Starting phenix.real_space_refine on Sat Jul 4 22:35:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9veg_65007/07_2026/9veg_65007.cif Found real_map, /net/cci-nas-00/data/ceres_data/9veg_65007/07_2026/9veg_65007.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9veg_65007/07_2026/9veg_65007.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9veg_65007/07_2026/9veg_65007.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9veg_65007/07_2026/9veg_65007.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9veg_65007/07_2026/9veg_65007.map" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 14 9.91 5 S 62 5.16 5 C 14421 2.51 5 N 3828 2.21 5 O 4733 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23058 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 3982 Classifications: {'peptide': 511} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 491} Chain breaks: 1 Chain: "B" Number of atoms: 3947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3947 Classifications: {'peptide': 506} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 486} Chain breaks: 1 Chain: "C" Number of atoms: 3934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3934 Classifications: {'peptide': 504} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 484} Chain breaks: 1 Chain: "F" Number of atoms: 4004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 4004 Classifications: {'peptide': 514} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 494} Chain breaks: 1 Chain: "G" Number of atoms: 3989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3989 Classifications: {'peptide': 512} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 492} Chain breaks: 1 Chain: "H" Number of atoms: 3188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3188 Classifications: {'peptide': 400} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 390} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Time building chain proxies: 4.72, per 1000 atoms: 0.20 Number of scatterers: 23058 At special positions: 0 Unit cell: (158.76, 167.16, 184.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 14 19.99 S 62 16.00 O 4733 8.00 N 3828 7.00 C 14421 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.60 Conformation dependent library (CDL) restraints added in 953.9 milliseconds 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5534 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 60 sheets defined 20.9% alpha, 31.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 234 through 241 Processing helix chain 'A' and resid 253 through 260 removed outlier: 3.558A pdb=" N GLY A 260 " --> pdb=" O ALA A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 286 Processing helix chain 'A' and resid 293 through 297 removed outlier: 3.926A pdb=" N PHE A 297 " --> pdb=" O LYS A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 472 Processing helix chain 'A' and resid 505 through 512 Processing helix chain 'A' and resid 545 through 554 Processing helix chain 'A' and resid 573 through 575 No H-bonds generated for 'chain 'A' and resid 573 through 575' Processing helix chain 'A' and resid 582 through 594 Processing helix chain 'A' and resid 605 through 609 Processing helix chain 'A' and resid 668 through 674 Processing helix chain 'A' and resid 766 through 771 removed outlier: 4.051A pdb=" N GLN A 770 " --> pdb=" O ASP A 766 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 241 Processing helix chain 'B' and resid 253 through 260 removed outlier: 3.505A pdb=" N GLY B 260 " --> pdb=" O ALA B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 285 Processing helix chain 'B' and resid 293 through 297 removed outlier: 3.742A pdb=" N PHE B 297 " --> pdb=" O LYS B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 472 Processing helix chain 'B' and resid 504 through 512 removed outlier: 4.246A pdb=" N GLN B 508 " --> pdb=" O GLY B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 554 removed outlier: 3.537A pdb=" N TYR B 554 " --> pdb=" O LEU B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 575 No H-bonds generated for 'chain 'B' and resid 573 through 575' Processing helix chain 'B' and resid 582 through 595 Processing helix chain 'B' and resid 605 through 609 removed outlier: 3.539A pdb=" N ASP B 608 " --> pdb=" O HIS B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 675 Processing helix chain 'C' and resid 234 through 241 Processing helix chain 'C' and resid 253 through 260 removed outlier: 3.796A pdb=" N GLY C 260 " --> pdb=" O ALA C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 285 Processing helix chain 'C' and resid 293 through 297 removed outlier: 3.628A pdb=" N PHE C 297 " --> pdb=" O LYS C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.880A pdb=" N THR C 429 " --> pdb=" O SER C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 472 Processing helix chain 'C' and resid 504 through 512 removed outlier: 4.263A pdb=" N GLN C 508 " --> pdb=" O GLY C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 554 Processing helix chain 'C' and resid 573 through 575 No H-bonds generated for 'chain 'C' and resid 573 through 575' Processing helix chain 'C' and resid 582 through 595 Processing helix chain 'C' and resid 605 through 609 Processing helix chain 'C' and resid 668 through 674 Processing helix chain 'C' and resid 766 through 770 Processing helix chain 'F' and resid 234 through 241 Processing helix chain 'F' and resid 253 through 260 removed outlier: 3.615A pdb=" N GLY F 260 " --> pdb=" O ALA F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 285 Processing helix chain 'F' and resid 293 through 297 removed outlier: 3.791A pdb=" N PHE F 297 " --> pdb=" O LYS F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 463 through 472 Processing helix chain 'F' and resid 502 through 512 removed outlier: 4.590A pdb=" N GLN F 507 " --> pdb=" O ASN F 503 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N GLN F 508 " --> pdb=" O GLY F 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 545 through 553 Processing helix chain 'F' and resid 573 through 577 Processing helix chain 'F' and resid 582 through 595 Processing helix chain 'F' and resid 605 through 609 Processing helix chain 'F' and resid 668 through 675 removed outlier: 3.671A pdb=" N LEU F 675 " --> pdb=" O ALA F 671 " (cutoff:3.500A) Processing helix chain 'F' and resid 760 through 764 Processing helix chain 'F' and resid 766 through 770 Processing helix chain 'G' and resid 234 through 241 Processing helix chain 'G' and resid 253 through 258 Processing helix chain 'G' and resid 279 through 285 Processing helix chain 'G' and resid 293 through 297 removed outlier: 3.940A pdb=" N PHE G 297 " --> pdb=" O LYS G 294 " (cutoff:3.500A) Processing helix chain 'G' and resid 463 through 472 Processing helix chain 'G' and resid 505 through 512 Processing helix chain 'G' and resid 545 through 554 Processing helix chain 'G' and resid 573 through 575 No H-bonds generated for 'chain 'G' and resid 573 through 575' Processing helix chain 'G' and resid 582 through 595 Processing helix chain 'G' and resid 605 through 609 Processing helix chain 'G' and resid 668 through 675 removed outlier: 3.540A pdb=" N LEU G 675 " --> pdb=" O ALA G 671 " (cutoff:3.500A) Processing helix chain 'G' and resid 760 through 764 Processing helix chain 'H' and resid 70 through 85 removed outlier: 3.585A pdb=" N TRP H 76 " --> pdb=" O LYS H 72 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU H 83 " --> pdb=" O GLU H 79 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TRP H 84 " --> pdb=" O LYS H 80 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS H 85 " --> pdb=" O GLU H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 104 removed outlier: 3.927A pdb=" N LYS H 103 " --> pdb=" O ASP H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 113 Processing helix chain 'H' and resid 119 through 135 Processing helix chain 'H' and resid 149 through 154 Processing helix chain 'H' and resid 166 through 178 Processing helix chain 'H' and resid 275 through 290 removed outlier: 5.471A pdb=" N GLY H 286 " --> pdb=" O LYS H 282 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N TRP H 287 " --> pdb=" O ASN H 283 " (cutoff:3.500A) Processing helix chain 'H' and resid 292 through 304 Processing helix chain 'H' and