Starting phenix.real_space_refine on Sun Aug 24 03:41:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iuz_35734/08_2025/8iuz_35734.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iuz_35734/08_2025/8iuz_35734.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8iuz_35734/08_2025/8iuz_35734.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iuz_35734/08_2025/8iuz_35734.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8iuz_35734/08_2025/8iuz_35734.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iuz_35734/08_2025/8iuz_35734.map" } resolution = 3.0 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: 4 Type Number sf(0) Gaussians S 87 5.16 5 C 10413 2.51 5 N 2892 2.21 5 O 3300 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16692 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3782 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 469} Chain breaks: 1 Chain: "B" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 927 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "C" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: D, G, E, H, F, I Time building chain proxies: 4.23, per 1000 atoms: 0.25 Number of scatterers: 16692 At special positions: 0 Unit cell: (154.944, 150.64, 150.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 87 16.00 O 3300 8.00 N 2892 7.00 C 10413 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 5 " - pdb=" SG CYS A 463 " distance=2.04 Simple disulfide: pdb=" SG CYS A 43 " - pdb=" SG CYS A 269 " distance=2.02 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 67 " distance=2.03 Simple disulfide: pdb=" SG CYS A 88 " - pdb=" SG CYS A 130 " distance=2.02 Simple disulfide: pdb=" SG CYS A 273 " - pdb=" SG CYS A 297 " distance=2.02 Simple disulfide: pdb=" SG CYS A 470 " - pdb=" SG CYS A 474 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 5 " - pdb=" SG CYS D 463 " distance=2.03 Simple disulfide: pdb=" SG CYS G 5 " - pdb=" SG CYS G 463 " distance=2.03 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 269 " distance=2.02 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 269 " distance=2.02 Simple disulfide: pdb=" SG CYS D 55 " - pdb=" SG CYS D 67 " distance=2.03 Simple disulfide: pdb=" SG CYS G 55 " - pdb=" SG CYS G 67 " distance=2.03 Simple disulfide: pdb=" SG CYS D 88 " - pdb=" SG CYS D 130 " distance=2.02 Simple disulfide: pdb=" SG CYS G 88 " - pdb=" SG CYS G 130 " distance=2.02 Simple disulfide: pdb=" SG CYS D 273 " - pdb=" SG CYS D 297 " distance=2.02 Simple disulfide: pdb=" SG CYS G 273 " - pdb=" SG CYS G 297 " distance=2.02 Simple disulfide: pdb=" SG CYS D 470 " - pdb=" SG CYS D 474 " distance=2.03 Simple disulfide: pdb=" SG CYS G 470 " - pdb=" SG CYS G 474 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 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=3, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 408 " " NAG A 502 " - " ASN A 29 " " NAG A 503 " - " ASN A 480 " " NAG D 501 " - " ASN D 408 " " NAG D 502 " - " ASN D 29 " " NAG D 503 " - " ASN D 480 " " NAG G 501 " - " ASN G 408 " " NAG G 502 " - " ASN G 29 " " NAG G 503 " - " ASN G 480 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.33 Conformation dependent library (CDL) restraints added in 970.9 milliseconds Enol-peptide restraints added in 1.2 microseconds 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3870 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 57 sheets defined 16.6% alpha, 26.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 56 through 60 removed outlier: 3.854A pdb=" N THR A 60 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 71 removed outlier: 3.992A pdb=" N LEU A 71 " --> pdb=" O ASP A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 103 removed outlier: 3.521A pdb=" N LEU A 99 " --> pdb=" O ASN A 95 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 removed outlier: 3.583A pdb=" N LYS A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 382 removed outlier: 3.901A pdb=" N ASP A 372 " --> pdb=" O GLN A 368 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLN A 373 " --> pdb=" O SER A 369 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 452 removed outlier: 3.628A pdb=" N VAL A 406 " --> pdb=" O GLN A 402 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 417 " --> pdb=" O SER A 413 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS A 432 " --> pdb=" O MET A 428 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 434 " --> pdb=" O ASN A 430 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASP A 435 " --> pdb=" O GLN A 431 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA A 437 " --> pdb=" O THR A 433 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N MET A 441 " --> pdb=" O ALA A 437 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 444 " --> pdb=" O GLU A 440 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS A 449 " --> pdb=" O TYR A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 478 removed outlier: 3.530A pdb=" N ILE A 478 " --> pdb=" O CYS A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 488 Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.699A pdb=" N ASP B 90 " --> pdb=" O THR B 87 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR B 91 " --> pdb=" O THR B 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 87 through 91' Processing helix chain 'C' and resid 79 through 83 removed outlier: 4.175A pdb=" N ILE C 83 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 60 removed outlier: 3.854A pdb=" N THR D 60 " --> pdb=" O LEU D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 71 removed outlier: 3.992A pdb=" N LEU D 71 " --> pdb=" O ASP D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 103 removed outlier: 3.520A pdb=" N LEU D 99 " --> pdb=" O ASN D 95 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU D 103 " --> pdb=" O LEU D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 185 removed outlier: 3.584A pdb=" N LYS D 185 " --> pdb=" O ALA D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 382 removed outlier: 