resid 306 through 316 Processing helix chain 'H' and resid 324 through 337 removed outlier: 4.175A pdb=" N GLN H 328 " --> pdb=" O LYS H 324 " (cutoff:3.500A) Processing helix chain 'H' and resid 352 through 357 Processing helix chain 'H' and resid 366 through 375 Processing helix chain 'H' and resid 416 through 420 Processing sheet with id=AA1, first strand: chain 'A' and resid 242 through 245 Processing sheet with id=AA2, first strand: chain 'A' and resid 307 through 318 removed outlier: 5.701A pdb=" N VAL A 309 " --> pdb=" O ASN A 396 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ASN A 396 " --> pdb=" O VAL A 309 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N MET A 311 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ARG A 394 " --> pdb=" O MET A 311 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 438 through 439 removed outlier: 4.705A pdb=" N ILE A 460 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 379 through 382 removed outlier: 4.185A pdb=" N ASN A 377 " --> pdb=" O VAL G 326 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER A 379 " --> pdb=" O ASN G 324 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER G 379 " --> pdb=" O ASN F 324 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 403 through 406 removed outlier: 6.964A pdb=" N TYR A 404 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ASN A 432 " --> pdb=" O TYR A 404 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 417 through 423 removed outlier: 5.376A pdb=" N THR A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LEU A 414 " --> pdb=" O THR A 418 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA A 420 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N THR A 409 " --> pdb=" O ASN A 481 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 486 through 490 removed outlier: 3.927A pdb=" N GLY A 500 " --> pdb=" O TYR A 487 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ILE A 489 " --> pdb=" O THR A 498 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N THR A 498 " --> pdb=" O ILE A 489 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 524 through 530 Processing sheet with id=AA9, first strand: chain 'A' and resid 558 through 561 Processing sheet with id=AB1, first strand: chain 'A' and resid 624 through 626 removed outlier: 6.467A pdb=" N ASP A 750 " --> pdb=" O LYS A 654 " (cutoff:3.500A) removed outlier: 12.296A pdb=" N LYS A 654 " --> pdb=" O ASP A 750 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL A 646 " --> pdb=" O GLN A 655 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 624 through 626 removed outlier: 4.342A pdb=" N VAL A 751 " --> pdb=" O SER A 684 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N SER A 684 " --> pdb=" O VAL A 751 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE A 753 " --> pdb=" O TYR A 682 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TYR A 682 " --> pdb=" O ILE A 753 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N GLU A 755 " --> pdb=" O ASN A 680 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N ASN A 680 " --> pdb=" O GLU A 755 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 639 through 641 removed outlier: 3.525A pdb=" N ALA A 663 " --> pdb=" O ILE A 738 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 242 through 245 Processing sheet with id=AB5, first strand: chain 'B' and resid 307 through 318 removed outlier: 5.604A pdb=" N VAL B 309 " --> pdb=" O ASN B 396 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ASN B 396 " --> pdb=" O VAL B 309 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N MET B 311 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ARG B 394 " --> pdb=" O MET B 311 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 438 through 439 removed outlier: 4.709A pdb=" N ILE B 460 " --> pdb=" O LEU B 389 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 321 through 322 Processing sheet with id=AB8, first strand: chain 'B' and resid 403 through 406 removed outlier: 6.975A pdb=" N TYR B 404 " --> pdb=" O ASN B 432 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ASN B 432 " --> pdb=" O TYR B 404 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 417 through 423 removed outlier: 5.196A pdb=" N THR B 418 " --> pdb=" O LEU B 414 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU B 414 " --> pdb=" O THR B 418 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA B 420 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N THR B 409 " --> pdb=" O ASN B 481 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 486 through 490 removed outlier: 3.879A pdb=" N GLY B 500 " --> pdb=" O TYR B 487 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ILE B 489 " --> pdb=" O THR B 498 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N THR B 498 " --> pdb=" O ILE B 489 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 524 through 530 Processing sheet with id=AC3, first strand: chain 'B' and resid 558 through 561 Processing sheet with id=AC4, first strand: chain 'B' and resid 624 through 626 removed outlier: 6.464A pdb=" N ASP B 750 " --> pdb=" O LYS B 654 " (cutoff:3.500A) removed outlier: 12.396A pdb=" N LYS B 654 " --> pdb=" O ASP B 750 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 624 through 626 removed outlier: 4.271A pdb=" N VAL B 751 " --> pdb=" O SER B 684 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N SER B 684 " --> pdb=" O VAL B 751 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE B 753 " --> pdb=" O TYR B 682 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N TYR B 682 " --> pdb=" O ILE B 753 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 638 through 641 removed outlier: 6.429A pdb=" N VAL B 697 " --> pdb=" O SER B 708 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER B 708 " --> pdb=" O VAL B 697 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL B 699 " --> pdb=" O ILE B 706 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ILE B 706 " --> pdb=" O VAL B 699 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 242 through 245 Processing sheet with id=AC8, first strand: chain 'C' and resid 310 through 318 removed outlier: 6.550A pdb=" N ASN C 392 " --> pdb=" O GLU C 312 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL C 314 " --> pdb=" O ASN C 390 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ASN C 390 " --> pdb=" O VAL C 314 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU C 316 " --> pdb=" O TYR C 388 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N TYR C 388 " --> pdb=" O LEU C 316 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 310 through 318 removed outlier: 6.550A pdb=" N ASN C 392 " --> pdb=" O GLU C 312 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL C 314 " --> pdb=" O ASN C 390 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ASN C 390 " --> pdb=" O VAL C 314 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU C 316 " --> pdb=" O TYR C 388 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N TYR C 388 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE C 460 " --> pdb=" O LEU C 389 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 417 through 423 removed outlier: 5.103A pdb=" N THR C 418 " --> pdb=" O LEU C 414 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU C 414 " --> pdb=" O THR C 418 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA C 420 " --> pdb=" O PHE C 412 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLU C 405 " --> pdb=" O GLY C 485 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLY C 485 " --> pdb=" O GLU C 405 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LYS C 407 " --> pdb=" O THR C 483 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N THR C 483 " --> pdb=" O LYS C 407 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N THR C 409 " --> pdb=" O ASN C 481 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N GLY C 485 " --> pdb=" O GLU C 501 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU C 501 " --> pdb=" O GLY C 485 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N TYR C 487 " --> pdb=" O GLY C 499 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 524 through 530 removed outlier: 3.526A pdb=" N MET C 621 " --> pdb=" O ASP C 519 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 