3.901A pdb=" N ASP D 372 " --> pdb=" O GLN D 368 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLN D 373 " --> pdb=" O SER D 369 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE D 374 " --> pdb=" O ALA D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 452 removed outlier: 3.628A pdb=" N VAL D 406 " --> pdb=" O GLN D 402 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL D 417 " --> pdb=" O SER D 413 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU D 423 " --> pdb=" O SER D 419 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS D 432 " --> pdb=" O MET D 428 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE D 434 " --> pdb=" O ASN D 430 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASP D 435 " --> pdb=" O GLN D 431 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA D 437 " --> pdb=" O THR D 433 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N MET D 441 " --> pdb=" O ALA D 437 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU D 444 " --> pdb=" O GLU D 440 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL D 448 " --> pdb=" O LEU D 444 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS D 449 " --> pdb=" O TYR D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 478 removed outlier: 3.530A pdb=" N ILE D 478 " --> pdb=" O CYS D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 488 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.699A pdb=" N ASP E 90 " --> pdb=" O THR E 87 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR E 91 " --> pdb=" O THR E 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 91' Processing helix chain 'F' and resid 79 through 83 removed outlier: 4.175A pdb=" N ILE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 60 removed outlier: 3.854A pdb=" N THR G 60 " --> pdb=" O LEU G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 71 removed outlier: 3.992A pdb=" N LEU G 71 " --> pdb=" O ASP G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 103 removed outlier: 3.520A pdb=" N LEU G 99 " --> pdb=" O ASN G 95 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU G 103 " --> pdb=" O LEU G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 185 removed outlier: 3.583A pdb=" N LYS G 185 " --> pdb=" O ALA G 181 " (cutoff:3.500A) Processing helix chain 'G' and resid 364 through 382 removed outlier: 3.901A pdb=" N ASP G 372 " --> pdb=" O GLN G 368 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLN G 373 " --> pdb=" O SER G 369 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE G 374 " --> pdb=" O ALA G 370 " (cutoff:3.500A) Processing helix chain 'G' and resid 400 through 452 removed outlier: 3.629A pdb=" N VAL G 406 " --> pdb=" O GLN G 402 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL G 417 " --> pdb=" O SER G 413 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU G 423 " --> pdb=" O SER G 419 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS G 432 " --> pdb=" O MET G 428 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE G 434 " --> pdb=" O ASN G 430 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASP G 435 " --> pdb=" O GLN G 431 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA G 437 " --> pdb=" O THR G 433 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N MET G 441 " --> pdb=" O ALA G 437 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU G 444 " --> pdb=" O GLU G 440 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL G 448 " --> pdb=" O LEU G 444 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS G 449 " --> pdb=" O TYR G 445 " (cutoff:3.500A) Processing helix chain 'G' and resid 473 through 478 removed outlier: 3.530A pdb=" N ILE G 478 " --> pdb=" O CYS G 474 " (cutoff:3.500A) Processing helix chain 'G' and resid 484 through 488 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.700A pdb=" N ASP H 90 " --> pdb=" O THR H 87 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR H 91 " --> pdb=" O THR H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing helix chain 'I' and resid 79 through 83 removed outlier: 4.175A pdb=" N ILE I 83 " --> pdb=" O PRO I 80 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.910A pdb=" N GLY A 359 " --> pdb=" O HIS A 352 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASN A 354 " --> pdb=" O GLY A 357 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 3 through 7 removed outlier: 4.702A pdb=" N TYR A 348 " --> pdb=" O ASP A 363 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 15 through 17 Processing sheet with id=4, first strand: chain 'A' and resid 30 through 31 Processing sheet with id=5, first strand: chain 'A' and resid 34 through 35 Processing sheet with id=6, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.860A pdb=" N ILE A 42 " --> pdb=" O ASP A 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=6 Processing sheet with id=7, first strand: chain 'A' and resid 49 through 51 removed outlier: 3.540A pdb=" N ILE A 259 " --> pdb=" O ILE A 78 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU A 80 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'A' and resid 91 through 92 removed outlier: 6.695A pdb=" N LYS A 92 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N TRP A 226 " --> pdb=" O LYS A 92 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE A 170 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'A' and resid 110 through 113 removed outlier: 3.604A pdb=" N GLU A 112 " --> pdb=" O ALA A 249 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'A' and resid 121 through 122 removed outlier: 3.578A pdb=" N LEU A 145 " --> pdb=" O ARG A 122 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'A' and resid 156 through 161 Processing sheet with id=12, first strand: chain 'A' and resid 278 through 280 removed outlier: 4.122A pdb=" N CYS A 273 " --> pdb=" O ILE A 280 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL A 294 " --> pdb=" O TYR A 274 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'A' and resid 456 through 458 removed outlier: 3.592A