558 through 561 Processing sheet with id=AD4, first strand: chain 'C' and resid 624 through 626 removed outlier: 6.535A pdb=" N ASP C 750 " --> pdb=" O LYS C 654 " (cutoff:3.500A) removed outlier: 12.450A pdb=" N LYS C 654 " --> pdb=" O ASP C 750 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 624 through 626 removed outlier: 4.957A pdb=" N TRP C 748 " --> pdb=" O LYS C 688 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LYS C 688 " --> pdb=" O TRP C 748 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ASP C 750 " --> pdb=" O TYR C 686 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR C 686 " --> pdb=" O ASP C 750 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 638 through 641 removed outlier: 3.680A pdb=" N ALA C 663 " --> pdb=" O ILE C 738 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL C 697 " --> pdb=" O LYS C 709 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS C 709 " --> pdb=" O VAL C 697 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 242 through 245 Processing sheet with id=AD8, first strand: chain 'F' and resid 307 through 318 removed outlier: 5.456A pdb=" N VAL F 309 " --> pdb=" O ASN F 396 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ASN F 396 " --> pdb=" O VAL F 309 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N MET F 311 " --> pdb=" O ARG F 394 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ARG F 394 " --> pdb=" O MET F 311 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 438 through 439 removed outlier: 4.599A pdb=" N ILE F 460 " --> pdb=" O LEU F 389 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 418 through 423 removed outlier: 3.885A pdb=" N ALA F 420 " --> pdb=" O PHE F 412 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N TYR F 404 " --> pdb=" O ASN F 432 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ASN F 432 " --> pdb=" O TYR F 404 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 418 through 423 removed outlier: 3.885A pdb=" N ALA F 420 " --> pdb=" O PHE F 412 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N ILE F 403 " --> pdb=" O TYR F 487 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N TYR F 487 " --> pdb=" O ILE F 403 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N GLU F 405 " --> pdb=" O GLY F 485 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY F 485 " --> pdb=" O GLU F 405 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LYS F 407 " --> pdb=" O THR F 483 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N THR F 483 " --> pdb=" O LYS F 407 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N THR F 409 " --> pdb=" O ASN F 481 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY F 500 " --> pdb=" O TYR F 487 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ILE F 489 " --> pdb=" O THR F 498 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N THR F 498 " --> pdb=" O ILE F 489 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 524 through 530 removed outlier: 9.109A pdb=" N PHE F 617 " --> pdb=" O THR F 513 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N SER F 515 " --> pdb=" O PHE F 617 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ILE F 619 " --> pdb=" O SER F 515 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE F 517 " --> pdb=" O ILE F 619 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 558 through 561 Processing sheet with id=AE5, first strand: chain 'F' and resid 624 through 626 removed outlier: 6.849A pdb=" N ASP F 750 " --> pdb=" O LYS F 654 " (cutoff:3.500A) removed outlier: 12.527A pdb=" N LYS F 654 " --> pdb=" O ASP F 750 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 624 through 626 removed outlier: 5.265A pdb=" N TRP F 748 " --> pdb=" O LYS F 688 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LYS F 688 " --> pdb=" O TRP F 748 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N ASP F 750 " --> pdb=" O TYR F 686 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR F 686 " --> pdb=" O ASP F 750 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL F 725 " --> pdb=" O TYR F 681 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 639 through 641 removed outlier: 4.163A pdb=" N VAL F 699 " --> pdb=" O ILE F 706 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE F 706 " --> pdb=" O VAL F 699 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 242 through 245 Processing sheet with id=AE9, first strand: chain 'G' and resid 310 through 318 removed outlier: 5.257A pdb=" N MET G 311 " --> pdb=" O ARG G 394 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ARG G 394 " --> pdb=" O MET G 311 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 438 through 439 removed outlier: 3.611A pdb=" N TYR G 439 " --> pdb=" O TYR G 395 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ILE G 460 " --> pdb=" O LEU G 389 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 403 through 406 removed outlier: 7.056A pdb=" N TYR G 404 " --> pdb=" O ASN G 432 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ASN G 432 " --> pdb=" O TYR G 404 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 418 through 423 removed outlier: 5.383A pdb=" N THR G 418 " --> pdb=" O LEU G 414 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU G 414 " --> pdb=" O THR G 418 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA G 420 " --> pdb=" O PHE G 412 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN G 482 " --> pdb=" O THR G 409 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N SER G 411 " --> pdb=" O THR G 480 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N THR G 480 " --> pdb=" O SER G 411 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL G 413 " --> pdb=" O LEU G 478 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N LEU G 478 " --> pdb=" O VAL G 413 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 486 through 490 removed outlier: 6.874A pdb=" N TYR G 487 " --> pdb=" O GLY G 499 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 524 through 530 Processing sheet with id=AF6, first strand: chain 'G' and resid 558 through 561 Processing sheet with id=AF7, first strand: chain 'G' and resid 624 through 626 removed outlier: 6.405A pdb=" N ASP G 750 " --> pdb=" O LYS G 654 " (cutoff:3.500A) removed outlier: 12.331A pdb=" N LYS G 654 " --> pdb=" O ASP G 750 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 624 through 626 removed outlier: 5.042A pdb=" N TRP G 748 " --> pdb=" O LYS G 688 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LYS G 688 " --> pdb=" O TRP G 748 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ASP G 750 " --> pdb=" O TYR G 686 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N TYR G 686 " --> pdb=" O ASP G 750 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL G 679 " --> pdb=" O ASN G 727 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 638 through 641 removed outlier: 3.552A pdb=" N ALA G 663 " --> pdb=" O ILE G 738 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 142 through 148 removed outlier: 6.508A pdb=" N ILE H 204 " --> pdb=" O VAL H 258 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N GLY H 260 " --> pdb=" O ILE H 204 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LYS H 206 " --> pdb=" O GLY H 260 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N LEU H 262 " --> pdb=" O LYS H 206 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N THR H 208 " --> pdb=" O LEU H 262 " (cutoff:3.500A) removed outlier: 9.092A pdb=" N LYS H 264 " --> pdb=" O THR H 208 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N PHE H 253 " --> pdb=" O VAL H 249 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL H 249 " --> pdb=" O PHE H 253 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N CYS H 255 " --> pdb=" O LYS H 247 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LYS H 247 " --> pdb=" O CYS H 255 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLN H 257 " --> pdb=" O VAL H 245 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N VAL H 245 " --> pdb=" O GLN H 257 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLU H 259 " --> pdb=" O ASP H 243 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG H 180 " --> pdb=" O VAL H 242 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 160 through 161 Processing sheet with id=AG3, first strand: chain 'H' and resid 188 through 191 Processing sheet with id=AG4, first strand: chain 'H' and resid 345 through 351 removed outlier: 3.768A pdb=" N ILE H 402 " --> pdb=" O CYS H 351 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ALA H 457 " --> pdb=" O ILE H 403 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ARG H 405 " --> pdb=" O ALA H 457 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N LEU H 459 " --> pdb=" O ARG H 405 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLN H 407 " --> pdb=" O LEU H 459 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N THR H 458 " --> pdb=" O ILE H 439 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N ILE H 439 " --> pdb=" O THR H 458 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'H' and resid 385 through 388 removed outlier: 3.800A pdb=" N MET H 385 " --> pdb=" O LEU H 431 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'H' and resid 444 through 447 841 hydrogen bonds defined for protein. 2100 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: 4.38 Time building geometry restraints manager: 2.18 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: 7565 1.34 - 1.46: 4027 1.46 - 1.58: 11728 1.58 - 1.69: 0 1.69 - 1.81: 122 Bond restraints: 23442 Sorted by residual: bond pdb=" CA ILE F 778 " pdb=" C ILE F 778 " ideal model delta sigma weight residual 1.524 1.504 0.020 1.16e-02 7.43e+03 2.95e+00 bond pdb=" CA LEU A 478 " pdb=" C LEU A 478 " ideal model delta sigma weight residual 1.522 1.504 0.018 1.22e-02 6.72e+03 2.17e+00 bond pdb=" N GLU A 479 " pdb=" CA GLU A 479 " ideal model delta sigma weight residual 1.455 1.438 0.017 1.25e-02 6.40e+03 1.92e+00 bond pdb=" CA THR B 752 " pdb=" C THR B 752 " ideal model delta sigma weight residual 1.521 1.505 0.016 1.24e-02 6.50e+03 1.70e+00 bond pdb=" CA ILE H 455 " pdb=" C ILE H 455 " ideal model delta sigma weight residual 1.522 1.509 0.014 1.08e-02 8.57e+03 1.61e+00 ... (remaining 23437 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 31207 1.80 - 3.61: 472 3.61 - 5.41: 47 5.41 - 7.22: 9 7.22 - 9.02: 2 Bond angle restraints: 31737 Sorted by residual: angle pdb=" N ILE G 772 " pdb=" CA ILE G 772 " pdb=" C ILE G 772 " ideal model delta sigma weight residual 112.96 108.32 4.64 1.00e+00 1.00e+00 2.16e+01 angle pdb=" CA GLN G 716 " pdb=" CB GLN G 716 " pdb=" CG GLN G 716 " ideal model delta sigma weight residual 114.10 121.15 -7.05 2.00e+00 2.50e-01 1.24e+01 angle pdb=" N SER C 765 " pdb=" CA SER C 765 " pdb=" C SER C 765 " ideal model delta sigma weight residual 113.89 108.33 5.56 1.58e+00 4.01e-01 1.24e+01 angle pdb=" N THR B 752 " pdb=" CA THR B 752 " pdb=" C THR B 752 " ideal model delta sigma weight residual 109.24 114.79 -5.55 1.67e+00 3.59e-01 1.11e+01 angle pdb=" N ILE F 778 " pdb=" CA ILE F 778 " pdb=" C ILE F 778 " ideal model delta sigma weight residual 110.23 106.85 3.38 1.04e+00 9.25e-01 1.06e+01 ... (remaining 31732 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.09: 12683 17.09 - 34.18: 1327 34.18 - 51.27: 239 51.27 - 68.37: 36 68.37 - 85.46: 13 Dihedral angle restraints: 14298 sinusoidal: 5673 harmonic: 8625 Sorted by residual: dihedral pdb=" CA ASN H 163 " pdb=" C ASN H 163 " pdb=" N THR H 164 " pdb=" CA THR H 164 " ideal model delta harmonic sigma weight residual 180.00 -160.78 -19.22 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA ASP H 312 " pdb=" C ASP H 312 " pdb=" N TYR H 313 " pdb=" CA TYR H 313 " ideal model delta harmonic sigma weight residual 180.00 161.50 18.50 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA LYS C 712 " pdb=" C LYS C 712 " pdb=" N LEU C 713 " pdb=" CA LEU C 713 " ideal model delta harmonic sigma weight residual -180.00 -161.62 -18.38 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 14295 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2194 0.036 - 0.071: 929 0.071 - 0.107: 344 0.107 - 0.142: 102 0.142 - 0.178: 3 Chirality restraints: 3572 Sorted by residual: chirality pdb=" CA ILE F 778 " pdb=" N ILE F 778 " pdb=" C ILE F 778 " pdb=" CB ILE F 778 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.91e-01 chirality pdb=" CA ILE G 736 " pdb=" N ILE G 736 " pdb=" C ILE G 736 " pdb=" CB ILE G 736 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.14e-01 chirality pdb=" CA ILE A 753 " pdb=" N ILE A 753 " pdb=" C ILE A 753 " pdb=" CB ILE A 753 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.22e-01 ... (remaining 3569 not shown) Planarity restraints: 4110 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 751 " 0.009 2.00e-02 2.50e+03 1.89e-02 3.58e+00 pdb=" C VAL C 751 " -0.033 2.00e-02 2.50e+03 pdb=" O VAL C 751 " 0.012 2.00e-02 2.50e+03 pdb=" N THR C 752 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU G 583 " -0.008 2.00e-02 2.50e+03 1.70e-02 2.88e+00 pdb=" CD GLU G 583 " 0.029 2.00e-02 2.50e+03 pdb=" OE1 GLU G 583 " -0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU G 583 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR F 612 " -0.028 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO F 613 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO F 613 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 613 " -0.023 5.00e-02 4.00e+02 ... (remaining 4107 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 153 2.65 - 3.21: 21930 3.21 - 3.77: 33617 3.77 - 4.34: 48622 4.34 - 4.90: 80145 Nonbonded interactions: 184467 Sorted by model distance: nonbonded pdb=" OE2 GLU A 238 " pdb="CA CA A 902 " model vdw 2.086 3.250 nonbonded pdb=" OD1 ASP A 229 " pdb="CA CA A 901 " model vdw 2.093 3.250 nonbonded pdb=" OD1 ASP B 229 " pdb="CA CA B 901 " model vdw 2.097 3.250 nonbonded pdb=" O ASP A 270 " pdb="CA CA A 902 " model vdw 2.113 3.250 nonbonded pdb=" OD1 ASP G 229 " pdb="CA CA G 901 " model vdw 2.113 3.250 ... (remaining 184462 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 223 through 323 or resid 380 through 902)) selection = (chain 'B' and (resid 223 through 323 or resid 380 through 902)) selection = (chain 'C' and resid 223 through 902) selection = (chain 'F' and (resid 223 through 323 or resid 380 through 902)) selection = (chain 'G' and (resid 223 through 323 or resid 380 through 902)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 13.080 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: 0.430 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 20.240 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 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 : 0.004 0.048 23442 Z= 0.173 Angle : 0.586 9.023 31737 Z= 0.336 Chirality : 0.046 0.178 3572 Planarity : 0.004 0.042 4110 Dihedral : 14.074 85.457 8764 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.08 % Allowed : 13.26 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.15), residues: 2925 helix: -0.77 (0.23), residues: 496 sheet: -0.28 (0.19), residues: 742 loop : -1.54 (0.14), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 730 TYR 0.016 0.001 TYR B 737 PHE 0.009 0.001 PHE H 268 TRP 0.023 0.001 TRP F 748 HIS 0.003 0.001 HIS A 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (23442) covalent geometry : angle 0.58586 / 0.34 (31737) hydrogen bonds : bond 0.13807 / 9.19 ( 815) hydrogen bonds : angle 6.70179 / 4.54 ( 2100) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 154 time to evaluate : 0.642 Fit side-chains revert: symmetry clash REVERT: A 476 MET cc_start: 0.8601 (ttt) cc_final: 0.8094 (ttt) REVERT: A 588 GLU cc_start: 0.8825 (tp30) cc_final: 0.8168 (tp30) REVERT: A 719 GLN cc_start: 0.8505 (tt0) cc_final: 0.8002 (tm-30) REVERT: C 270 ASP cc_start: 0.8659 (t0) cc_final: 0.8356 (t0) REVERT: C 732 LEU cc_start: 0.7927 (mt) cc_final: 0.7629 (tt) REVERT: C 735 LYS cc_start: 0.8626 (mtmt) cc_final: 0.8286 (mtpp) REVERT: C 736 ILE cc_start: 0.9572 (mp) cc_final: 0.9353 (tp) REVERT: F 681 TYR cc_start: 0.7352 (p90) cc_final: 0.6587 (p90) REVERT: G 582 ASP cc_start: 0.7314 (p0) cc_final: 0.7096 (p0) REVERT: G 602 ASP cc_start: 0.8860 (m-30) cc_final: 0.8134 (t0) REVERT: H 90 GLU cc_start: 0.6739 (mt-10) cc_final: 0.5577 (tp30) outliers start: 2 outliers final: 1 residues processed: 156 average time/residue: 0.1715 time to fit residues: 40.1362 Evaluate side-chains 146 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 145 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 455 