pdb=" N GLU A 457 " --> pdb=" O GLU A 465 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLU A 465 " --> pdb=" O GLU A 457 " (cutoff:3.500A) No H-bonds generated for sheet with id=13 Processing sheet with id=14, first strand: chain 'B' and resid 3 through 7 removed outlier: 3.507A pdb=" N GLN B 3 " --> pdb=" O THR B 25 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR B 21 " --> pdb=" O SER B 7 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'B' and resid 58 through 60 removed outlier: 3.576A pdb=" N SER B 59 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS B 45 " --> pdb=" O PHE B 41 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU B 47 " --> pdb=" O ARG B 39 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N TRP B 37 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N TYR B 51 " --> pdb=" O TRP B 35 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N TRP B 35 " --> pdb=" O TYR B 51 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'B' and resid 58 through 60 removed outlier: 3.576A pdb=" N SER B 59 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS B 45 " --> pdb=" O PHE B 41 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU B 47 " --> pdb=" O ARG B 39 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N TRP B 37 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N TYR B 51 " --> pdb=" O TRP B 35 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N TRP B 35 " --> pdb=" O TYR B 51 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.748A pdb=" N LEU C 11 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR C 102 " --> pdb=" O TYR C 86 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LEU C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N TYR C 49 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.748A pdb=" N LEU C 11 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR C 102 " --> pdb=" O TYR C 86 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN C 90 " --> pdb=" O THR C 97 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR C 97 " --> pdb=" O GLN C 90 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'C' and resid 22 through 23 removed outlier: 3.656A pdb=" N PHE C 71 " --> pdb=" O CYS C 23 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.910A pdb=" N GLY D 359 " --> pdb=" O HIS D 352 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASN D 354 " --> pdb=" O GLY D 357 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'D' and resid 3 through 7 removed outlier: 4.702A pdb=" N TYR D 348 " --> pdb=" O ASP D 363 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'D' and resid 15 through 17 Processing sheet with id=23, first strand: chain 'D' and resid 30 through 31 Processing sheet with id=24, first strand: chain 'D' and resid 34 through 35 Processing sheet with id=25, first strand: chain 'D' and resid 42 through 43 removed outlier: 5.861A pdb=" N ILE D 42 " --> pdb=" O ASP D 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=25 Processing sheet with id=26, first strand: chain 'D' and resid 49 through 51 removed outlier: 3.540A pdb=" N ILE D 259 " --> pdb=" O ILE D 78 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU D 80 " --> pdb=" O ILE D 259 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'D' and resid 91 through 92 removed outlier: 6.694A pdb=" N LYS D 92 " --> pdb=" O PHE D 224 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N TRP D 226 " --> pdb=" O LYS D 92 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE D 170 " --> pdb=" O LEU D 227 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'D' and resid 110 through 113 removed outlier: 3.605A pdb=" N GLU D 112 " --> pdb=" O ALA D 249 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'D' and resid 121 through 122 removed outlier: 3.579A pdb=" N LEU D 145 " --> pdb=" O ARG D 122 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'D' and resid 156 through 161 Processing sheet with id=31, first strand: chain 'D' and resid 278 through 280 removed outlier: 4.123A pdb=" N CYS D 273 " --> pdb=" O ILE D 280 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL D 294 " --> pdb=" O TYR D 274 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'D' and resid 456 through 458 removed outlier: 3.592A pdb=" N GLU D 457 " --> pdb=" O GLU D 465 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLU D 465 " --> pdb=" O GLU D 457 " (cutoff:3.500A) No H-bonds generated for sheet with id=32 Processing sheet with id=33, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.507A pdb=" N GLN E 3 " --> pdb=" O THR E 25 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'E' and resid 58 through 60 removed outlier: 3.576A pdb=" N SER E 59 " --> pdb=" O TYR E 51 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS E 45 " --> pdb=" O PHE E 41 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU E 47 " --> pdb=" O ARG E 39 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N TRP E 37 " --> pdb=" O MET E 49 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N TYR E 51 " --> pdb=" O TRP E 35 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N TRP E 35 " --> pdb=" O TYR E 51 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'E' and resid 58 through 60 removed outlier: 3.576A pdb=" N SER E 59 " --> pdb=" O TYR E 51 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS E 45 " --> pdb=" O PHE E 41 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU E 47 " --> pdb=" O ARG E 39 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N TRP E 37 " --> pdb=" O MET E 49 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N TYR E 51 " --> pdb=" O TRP E 35 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N TRP E 35 " --> pdb=" O TYR E 51 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.749A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR F 102 " --> pdb=" O TYR F 86 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=37, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.749A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR F 102 " --> pdb=" O TYR F 86 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN F 90 " --> pdb=" O THR F 97 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N THR F 97 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=38, first strand: chain 'F' and resid 22 through 23 removed outlier: 3.656A pdb=" N PHE F 71 " --> pdb=" O CYS F 23 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.910A pdb=" N GLY G 359 " --> pdb=" O HIS G 352 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASN G 354 " --> pdb=" O GLY G 357 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'G' and resid 3 through 7 removed outlier: 4.702A pdb=" N TYR G 348 " --> pdb=" O ASP G 363 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'G' and resid 15 through 17 Processing sheet with id=42, first strand: chain 'G' and resid 30 through 31 Processing sheet with id=43, first strand: chain 'G' and resid 34 through 35 Processing sheet with id=44, first strand: chain 'G' and resid 42 through 43 removed outlier: 5.860A pdb=" N ILE G 42 " --> pdb=" O ASP G 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=44 Processing sheet with id=45, first strand: chain 'G' and resid 49 through 51 removed outlier: 3.540A pdb=" N ILE G 259 " --> pdb=" O ILE G 78 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU G 80 " --> pdb=" O ILE G 259 " (cutoff:3.500A) Processing sheet with id=46, first strand: chain 'G' and resid 91 through 92 removed outlier: 6.695A pdb=" N LYS G 92 " --> pdb=" O PHE G 224 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N TRP G 226 " --> pdb=" O LYS G 92 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE G 170 " --> pdb=" O LEU G 227 " (cutoff:3.500A) Processing sheet with id=47, first strand: chain 'G' and resid 110 through 113 removed outlier: 3.604A pdb=" N GLU G 112 " --> pdb=" O ALA G 249 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'G' and resid 121 through 122 removed outlier: 3.577A pdb=" N LEU G 145 " --> pdb=" O ARG G 122 " (cutoff:3.500A) Processing sheet with id=49, first strand: chain 'G' and resid 156 through 161 Processing sheet with id=50, first strand: chain 'G' and resid 278 through 280 removed outlier: 4.122A pdb=" N CYS G 273 " --> pdb=" O ILE G 280 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL G 294 " --> pdb=" O TYR G 274 " (cutoff:3.500A) Processing sheet with id=51, first strand: chain 'G' and resid 456 through 458 removed outlier: 3.592A pdb=" N GLU G 457 " --> pdb=" O GLU G 465 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLU G 465 " --> pdb=" O GLU G 457 " (cutoff:3.500A) No H-bonds generated for sheet with id=51 Processing sheet with id=52, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.507A pdb=" N GLN H 3 " --> pdb=" O THR H 25 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) Processing sheet with id=53, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.576A pdb=" N SER H 59 " --> pdb=" O TYR H 51 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS H 45 " --> pdb=" O PHE H 41 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU H 47 " --> pdb=" O ARG H 39 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N TRP H 37 " --> pdb=" O MET H 49 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N TYR H 51 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N TRP H 35 " --> pdb=" O TYR H 51 " (cutoff:3.500A) Processing sheet with id=54, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.576A pdb=" N SER H 59 " --> pdb=" O TYR H 51 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS H 45 " --> pdb=" O PHE H 41 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU H 47 " --> pdb=" O ARG H 39 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N TRP H 37 " --> pdb=" O MET H 49 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N TYR H 51 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N TRP H 35 " --> pdb=" O TYR H 51 " (cutoff:3.500A) Processing sheet with id=55, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.748A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR I 102 " --> pdb=" O TYR I 86 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=56, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.748A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR I 102 " --> pdb=" O TYR I 86 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN I 90 " --> pdb=" O THR I 97 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR I 97 " --> pdb=" O GLN I 90 " (cutoff:3.500A) Processing sheet with id=57, first strand: chain 'I' and resid 22 through 23 removed outlier: 3.656A pdb=" N PHE I 71 " --> pdb=" O CYS I 23 " (cutoff:3.500A) 501 hydrogen bonds defined for protein. 1305 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: 3.58 Time building geometry restraints manager: 1.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3819 1.33 - 1.45: 4174 1.45 - 1.58: 8918 1.58 - 1.70: 0 1.70 - 1.82: 126 Bond restraints: 17037 Sorted by residual: bond pdb=" CB VAL A 235 " pdb=" CG2 VAL A 235 " ideal model delta sigma weight residual 1.521 1.422 0.099 3.30e-02 9.18e+02 9.05e+00 bond pdb=" CB VAL G 235 " pdb=" CG2 VAL G 235 " ideal model delta sigma weight residual 1.521 1.422 0.099 3.30e-02 9.18e+02 9.04e+00 bond pdb=" CB VAL D 235 " pdb=" CG2 VAL D 235 " ideal model delta sigma weight residual 1.521 1.422 0.099 3.30e-02 9.18e+02 9.04e+00 bond pdb=" C1 NAG D 503 " pdb=" O5 NAG D 503 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 6.90e+00 bond pdb=" C1 NAG A 503 " pdb=" O5 NAG A 503 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.77e+00 ... (remaining 17032 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 22073 2.88 - 5.77: 883 5.77 - 8.65: 88 8.65 - 11.54: 23 11.54 - 14.42: 12 Bond angle restraints: 23079 Sorted by residual: angle pdb=" C ILE I 29 " pdb=" N ASN I 30 " pdb=" CA ASN I 30 " ideal model delta sigma weight residual 121.54 133.47 -11.93 1.91e+00 2.74e-01 3.90e+01 angle pdb=" C ILE F 29 " pdb=" N ASN F 30 " pdb=" CA ASN F 30 " ideal model delta sigma weight residual 121.54 133.46 -11.92 