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 507 GLN A 662 ASN ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 507 GLN ** G 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.124361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.072742 restraints weight = 48918.377| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.93 r_work: 0.2944 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.0729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23442 Z= 0.127 Angle : 0.495 6.241 31737 Z= 0.272 Chirality : 0.045 0.151 3572 Planarity : 0.004 0.058 4110 Dihedral : 4.410 20.239 3144 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.31 % Allowed : 13.64 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.15), residues: 2925 helix: -0.28 (0.24), residues: 498 sheet: -0.04 (0.19), residues: 743 loop : -1.39 (0.14), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 400 TYR 0.012 0.001 TYR H 437 PHE 0.016 0.001 PHE A 773 TRP 0.014 0.001 TRP C 237 HIS 0.003 0.001 HIS A 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (23442) covalent geometry : angle 0.49492 / 0.27 (31737) hydrogen bonds : bond 0.03358 / 2.20 ( 815) hydrogen bonds : angle 5.18889 / 3.57 ( 2100) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 158 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 588 GLU cc_start: 0.9041 (tp30) cc_final: 0.8542 (tp30) REVERT: A 719 GLN cc_start: 0.8826 (tt0) cc_final: 0.8358 (tm-30) REVERT: C 477 MET cc_start: 0.8873 (mmm) cc_final: 0.8345 (mpp) REVERT: C 615 MET cc_start: 0.9159 (mtt) cc_final: 0.8861 (mtt) REVERT: C 732 LEU cc_start: 0.8013 (mt) cc_final: 0.7683 (tt) REVERT: C 736 ILE cc_start: 0.9582 (mp) cc_final: 0.9328 (tp) REVERT: F 578 MET cc_start: 0.7611 (mmm) cc_final: 0.7313 (mmm) REVERT: G 477 MET cc_start: 0.8929 (mmm) cc_final: 0.8649 (mmm) REVERT: G 602 ASP cc_start: 0.9067 (m-30) cc_final: 0.8337 (t0) outliers start: 34 outliers final: 14 residues processed: 186 average time/residue: 0.1567 time to fit residues: 45.0824 Evaluate side-chains 159 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 747 TYR Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain C residue 764 LEU Chi-restraints excluded: chain F residue 478 LEU Chi-restraints excluded: chain F residue 483 THR Chi-restraints excluded: chain F residue 665 VAL Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain G residue 687 MET Chi-restraints excluded: chain G residue 697 VAL Chi-restraints excluded: chain G residue 736 ILE Chi-restraints excluded: chain G residue 747 TYR Chi-restraints excluded: chain H residue 193 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 178 optimal weight: 8.9990 chunk 194 optimal weight: 0.7980 chunk 274 optimal weight: 5.9990 chunk 199 optimal weight: 20.0000 chunk 8 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 196 optimal weight: 8.9990 chunk 25 optimal weight: 0.8980 chunk 89 optimal weight: 9.9990 chunk 225 optimal weight: 0.0470 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 507 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.125321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.074159 restraints weight = 49001.788| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.89 r_work: 0.2968 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 23442 Z= 0.099 Angle : 0.463 7.369 31737 Z= 0.253 Chirality : 0.044 0.180 3572 Planarity : 0.003 0.057 4110 Dihedral : 4.130 19.265 3142 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.46 % Allowed : 14.18 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.15), residues: 2925 helix: -0.05 (0.24), residues: 499 sheet: 0.14 (0.19), residues: 738 loop : -1.31 (0.14), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 730 TYR 0.011 0.001 TYR C 747 PHE 0.012 0.001 PHE H 397 TRP 0.017 0.001 TRP F 748 HIS 0.002 0.000 HIS B 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (23442) covalent geometry : angle 0.46311 / 0.25 (31737) hydrogen bonds : bond 0.02922 / 1.92 ( 815) hydrogen bonds : angle 4.84808 / 3.34 ( 2100) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 178 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 719 GLN cc_start: 0.8741 (tt0) cc_final: 0.8321 (tm-30) REVERT: C 477 MET cc_start: 0.8879 (mmm) cc_final: 0.8390 (mpt) REVERT: C 615 MET cc_start: 0.9095 (mtt) cc_final: 0.8876 (mtt) REVERT: C 685 MET cc_start: 0.9063 (mtm) cc_final: 0.8587 (tmm) REVERT: C 732 LEU cc_start: 0.8030 (mt) cc_final: 0.7678 (tt) REVERT: F 495 ASN cc_start: 0.8251 (p0) cc_final: 0.8039 (p0) REVERT: F 523 ARG cc_start: 0.8709 (ttp80) cc_final: 0.8341 (ttp80) REVERT: G 310 ASN cc_start: 0.8483 (t0) cc_final: 0.8268 (t0) REVERT: G 477 MET cc_start: 0.8951 (mmm) cc_final: 0.8662 (mmm) REVERT: G 602 ASP cc_start: 0.9065 (m-30) cc_final: 0.8362 (t0) REVERT: H 131 LYS cc_start: 0.7887 (mmtm) cc_final: 0.7605 (ptmt) REVERT: H 385 MET cc_start: 0.7845 (mmm) cc_final: 0.7640 (mmt) outliers start: 38 outliers final: 20 residues processed: 210 average time/residue: 0.1489 time to fit residues: 48.5151 Evaluate side-chains 172 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 747 TYR Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 764 LEU Chi-restraints excluded: chain F residue 478 LEU Chi-restraints excluded: chain F residue 483 THR Chi-restraints excluded: chain F residue 621 MET Chi-restraints excluded: chain F residue 665 VAL Chi-restraints excluded: chain F residue 699 VAL Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain G residue 687 MET Chi-restraints excluded: chain G residue 697 VAL Chi-restraints excluded: chain G residue 736 ILE Chi-restraints excluded: chain G residue 747 TYR Chi-restraints excluded: chain G residue 751 VAL Chi-restraints excluded: chain H residue 193 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 6 optimal weight: 0.0370 chunk 10 optimal weight: 9.9990 chunk 200 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 171 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 262 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 124 optimal weight: 0.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 507 GLN ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 432 ASN ** G 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.125555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.073969 restraints weight = 48798.077| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.96 r_work: 0.2968 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 23442 Z= 0.098 Angle : 0.454 7.233 31737 Z= 0.248 Chirality : 0.044 0.217 3572 Planarity : 0.003 0.052 4110 Dihedral : 3.991 18.793 3142 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.46 % Allowed : 15.38 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.15), residues: 2925 helix: 0.08 (0.24), residues: 499 sheet: 0.19 (0.19), residues: 774 loop : -1.25 (0.15), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 730 TYR 0.014 0.001 TYR F 686 PHE 0.008 0.001 PHE H 356 TRP 0.024 0.001 TRP C 748 HIS 0.004 0.000 HIS C 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (23442) covalent geometry : angle 0.45444 / 0.25 (31737) hydrogen bonds : bond 0.02780 / 1.79 ( 815) hydrogen bonds : angle 4.69208 / 3.24 ( 2100) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 174 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 719 GLN cc_start: 0.8649 (tt0) cc_final: 0.8265 (tm-30) REVERT: B 640 TRP cc_start: 0.7059 (m100) cc_final: 0.6768 (m100) REVERT: C 477 MET cc_start: 0.8774 (mmm) cc_final: 0.8317 (mpp) REVERT: C 685 MET cc_start: 0.9024 (mtm) cc_final: 0.8545 (tmm) REVERT: C 732 LEU cc_start: 0.8017 (mt) cc_final: 0.7730 (tt) REVERT: F 477 MET cc_start: 0.9002 (mmt) cc_final: 0.8716 (mpp) REVERT: F 495 ASN cc_start: 0.8113 (p0) cc_final: 0.7901 (p0) REVERT: F 513 THR cc_start: 0.9257 (p) cc_final: 0.9050 (t) REVERT: F 523 ARG cc_start: 0.8692 (ttp80) cc_final: 0.8371 (ttp80) REVERT: G 310 ASN cc_start: 0.8423 (t0) cc_final: 0.8191 (t0) REVERT: G 477 MET cc_start: 0.8909 (mmm) cc_final: 0.8584 (mmm) REVERT: G 602 ASP cc_start: 0.9112 (m-30) cc_final: 0.8394 (t0) REVERT: H 119 PHE cc_start: 0.6465 (m-80) cc_final: 0.5484 (p90) REVERT: H 131 LYS cc_start: 0.7889 (mmtm) cc_final: 0.7605 (ptmt) REVERT: H 132 MET cc_start: 0.6721 (mpp) cc_final: 0.6499 (mpp) REVERT: H 385 MET cc_start: 0.7938 (mmm) cc_final: 0.7736 (mmt) outliers start: 38 outliers final: 23 residues processed: 207 average time/residue: 0.1636 time to fit residues: 52.5700 Evaluate side-chains 187 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 747 TYR Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 752 THR Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 764 LEU Chi-restraints excluded: chain F residue 266 SER Chi-restraints excluded: chain F residue 478 LEU Chi-restraints excluded: chain F residue 483 THR Chi-restraints excluded: chain F residue 621 MET Chi-restraints excluded: chain F residue 665 VAL Chi-restraints excluded: chain F residue 699 VAL Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain G residue 697 VAL Chi-restraints excluded: chain G residue 736 ILE Chi-restraints excluded: chain G residue 747 TYR Chi-restraints excluded: chain G residue 751 VAL Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 312 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 111 optimal weight: 9.9990 chunk 99 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 202 optimal weight: 4.9990 chunk 145 optimal weight: 10.0000 chunk 62 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 188 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 ASN ** F 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.121891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.069895 restraints weight = 48956.698| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.02 r_work: 0.2857 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 23442 Z= 0.227 Angle : 0.526 7.536 31737 Z= 0.285 Chirality : 0.046 0.183 3572 Planarity : 0.003 0.054 4110 Dihedral : 4.410 21.004 3142 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.89 % Allowed : 15.84 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.15), residues: 2925 helix: 0.02 (0.24), residues: 496 sheet: 0.13 (0.19), residues: 768 loop : -1.30 (0.14), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 400 TYR 0.023 0.001 TYR F 686 PHE 0.014 0.001 PHE B 264 TRP 0.023 0.002 TRP C 748 HIS 0.005 0.001 HIS G 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.23 (23442) covalent geometry : angle 0.52601 / 0.28 (31737) hydrogen bonds : bond 0.03362 / 2.17 ( 815) hydrogen bonds : angle 4.85325 / 3.36 ( 2100) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 164 time to evaluate : 0.985 Fit side-chains revert: symmetry clash REVERT: A 224 GLU cc_start: 0.8553 (mp0) cc_final: 0.8283 (mp0) REVERT: A 588 GLU cc_start: 0.8879 (mm-30) cc_final: 0.8613 (mp0) REVERT: A 719 GLN cc_start: 0.8500 (tt0) cc_final: 0.8076 (tm-30) REVERT: C 270 ASP cc_start: 0.8881 (t0) cc_final: 0.8324 (t0) REVERT: C 439 TYR cc_start: 0.8535 (t80) cc_final: 0.8215 (t80) REVERT: C 477 MET cc_start: 0.8497 (mmm) cc_final: 0.7944 (mpt) REVERT: C 685 MET cc_start: 0.9003 (mtm) cc_final: 0.8541 (tmm) REVERT: C 735 LYS cc_start: 0.8563 (mtmt) cc_final: 0.8154 (mtpp) REVERT: F 477 MET cc_start: 0.8946 (mmt) cc_final: 0.8663 (mpp) REVERT: G 477 MET cc_start: 0.8708 (mmm) cc_final: 0.8314 (mmm) REVERT: G 602 ASP cc_start: 0.9109 (m-30) cc_final: 0.8347 (t0) REVERT: G 664 TYR cc_start: 0.8242 (p90) cc_final: 0.7976 (p90) REVERT: H 131 LYS cc_start: 0.7933 (mmtm) cc_final: 0.7613 (ptmt) REVERT: H 447 ILE cc_start: 0.1754 (OUTLIER) cc_final: 0.0509 (mm) REVERT: H 452 ARG cc_start: 0.4001 (mpt-90) cc_final: 0.3271 (ttm110) outliers start: 49 outliers final: 31 residues processed: 205 average time/residue: 0.1668 time to fit residues: 52.4968 Evaluate side-chains 188 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 747 TYR Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 752 THR Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain F residue 266 SER Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 438 SER Chi-restraints excluded: chain F residue 478 LEU Chi-restraints excluded: chain F residue 483 THR Chi-restraints excluded: chain F residue 621 MET Chi-restraints excluded: chain F residue 665 VAL Chi-restraints excluded: chain F residue 686 TYR Chi-restraints excluded: chain F residue 699 VAL Chi-restraints excluded: chain F residue 721 VAL Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain G residue 687 MET Chi-restraints excluded: chain G residue 697 VAL Chi-restraints excluded: chain G residue 736 ILE Chi-restraints excluded: chain G residue 747 TYR Chi-restraints excluded: chain G residue 751 VAL Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 224 ILE Chi-restraints excluded: chain H residue 312 ASP Chi-restraints excluded: chain H residue 408 VAL Chi-restraints excluded: chain H residue 445 VAL Chi-restraints excluded: chain H residue 447 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 29 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 chunk 216 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 156 optimal weight: 2.9990 chunk 282 optimal weight: 20.0000 chunk 43 optimal weight: 10.0000 chunk 274 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 178 optimal weight: 6.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.120224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.067678 restraints weight = 48393.495| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.12 r_work: 0.2859 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 23442 Z= 0.173 Angle : 0.496 9.057 31737 Z= 0.269 Chirality : 0.045 0.209 3572 Planarity : 0.003 0.053 4110 Dihedral : 4.305 20.441 3142 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.85 % Allowed : 16.42 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.15), residues: 2925 helix: -0.00 (0.24), residues: 502 sheet: 0.12 (0.19), residues: 775 loop : -1.26 (0.14), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 730 TYR 0.022 0.001 TYR G 664 PHE 0.012 0.001 PHE C 656 TRP 0.024 0.001 TRP C 748 HIS 0.004 0.001 HIS A 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.17 (23442) covalent geometry : angle 0.49614 / 0.27 (31737) hydrogen bonds : bond 0.03077 / 1.99 ( 815) hydrogen bonds : angle 4.78247 / 3.32 ( 2100) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 168 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 719 GLN cc_start: 0.8368 (tt0) cc_final: 0.7980 (tm-30) REVERT: B 640 TRP cc_start: 0.7065 (m100) cc_final: 0.6728 (m100) REVERT: C 270 ASP cc_start: 0.8739 (t0) cc_final: 0.8133 (t0) REVERT: C 439 TYR cc_start: 0.8480 (t80) cc_final: 0.8153 (t80) REVERT: C 477 MET cc_start: 0.8340 (mmm) cc_final: 0.7741 (mpp) REVERT: C 685 MET cc_start: 0.8937 (mtm) cc_final: 0.8494 (tmm) REVERT: F 477 MET cc_start: 0.8972 (mmt) cc_final: 0.8688 (mpp) REVERT: F 523 ARG cc_start: 0.8325 (ttp80) cc_final: 0.7880 (ttp80) REVERT: G 310 ASN cc_start: 0.8115 (t0) cc_final: 0.7796 (t0) REVERT: G 454 ASP cc_start: 0.8479 (m-30) cc_final: 0.8181 (m-30) REVERT: G 477 MET cc_start: 0.8559 (mmm) cc_final: 0.8164 (mmm) REVERT: G 508 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.8227 (mp10) REVERT: G 602 ASP cc_start: 0.9146 (m-30) cc_final: 0.8344 (t0) REVERT: G 664 TYR cc_start: 0.8120 (p90) cc_final: 0.7855 (p90) outliers start: 48 outliers final: 33 residues processed: 206 average time/residue: 0.1610 time to fit residues: 51.1976 Evaluate side-chains 189 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 155 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 747 TYR Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 685 MET Chi-restraints excluded: chain B residue 706 ILE Chi-restraints excluded: chain B residue 752 THR Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 736 ILE Chi-restraints excluded: chain C residue 747 TYR Chi-restraints excluded: chain F residue 266 SER Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 478 LEU Chi-restraints excluded: chain F residue 483 THR Chi-restraints excluded: chain F residue 621 MET Chi-restraints excluded: chain F residue 665 VAL Chi-restraints excluded: chain F residue 686 TYR Chi-restraints excluded: chain F residue 699 VAL Chi-restraints excluded: chain G residue 508 GLN Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain G residue 687 MET Chi-restraints excluded: chain G residue 697 VAL Chi-restraints excluded: chain G residue 736 ILE Chi-restraints excluded: chain G residue 747 TYR Chi-restraints excluded: chain G residue 751 VAL Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 312 ASP Chi-restraints excluded: chain H residue 445 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 126 optimal weight: 2.9990 chunk 235 optimal weight: 0.0030 chunk 131 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 220 optimal weight: 0.9990 chunk 244 optimal weight: 0.6980 chunk 263 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 289 optimal weight: 6.