1.91e+00 2.74e-01 3.90e+01 angle pdb=" C ILE C 29 " pdb=" N ASN C 30 " pdb=" CA ASN C 30 " ideal model delta sigma weight residual 121.54 133.44 -11.90 1.91e+00 2.74e-01 3.88e+01 angle pdb=" N ILE F 29 " pdb=" CA ILE F 29 " pdb=" C ILE F 29 " ideal model delta sigma weight residual 113.71 108.88 4.83 9.50e-01 1.11e+00 2.59e+01 angle pdb=" N ILE I 29 " pdb=" CA ILE I 29 " pdb=" C ILE I 29 " ideal model delta sigma weight residual 113.71 108.89 4.82 9.50e-01 1.11e+00 2.58e+01 ... (remaining 23074 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.02: 9270 16.02 - 32.05: 804 32.05 - 48.07: 156 48.07 - 64.09: 33 64.09 - 80.12: 15 Dihedral angle restraints: 10278 sinusoidal: 4212 harmonic: 6066 Sorted by residual: dihedral pdb=" CA ASN G 397 " pdb=" C ASN G 397 " pdb=" N GLU G 398 " pdb=" CA GLU G 398 " ideal model delta harmonic sigma weight residual 180.00 137.42 42.58 0 5.00e+00 4.00e-02 7.25e+01 dihedral pdb=" CA ASN A 397 " pdb=" C ASN A 397 " pdb=" N GLU A 398 " pdb=" CA GLU A 398 " ideal model delta harmonic sigma weight residual 180.00 137.47 42.53 0 5.00e+00 4.00e-02 7.23e+01 dihedral pdb=" CA ASN D 397 " pdb=" C ASN D 397 " pdb=" N GLU D 398 " pdb=" CA GLU D 398 " ideal model delta harmonic sigma weight residual 180.00 137.53 42.47 0 5.00e+00 4.00e-02 7.21e+01 ... (remaining 10275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 2329 0.119 - 0.238: 194 0.238 - 0.358: 21 0.358 - 0.477: 0 0.477 - 0.596: 3 Chirality restraints: 2547 Sorted by residual: chirality pdb=" CB ILE A 4 " pdb=" CA ILE A 4 " pdb=" CG1 ILE A 4 " pdb=" CG2 ILE A 4 " both_signs ideal model delta sigma weight residual False 2.64 2.05 0.60 2.00e-01 2.50e+01 8.88e+00 chirality pdb=" CB ILE D 4 " pdb=" CA ILE D 4 " pdb=" CG1 ILE D 4 " pdb=" CG2 ILE D 4 " both_signs ideal model delta sigma weight residual False 2.64 2.05 0.60 2.00e-01 2.50e+01 8.87e+00 chirality pdb=" CB ILE G 4 " pdb=" CA ILE G 4 " pdb=" CG1 ILE G 4 " pdb=" CG2 ILE G 4 " both_signs ideal model delta sigma weight residual False 2.64 2.05 0.60 2.00e-01 2.50e+01 8.86e+00 ... (remaining 2544 not shown) Planarity restraints: 3003 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP G 143 " -0.025 2.00e-02 2.50e+03 1.97e-02 9.68e+00 pdb=" CG TRP G 143 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP G 143 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP G 143 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP G 143 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP G 143 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP G 143 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 143 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 143 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP G 143 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 143 " 0.025 2.00e-02 2.50e+03 1.97e-02 9.67e+00 pdb=" CG TRP A 143 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP A 143 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP A 143 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 143 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 143 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 143 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 143 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 143 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 143 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 143 " 0.026 2.00e-02 2.50e+03 1.97e-02 9.67e+00 pdb=" CG TRP D 143 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP D 143 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP D 143 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 143 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP D 143 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP D 143 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 143 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 143 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 143 " 0.004 2.00e-02 2.50e+03 ... (remaining 3000 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.99: 3 1.99 - 2.71: 1253 2.71 - 3.44: 21728 3.44 - 4.17: 38588 4.17 - 4.90: 69014 Nonbonded interactions: 130586 Sorted by model distance: nonbonded pdb=" OE1 GLU D 457 " pdb=" NH2 ARG G 453 " model vdw 1.257 3.120 nonbonded pdb=" NH2 ARG A 453 " pdb=" OE1 GLU G 457 " model vdw 1.257 3.120 nonbonded pdb=" OE1 GLU A 457 " pdb=" NH2 ARG D 453 " model vdw 1.257 3.120 nonbonded pdb=" CD GLU A 457 " pdb=" NH2 ARG D 453 " model vdw 2.063 3.350 nonbonded pdb=" CD GLU D 457 " pdb=" NH2 ARG G 453 " model vdw 2.063 3.350 ... (remaining 130581 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' } 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: 6.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.190 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4861 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 : 0.012 0.458 17073 Z= 0.755 Angle : 1.360 17.429 23154 Z= 0.749 Chirality : 0.074 0.596 2547 Planarity : 0.008 0.074 2994 Dihedral : 12.686 80.118 6336 Min Nonbonded Distance : 1.257 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.17 % Favored : 87.83 % Rotamer: Outliers : 0.99 % Allowed : 4.28 % Favored : 94.