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.124529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.072515 restraints weight = 48371.740| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 3.05 r_work: 0.2914 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 23442 Z= 0.102 Angle : 0.469 9.853 31737 Z= 0.254 Chirality : 0.044 0.188 3572 Planarity : 0.003 0.049 4110 Dihedral : 4.025 18.944 3142 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.54 % Allowed : 17.19 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.15), residues: 2925 helix: 0.12 (0.24), residues: 504 sheet: 0.20 (0.19), residues: 780 loop : -1.15 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 730 TYR 0.022 0.001 TYR F 686 PHE 0.011 0.001 PHE C 656 TRP 0.026 0.001 TRP C 748 HIS 0.002 0.000 HIS B 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 (23442) covalent geometry : angle 0.46886 / 0.25 (31737) hydrogen bonds : bond 0.02720 / 1.76 ( 815) hydrogen bonds : angle 4.64553 / 3.23 ( 2100) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 168 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 719 GLN cc_start: 0.8398 (tt0) cc_final: 0.8060 (tm-30) REVERT: B 270 ASP cc_start: 0.9090 (t0) cc_final: 0.8812 (t0) REVERT: B 640 TRP cc_start: 0.7061 (m100) cc_final: 0.6818 (m100) REVERT: C 270 ASP cc_start: 0.8783 (t0) cc_final: 0.8196 (t0) REVERT: C 477 MET cc_start: 0.8504 (mmm) cc_final: 0.7986 (mpp) REVERT: C 685 MET cc_start: 0.8973 (mtm) cc_final: 0.8490 (tmm) REVERT: F 477 MET cc_start: 0.8986 (mmt) cc_final: 0.8627 (mpp) REVERT: F 495 ASN cc_start: 0.7919 (p0) cc_final: 0.7702 (p0) REVERT: F 513 THR cc_start: 0.9177 (p) cc_final: 0.8866 (t) REVERT: F 523 ARG cc_start: 0.8550 (ttp80) cc_final: 0.8036 (ttp80) REVERT: G 310 ASN cc_start: 0.8204 (t0) cc_final: 0.7932 (t0) REVERT: G 454 ASP cc_start: 0.8544 (m-30) cc_final: 0.8238 (m-30) REVERT: G 477 MET cc_start: 0.8686 (mmm) cc_final: 0.8306 (mmm) REVERT: G 508 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8439 (mp10) REVERT: G 602 ASP cc_start: 0.9094 (m-30) cc_final: 0.8324 (t0) outliers start: 40 outliers final: 29 residues processed: 201 average time/residue: 0.1561 time to fit residues: 48.5160 Evaluate side-chains 186 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 156 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 747 TYR Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 752 THR Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 736 ILE Chi-restraints excluded: chain C residue 747 TYR Chi-restraints excluded: chain F residue 266 SER Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 438 SER Chi-restraints excluded: chain F residue 478 LEU Chi-restraints excluded: chain F residue 483 THR Chi-restraints excluded: chain F residue 621 MET Chi-restraints excluded: chain F residue 665 VAL Chi-restraints excluded: chain F residue 699 VAL Chi-restraints excluded: chain G residue 508 GLN Chi-restraints excluded: chain G residue 687 MET Chi-restraints excluded: chain G residue 697 VAL Chi-restraints excluded: chain G residue 736 ILE Chi-restraints excluded: chain G residue 747 TYR Chi-restraints excluded: chain G residue 751 VAL Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 268 PHE Chi-restraints excluded: chain H residue 312 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 55 optimal weight: 0.5980 chunk 248 optimal weight: 8.9990 chunk 228 optimal weight: 0.0970 chunk 255 optimal weight: 8.9990 chunk 180 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 292 optimal weight: 7.9990 chunk 188 optimal weight: 6.9990 overall best weight: 1.0580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 432 ASN F 714 ASN G 507 GLN G 770 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.124136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.072511 restraints weight = 48493.688| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 3.04 r_work: 0.2900 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23442 Z= 0.128 Angle : 0.480 11.687 31737 Z= 0.258 Chirality : 0.045 0.181 3572 Planarity : 0.003 0.048 4110 Dihedral : 4.046 19.068 3142 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.70 % Allowed : 17.11 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.15), residues: 2925 helix: 0.17 (0.24), residues: 505 sheet: 0.25 (0.19), residues: 773 loop : -1.10 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 730 TYR 0.015 0.001 TYR G 664 PHE 0.012 0.001 PHE C 656 TRP 0.023 0.001 TRP C 748 HIS 0.003 0.001 HIS A 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (23442) covalent geometry : angle 0.47989 / 0.26 (31737) hydrogen bonds : bond 0.02845 / 1.84 ( 815) hydrogen bonds : angle 4.61957 / 3.21 ( 2100) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 168 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 GLU cc_start: 0.8533 (mp0) cc_final: 0.8244 (mp0) REVERT: A 719 GLN cc_start: 0.8369 (tt0) cc_final: 0.8030 (tm-30) REVERT: B 270 ASP cc_start: 0.9128 (t0) cc_final: 0.8823 (t0) REVERT: B 640 TRP cc_start: 0.7083 (m100) cc_final: 0.6773 (m100) REVERT: C 270 ASP cc_start: 0.8809 (t0) cc_final: 0.8240 (t0) REVERT: C 477 MET cc_start: 0.8499 (mmm) cc_final: 0.7951 (mpp) REVERT: C 770 GLN cc_start: 0.8545 (pm20) cc_final: 0.8015 (tp40) REVERT: F 477 MET cc_start: 0.8939 (mmt) cc_final: 0.8623 (mpp) REVERT: F 495 ASN cc_start: 0.7847 (p0) cc_final: 0.7626 (p0) REVERT: F 513 THR cc_start: 0.9188 (p) cc_final: 0.8883 (t) REVERT: F 523 ARG cc_start: 0.8562 (ttp80) cc_final: 0.7861 (ttp80) REVERT: G 310 ASN cc_start: 0.8218 (t0) cc_final: 0.7923 (t0) REVERT: G 454 ASP cc_start: 0.8542 (m-30) cc_final: 0.8230 (m-30) REVERT: G 477 MET cc_start: 0.8684 (mmm) cc_final: 0.8301 (mmm) REVERT: G 508 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8452 (mp10) REVERT: G 602 ASP cc_start: 0.9102 (m-30) cc_final: 0.8361 (t0) REVERT: G 770 GLN cc_start: 0.7887 (tm130) cc_final: 0.7444 (tm-30) outliers start: 44 outliers final: 30 residues processed: 205 average time/residue: 0.1512 time to fit residues: 48.2488 Evaluate side-chains 191 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 160 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 747 TYR Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 752 THR Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 736 ILE Chi-restraints excluded: chain F residue 266 SER Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 438 SER Chi-restraints excluded: chain F residue 478 LEU Chi-restraints excluded: chain F residue 483 THR Chi-restraints excluded: chain F residue 621 MET Chi-restraints excluded: chain F residue 665 VAL Chi-restraints excluded: chain F residue 686 TYR Chi-restraints excluded: chain F residue 699 VAL Chi-restraints excluded: chain G residue 508 GLN Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain G residue 687 MET Chi-restraints excluded: chain G residue 697 VAL Chi-restraints excluded: chain G residue 736 ILE Chi-restraints excluded: chain G residue 747 TYR Chi-restraints excluded: chain G residue 751 VAL Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 312 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 213 optimal weight: 6.9990 chunk 171 optimal weight: 4.9990 chunk 286 optimal weight: 9.9990 chunk 164 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 249 optimal weight: 2.9990 chunk 175 optimal weight: 5.9990 chunk 93 optimal weight: 8.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 432 ASN G 507 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.123337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.070933 restraints weight = 48843.069| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 3.07 r_work: 0.2880 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23442 Z= 0.158 Angle : 0.498 12.165 31737 Z= 0.268 Chirality : 0.045 0.202 3572 Planarity : 0.003 0.047 4110 Dihedral : 4.152 19.398 3142 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.50 % Allowed : 17.50 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.15), residues: 2925 helix: 0.14 (0.24), residues: 504 sheet: 0.25 (0.19), residues: 783 loop : -1.13 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 730 TYR 0.013 0.001 TYR H 384 PHE 0.014 0.001 PHE C 656 TRP 0.050 0.002 TRP C 748 HIS 0.004 0.001 HIS A 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (23442) covalent geometry : angle 0.49817 / 0.27 (31737) hydrogen bonds : bond 0.02990 / 1.94 ( 815) hydrogen bonds : angle 4.70825 / 3.28 ( 2100) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 166 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 GLU cc_start: 0.8546 (mp0) cc_final: 0.8265 (mp0) REVERT: A 588 GLU cc_start: 0.8889 (mm-30) cc_final: 0.8672 (mp0) REVERT: A 719 GLN cc_start: 0.8393 (tt0) cc_final: 0.8042 (tm-30) REVERT: B 270 ASP cc_start: 0.9133 (t0) cc_final: 0.8824 (t0) REVERT: C 270 ASP cc_start: 0.8832 (t0) cc_final: 0.8237 (t0) REVERT: C 477 MET cc_start: 0.8526 (mmm) cc_final: 0.7897 (mpp) REVERT: C 770 GLN cc_start: 0.8548 (pm20) cc_final: 0.8002 (tp40) REVERT: C 780 TYR cc_start: 0.6427 (t80) cc_final: 0.6187 (t80) REVERT: F 477 MET cc_start: 0.8971 (mmt) cc_final: 0.8635 (mpp) REVERT: F 495 ASN cc_start: 0.7900 (p0) cc_final: 0.7675 (p0) REVERT: F 513 THR cc_start: 0.9249 (p) cc_final: 0.8936 (t) REVERT: F 523 ARG cc_start: 0.8380 (ttp80) cc_final: 0.7771 (ttp80) REVERT: G 310 ASN cc_start: 0.8288 (t0) cc_final: 0.7980 (t0) REVERT: G 454 ASP cc_start: 0.8544 (m-30) cc_final: 0.8247 (m-30) REVERT: G 477 MET cc_start: 0.8695 (mmm) cc_final: 0.8314 (mmm) REVERT: G 508 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8470 (mp10) REVERT: G 602 ASP cc_start: 0.9111 (m-30) cc_final: 0.8375 (t0) REVERT: G 770 GLN cc_start: 0.7924 (tm130) cc_final: 0.7446 (tm-30) outliers start: 39 outliers final: 33 residues processed: 196 average time/residue: 0.1656 time to fit residues: 50.5324 Evaluate side-chains 194 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 160 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 747 TYR Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 752 THR Chi-restraints excluded: chain C residue 656 PHE Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 736 ILE Chi-restraints excluded: chain C residue 747 TYR Chi-restraints excluded: chain F residue 266 SER Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 438 SER Chi-restraints excluded: chain F residue 478 LEU Chi-restraints excluded: chain F residue 483 THR Chi-restraints excluded: chain F residue 621 MET Chi-restraints excluded: chain F residue 665 VAL Chi-restraints excluded: chain F residue 686 TYR Chi-restraints excluded: chain F residue 699 VAL Chi-restraints excluded: chain G residue 508 GLN Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain G residue 687 MET Chi-restraints excluded: chain G residue 697 VAL Chi-restraints excluded: chain G residue 747 TYR Chi-restraints excluded: chain G residue 751 VAL Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 268 PHE Chi-restraints excluded: chain H residue 312 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 57 optimal weight: 0.0170 chunk 59 optimal weight: 1.9990 chunk 261 optimal weight: 8.9990 chunk 159 optimal weight: 2.9990 chunk 263 optimal weight: 4.9990 chunk 248 optimal weight: 1.9990 chunk 286 optimal weight: 7.9990 chunk 136 optimal weight: 6.9990 chunk 285 optimal weight: 30.0000 chunk 178 optimal weight: 4.9990 chunk 194 optimal weight: 7.9990 overall best weight: 2.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 731 ASN ** F 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.118925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.066395 restraints weight = 48427.323| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 3.12 r_work: 0.2826 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 23442 Z= 0.259 Angle : 0.565 12.938 31737 Z= 0.302 Chirality : 0.047 0.202 3572 Planarity : 0.004 0.046 4110 Dihedral : 4.548 21.227 3142 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.39 % Allowed : 17.69 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.15), residues: 2925 helix: -0.03 (0.24), residues: 504 sheet: 0.17 (0.19), residues: 772 loop : -1.24 (0.14), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 730 TYR 0.013 0.002 TYR G 737 PHE 0.012 0.002 PHE B 264 TRP 0.058 0.002 TRP C 748 HIS 0.007 0.001 HIS G 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00620 / 0.26 (23442) covalent geometry : angle 0.56503 / 0.30 (31737) hydrogen bonds : bond 0.03469 / 2.25 ( 815) hydrogen bonds : angle 4.90776 / 3.41 ( 2100) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 150 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 224 GLU cc_start: 0.8594 (mp0) cc_final: 0.8309 (mp0) REVERT: A 442 LYS cc_start: 0.9080 (mmtm) cc_final: 0.8857 (mmtm) REVERT: A 719 GLN cc_start: 0.8363 (tt0) cc_final: 0.8006 (tm-30) REVERT: B 270 ASP cc_start: 0.9083 (t0) cc_final: 0.8613 (t0) REVERT: C 270 ASP cc_start: 0.8792 (t0) cc_final: 0.8217 (t0) REVERT: C 439 TYR cc_start: 0.8531 (t80) cc_final: 0.8288 (t80) REVERT: C 477 MET cc_start: 0.8343 (mmm) cc_final: 0.7710 (mpp) REVERT: C 735 LYS cc_start: 0.8538 (mtmt) cc_final: 0.8246 (tttt) REVERT: C 780 TYR cc_start: 0.6329 (t80) cc_final: 0.6088 (t80) REVERT: F 477 MET cc_start: 0.8980 (mmt) cc_final: 0.8659 (mpp) REVERT: F 523 ARG cc_start: 0.8235 (ttp80) cc_final: 0.7644 (ttp80) REVERT: G 454 ASP cc_start: 0.8450 (m-30) cc_final: 0.8147 (m-30) REVERT: G 477 MET cc_start: 0.8597 (mmm) cc_final: 0.8191 (mmm) REVERT: G 602 ASP cc_start: 0.9153 (m-30) cc_final: 0.8386 (t0) outliers start: 36 outliers final: 35 residues processed: 180 average time/residue: 0.1577 time to fit residues: 44.0797 Evaluate side-chains 182 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 147 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 747 TYR Chi-restraints excluded: chain A residue 751 VAL Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 752 THR Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 656 PHE Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 736 ILE Chi-restraints excluded: chain F residue 266 SER Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 438 SER Chi-restraints excluded: chain F residue 478 LEU Chi-restraints excluded: chain F residue 483 THR Chi-restraints excluded: chain F residue 621 MET Chi-restraints excluded: chain F residue 665 VAL Chi-restraints excluded: chain F residue 686 TYR Chi-restraints excluded: chain F residue 699 VAL Chi-restraints excluded: chain F residue 770 GLN Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain G residue 697 VAL Chi-restraints excluded: chain G residue 747 TYR Chi-restraints excluded: chain G residue 751 VAL Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 268 PHE Chi-restraints excluded: chain H residue 312 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 61 optimal weight: 7.9990 chunk 57 optimal weight: 0.0970 chunk 15 optimal weight: 2.9990 chunk 287 optimal weight: 10.0000 chunk 284 optimal weight: 9.9990 chunk 192 optimal weight: 1.9990 chunk 162 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 224 optimal weight: 2.9990 chunk 199 optimal weight: 6.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.119734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.067203 restraints weight = 48316.623| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 3.14 r_work: 0.2844 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 23442 Z= 0.195 Angle : 0.525 12.923 31737 Z= 0.281 Chirality : 0.046 0.182 3572 Planarity : 0.003 0.045 4110 Dihedral : 4.413 21.085 3142 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.54 % Allowed : 17.73 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.15), residues: 2925 helix: -0.00 (0.24), residues: 504 sheet: 0.19 (0.19), residues: 776 loop : -1.22 (0.15), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 730 TYR 0.011 0.001 TYR H 437 PHE 0.013 0.001 PHE C 656 TRP 0.025 0.002 TRP C 748 HIS 0.004 0.001 HIS A 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.19 (23442) covalent geometry : angle 0.52548 / 0.28 (31737) hydrogen bonds : bond 0.03164 / 2.06 ( 815) hydrogen bonds : angle 4.84157 / 3.37 ( 2100) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7220.46 seconds wall clock time: 124 minutes 8.46 seconds (7448.46 seconds total)