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % 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 aren not related in a simple way. whole: -4.45 (0.15), residues: 2103 helix: -3.45 (0.19), residues: 291 sheet: -2.80 (0.18), residues: 663 loop : -2.93 (0.15), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.002 ARG D 450 TYR 0.052 0.004 TYR E 102 PHE 0.036 0.006 PHE G 335 TRP 0.052 0.005 TRP G 143 HIS 0.013 0.004 HIS D 175 Details of bonding type rmsd covalent geometry : bond 0.01006 (17037) covalent geometry : angle 1.33708 (23079) SS BOND : bond 0.00512 ( 24) SS BOND : angle 2.01678 ( 48) hydrogen bonds : bond 0.30501 ( 450) hydrogen bonds : angle 10.31721 ( 1305) Misc. bond : bond 0.45787 ( 3) link_NAG-ASN : bond 0.00538 ( 9) link_NAG-ASN : angle 7.10285 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 355 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 ASN cc_start: 0.8468 (t0) cc_final: 0.8186 (t0) REVERT: B 67 ARG cc_start: 0.6017 (ptp-110) cc_final: 0.5638 (ptt180) REVERT: C 5 ASN cc_start: 0.6169 (m-40) cc_final: 0.5912 (m-40) REVERT: C 50 LYS cc_start: 0.6404 (mttt) cc_final: 0.6195 (mttt) REVERT: D 310 THR cc_start: 0.1801 (OUTLIER) cc_final: 0.1381 (m) REVERT: D 401 LYS cc_start: 0.4301 (mppt) cc_final: 0.4066 (mtmm) REVERT: D 412 ASP cc_start: 0.4848 (t70) cc_final: 0.4625 (t0) REVERT: G 87 VAL cc_start: 0.6014 (m) cc_final: 0.5654 (p) REVERT: G 408 ASN cc_start: 0.4323 (m-40) cc_final: 0.3933 (t160) REVERT: I 67 SER cc_start: 0.2164 (p) cc_final: 0.1766 (m) outliers start: 18 outliers final: 1 residues processed: 368 average time/residue: 0.5082 time to fit residues: 211.4624 Evaluate side-chains 204 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 202 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 310 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.0970 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 0.3980 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 6.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN A 124 ASN A 155 GLN A 268 ASN A 421 ASN A 430 ASN A 455 ASN A 468 HIS A 481 ASN A 485 HIS A 495 ASN B 61 ASN B 104 HIS C 42 ASN C 53 ASN D 69 GLN D 155 GLN D 175 HIS D 225 HIS D 353 GLN D 388 GLN D 430 ASN D 455 ASN D 481 ASN D 495 ASN E 104 HIS F 42 ASN F 53 ASN ** G 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 288 ASN G 373 GLN G 421 ASN G 430 ASN G 455 ASN G 481 ASN G 485 HIS G 495 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 HIS I 42 ASN I 53 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5084 r_free = 0.5084 target = 0.206388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.173674 restraints weight = 28928.015| |-----------------------------------------------------------------------------| r_work (start): 0.4723 rms_B_bonded: 3.20 r_work: 0.4625 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.4625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5744 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 17073 Z= 0.169 Angle : 0.770 9.816 23154 Z= 0.401 Chirality : 0.048 0.204 2547 Planarity : 0.006 0.059 2994 Dihedral : 7.543 71.461 2489 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.34 % Allowed : 12.45 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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 aren not related in a simple way. whole: -3.28 (0.16), residues: 2103 helix: -1.21 (0.28), residues: 321 sheet: -1.98 (0.21), residues: 546 loop : -2.63 (0.15), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 212 TYR 0.017 0.002 TYR D 488 PHE 0.026 0.002 PHE G 137 TRP 0.017 0.002 TRP G 418 HIS 0.006 0.001 HIS G 275 Details of bonding type rmsd covalent geometry : bond 0.00359 (17037) covalent geometry : angle 0.75607 (23079) SS BOND : bond 0.00680 ( 24) SS BOND : angle 1.62918 ( 48) hydrogen bonds : bond 0.05229 ( 450) hydrogen bonds : angle 5.88294 ( 1305) Misc. bond : bond 0.00230 ( 3) link_NAG-ASN : bond 0.01605 ( 9) link_NAG-ASN : angle 3.82066 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 263 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.7320 (tp30) cc_final: 0.7116 (tp30) REVERT: A 119 ASN cc_start: 0.7331 (p0) cc_final: 0.6691 (t0) REVERT: A 170 ILE cc_start: 0.7345 (OUTLIER) cc_final: 0.6919 (mp) REVERT: C 5 ASN cc_start: 0.5961 (m-40) cc_final: 0.5750 (m-40) REVERT: D 141 MET cc_start: 0.4950 (mmt) cc_final: 0.4273 (mmm) REVERT: D 174 ILE cc_start: 0.6511 (OUTLIER) cc_final: 0.5736 (mm) REVERT: D 412 ASP cc_start: 0.7141 (t70) cc_final: 0.6751 (t0) REVERT: D 493 MET cc_start: 0.5954 (OUTLIER) cc_final: 0.5214 (ppp) REVERT: E 1 MET cc_start: 0.1004 (tmt) cc_final: 0.0623 (tpp) REVERT: E 47 GLU cc_start: 0.5160 (OUTLIER) cc_final: 0.4111 (tt0) REVERT: E 49 MET cc_start: 0.6308 (mmm) cc_final: 0.5618 (mmm) REVERT: E 68 MET cc_start: 0.6491 (tpp) cc_final: 0.6029 (mtm) REVERT: F 4 MET cc_start: 0.6856 (tpp) cc_final: 0.6558 (tpp) REVERT: F 38 LEU cc_start: 0.7193 (OUTLIER) cc_final: 0.6603 (mm) REVERT: G 19 THR cc_start: 0.7357 (t) cc_final: 0.7133 (t) REVERT: G 201 TYR cc_start: 0.4936 (OUTLIER) cc_final: 0.3697 (t80) REVERT: G 274 TYR cc_start: 0.4638 (OUTLIER) cc_final: 0.4353 (m-80) REVERT: G 386 ASN cc_start: 0.5359 (p0) cc_final: 0.5053 (p0) REVERT: I 4 MET cc_start: 0.3030 (tpp) cc_final: 0.2637 (tpt) outliers start: 61 outliers final: 18 residues processed: 300 average time/residue: 0.4584 time to fit residues: 158.8095 Evaluate side-chains 200 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 175 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain C residue 23 CYS Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 493 MET Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 201 TYR Chi-restraints excluded: chain G residue 274 TYR Chi-restraints excluded: chain G residue 446 GLU Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 38 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 115 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 172 optimal weight: 0.9990 chunk 137 optimal weight: 4.9990 chunk 131 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 201 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 HIS A 225 HIS A 495 ASN B 40 GLN D 9 HIS D 175 HIS D 368 GLN D 388 GLN D 432 HIS E 40 GLN G 54 GLN G 264 GLN G 432 HIS ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 40 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4853 r_free = 0.4853 target = 0.195773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.153646 restraints weight = 26511.155| |-----------------------------------------------------------------------------| r_work (start): 0.4294 rms_B_bonded: 3.38 r_work: 0.4177 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.4177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 moved from start: 0.7586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 17073 Z= 0.191 Angle : 0.820 11.336 23154 Z= 0.421 Chirality : 0.049 0.224 2547 Planarity : 0.006 0.067 2994 Dihedral : 7.381 59.999 2488 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 4.11 % Allowed : 15.19 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 aren not related in a simple way. whole: -2.89 (0.17), residues: 2103 helix: -0.92 (0.28), residues: 318 sheet: -1.77 (0.20), residues: 621 loop : -2.32 (0.16), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 486 TYR 0.032 0.002 TYR D 445 PHE 0.029 0.003 PHE G 205 TRP 0.037 0.002 TRP D 143 HIS 0.008 0.001 HIS D 9 Details of bonding type rmsd covalent geometry : bond 0.00418 (17037) covalent geometry : angle 0.80973 (23079) SS BOND : bond 0.01023 ( 24) SS BOND : angle 1.35877 ( 48) hydrogen bonds : bond 0.05339 ( 450) hydrogen bonds : angle 5.69899 ( 1305) Misc. bond : bond 0.00136 ( 3) link_NAG-ASN : bond 0.00816 ( 9) link_NAG-ASN : angle 3.55705 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 224 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.5758 (OUTLIER) cc_final: 0.4851 (mp0) REVERT: A 119 ASN cc_start: 0.7363 (p0) cc_final: 0.6598 (t0) REVERT: A 170 ILE cc_start: 0.7523 (OUTLIER) cc_final: 0.6898 (mp) REVERT: A 485 HIS cc_start: 0.7347 (p-80) cc_final: 0.6488 (p-80) REVERT: A 493 MET cc_start: 0.6822 (mtm) cc_final: 0.6595 (mtm) REVERT: C 4 MET cc_start: 0.5847 (mmm) cc_final: 0.5553 (mtm) REVERT: D 95 ASN cc_start: 0.8285 (t0) cc_final: 0.8079 (t0) REVERT: D 137 PHE cc_start: 0.4649 (t80) cc_final: 0.4305 (t80) REVERT: D 174 ILE cc_start: 0.7423 (OUTLIER) cc_final: 0.7044 (mm) REVERT: D 307 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8141 (mm) REVERT: D 380 ARG cc_start: 0.6833 (OUTLIER) cc_final: 0.6633 (ttp80) REVERT: D 442 ASP cc_start: 0.7231 (t0) cc_final: 0.6552 (t0) REVERT: D 467 PHE cc_start: 0.6228 (m-80) cc_final: 0.5971 (m-80) REVERT: E 49 MET cc_start: 0.5710 (mmm) cc_final: 0.4943 (mmm) REVERT: F 47 LEU cc_start: 0.4700 (mt) cc_final: 0.4371 (mm) REVERT: F 49 TYR cc_start: 0.5084 (p90) cc_final: 0.4692 (p90) REVERT: F 97 THR cc_start: 0.3833 (p) cc_final: 0.3534 (p) REVERT: G 54 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7751 (tm-30) REVERT: G 145 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.7108 (tt) REVERT: G 182 GLU cc_start: 0.5027 (tm-30) cc_final: 0.4654 (tp30) REVERT: G 201 TYR cc_start: 0.6773 (OUTLIER) cc_final: 0.6031 (m-80) REVERT: G 252 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8406 (mp) REVERT: G 436 LEU cc_start: 0.7320 (mp) cc_final: 0.7040 (mt) REVERT: G 457 GLU cc_start: 0.6998 (mt-10) cc_final: 0.5677 (mp0) REVERT: G 475 MET cc_start: 0.6296 (tpp) cc_final: 0.5995 (mmt) REVERT: G 486 ARG cc_start: 0.7579 (mmm160) cc_final: 0.6769 (tpm170) outliers start: 75 outliers final: 20 residues processed: 279 average time/residue: 0.4743 time to fit residues: 151.6736 Evaluate side-chains 188 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain C residue 23 CYS Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 380 ARG Chi-restraints excluded: chain D residue 493 MET Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain G residue 54 GLN Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 201 TYR Chi-restraints excluded: chain G residue 240 ASN Chi-restraints excluded: chain G residue 252 LEU Chi-restraints excluded: chain G residue 446 GLU Chi-restraints excluded: chain G residue 495 ASN Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain I residue 38 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 171 optimal weight: 0.0270 chunk 58 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 137 optimal weight: 0.9980 chunk 172 optimal weight: 0.0010 chunk 141 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 overall best weight: 0.4644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 495 ASN D 69 GLN ** D 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 54 GLN G 183 GLN G 214 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4805 r_free = 0.4805 target = 0.178809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.139539 restraints weight = 27451.122| |-----------------------------------------------------------------------------| r_work (start): 0.4314 rms_B_bonded: 3.22 r_work: 0.4216 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6625 moved from start: 0.8021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17073 Z= 0.118 Angle : 0.658 9.256 23154 Z= 0.336 Chirality : 0.045 0.243 2547 Planarity : 0.005 0.053 2994 Dihedral : 6.630 59.574 2487 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.18 % Allowed : 17.71 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 aren not related in a simple way. whole: -2.37 (0.18), residues: 2103 helix: -0.21 (0.30), residues: 318 sheet: -1.40 (0.20), residues: 627 loop : -2.10 (0.17), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 131 TYR 0.021 0.001 TYR D 420 PHE 0.026 0.002 PHE G 205 TRP 0.012 0.001 TRP G 143 HIS 0.005 0.001 HIS G 432 Details of bonding type rmsd covalent geometry : bond 0.00264 (17037) covalent geometry : angle 0.64676 (23079) SS BOND : bond 0.00313 ( 24) SS BOND : angle 1.45356 ( 48) hydrogen bonds : bond 0.03805 ( 450) hydrogen bonds : angle 5.03028 ( 1305) Misc. bond : bond 0.00090 ( 3) link_NAG-ASN : bond 0.00559 ( 9) link_NAG-ASN : angle 3.08442 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 199 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.5659 (OUTLIER) cc_final: 0.4774 (mp0) REVERT: A 119 ASN cc_start: 0.7469 (p0) cc_final: 0.6727 (t0) REVERT: A 170 ILE cc_start: 0.7404 (OUTLIER) cc_final: 0.6849 (mp) REVERT: A 299 ARG cc_start: 0.6698 (OUTLIER) cc_final: 0.5007 (mtp180) REVERT: A 493 MET cc_start: 0.6659 (mtm) cc_final: 0.6456 (mtm) REVERT: D 82 ARG cc_start: 0.7908 (mmm160) cc_final: 0.7628 (tpp-160) REVERT: D 95 ASN cc_start: 0.8318 (t0) cc_final: 0.8060 (t0) REVERT: D 119 ASN cc_start: 0.6865 (p0) cc_final: 0.5817 (t0) REVERT: D 127 THR cc_start: 0.8258 (p) cc_final: 0.7948 (t) REVERT: D 174 ILE cc_start: 0.7365 (OUTLIER) cc_final: 0.7018 (mm) REVERT: D 380 ARG cc_start: 0.6857 (OUTLIER) cc_final: 0.6655 (ttp80) REVERT: D 420 TYR cc_start: 0.7458 (t80) cc_final: 0.7257 (t80) REVERT: E 1 MET cc_start: 0.2233 (tmt) cc_final: 0.1761 (tpp) REVERT: F 49 TYR cc_start: 0.4925 (p90) cc_final: 0.4537 (p90) REVERT: G 54 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.7180 (tm-30) REVERT: G 119 ASN cc_start: 0.6276 (p0) cc_final: 0.5322 (p0) REVERT: G 145 LEU cc_start: 0.7516 (tp) cc_final: 0.7227 (tp) REVERT: G 156 MET cc_start: 0.6048 (mpp) cc_final: 0.5565 (mpp) REVERT: G 201 TYR cc_start: 0.6802 (OUTLIER) cc_final: 0.6207 (m-80) REVERT: G 299 ARG cc_start: 0.6826 (OUTLIER) cc_final: 0.6454 (mpp-170) REVERT: G 313 LYS cc_start: 0.6188 (OUTLIER) cc_final: 0.5798 (tptm) REVERT: G 454 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.6706 (tm-30) REVERT: G 463 CYS cc_start: 0.7985 (m) cc_final: 0.7718 (m) REVERT: G 467 PHE cc_start: 0.7231 (m-80) cc_final: 0.6798 (t80) REVERT: G 475 MET cc_start: 0.6320 (tpp) cc_final: 0.5876 (mmt) REVERT: G 486 ARG cc_start: 0.7410 (mmm160) cc_final: 0.7099 (tpm-80) REVERT: I 46 LEU cc_start: 0.2641 (OUTLIER) cc_final: 0.2301 (tm) outliers start: 58 outliers final: 16 residues processed: 248 average time/residue: 0.4781 time to fit residues: 136.4560 Evaluate side-chains 186 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 299 ARG Chi-restraints excluded: chain C residue 23 CYS Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 380 ARG Chi-restraints excluded: chain D residue 401 LYS Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 54 GLN Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 201 TYR Chi-restraints excluded: chain G residue 299 ARG Chi-restraints excluded: chain G residue 313 LYS Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 454 GLU Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 46 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 132 optimal weight: 0.0370 chunk 82 optimal weight: 5.9990 chunk 128 optimal weight: 8.9990 chunk 2 optimal weight: 0.3980 chunk 119 optimal weight: 9.9990 chunk 157 optimal weight: 5.9990 chunk 42 optimal weight: 0.1980 chunk 124 optimal weight: 4.9990 chunk 172 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 495 ASN D 69 GLN ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 101 GLN G 240 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4796 r_free = 0.4796 target = 0.181873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.140817 restraints weight = 26073.513| |-----------------------------------------------------------------------------| r_work (start): 0.4244 rms_B_bonded: 3.15 r_work: 0.4136 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6611 moved from start: 0.8501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17073 Z= 0.114 Angle : 0.640 10.324 23154 Z= 0.326 Chirality : 0.044 0.222 2547 Planarity : 0.005 0.065 2994 Dihedral : 6.349 58.591 2487 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.07 % Allowed : 18.91 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -2.03 (0.18), residues: 2103 helix: 0.07 (0.30), residues: 318 sheet: -1.08 (0.21), residues: 639 loop : -1.95 (0.17), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 122 TYR 0.023 0.001 TYR G 420 PHE 0.020 0.002 PHE G 93 TRP 0.012 0.001 TRP G 143 HIS 0.006 0.001 HIS G 432 Details of bonding type rmsd covalent geometry : bond 0.00256 (17037) covalent geometry : angle 0.63256 (23079) SS BOND : bond 0.00374 ( 24) SS BOND : angle 1.01738 ( 48) hydrogen bonds : bond 0.03629 ( 450) hydrogen bonds : angle 4.74964 ( 1305) Misc. bond : bond 0.00065 ( 3) link_NAG-ASN : bond 0.00417 ( 9) link_NAG-ASN : angle 2.74223 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 172 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.5509 (OUTLIER) cc_final: 0.4658 (mp0) REVERT: A 119 ASN cc_start: 0.7504 (p0) cc_final: 0.6844 (t0) REVERT: A 170 ILE cc_start: 0.7418 (OUTLIER) cc_final: 0.6829 (mp) REVERT: A 299 ARG cc_start: 0.6512 (OUTLIER) cc_final: 0.4832 (mpp-170) REVERT: A 337 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7194 (pm20) REVERT: A 485 HIS cc_start: 0.7471 (p90) cc_final: 0.7170 (p-80) REVERT: A 493 MET cc_start: 0.6687 (mtm) cc_final: 0.6468 (mtm) REVERT: D 95 ASN cc_start: 0.8317 (t0) cc_final: 0.8012 (t0) REVERT: D 114 MET cc_start: 0.7780 (ttm) cc_final: 0.7230 (ttm) REVERT: D 119 ASN cc_start: 0.6919 (p0) cc_final: 0.6020 (t0) REVERT: D 127 THR cc_start: 0.8416 (p) cc_final: 0.8196 (t) REVERT: D 146 SER cc_start: 0.8454 (t) cc_final: 0.8044 (p) REVERT: D 174 ILE cc_start: 0.7184 (OUTLIER) cc_final: 0.6912 (mm) REVERT: D 380 ARG cc_start: 0.6863 (OUTLIER) cc_final: 0.6611 (ttp80) REVERT: D 401 LYS cc_start: 0.6286 (OUTLIER) cc_final: 0.5996 (mppt) REVERT: D 446 GLU cc_start: 0.7072 (OUTLIER) cc_final: 0.6810 (pm20) REVERT: E 1 MET cc_start: 0.2336 (tmt) cc_final: 0.1843 (tpp) REVERT: E 68 MET cc_start: 0.6951 (ptm) cc_final: 0.6267 (ptm) REVERT: F 49 TYR cc_start: 0.4801 (p90) cc_final: 0.4367 (p90) REVERT: G 22 GLU cc_start: 0.6369 (OUTLIER) cc_final: 0.6067 (mp0) REVERT: G 54 GLN cc_start: 0.7756 (tm-30) cc_final: 0.7326 (tm-30) REVERT: G 119 ASN cc_start: 0.6354 (p0) cc_final: 0.5477 (p0) REVERT: G 201 TYR cc_start: 0.6727 (OUTLIER) cc_final: 0.6260 (m-80) REVERT: G 454 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7077 (tm-30) REVERT: G 475 MET cc_start: 0.5957 (tpp) cc_final: 0.5586 (mmt) REVERT: G 486 ARG cc_start: 0.7557 (mmm160) cc_final: 0.7196 (tpm-80) REVERT: H 79 PHE cc_start: 0.5118 (OUTLIER) cc_final: 0.4443 (p90) REVERT: I 21 ILE cc_start: 0.7111 (mt) cc_final: 0.6884 (tt) REVERT: I 50 LYS cc_start: 0.6142 (tptp) cc_final: 0.5639 (mmmt) outliers start: 56 outliers final: 18 residues processed: 218 average time/residue: 0.4812 time to fit residues: 120.5954 Evaluate side-chains 178 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 148 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 299 ARG Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain C residue 23 CYS Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 312 MET Chi-restraints excluded: chain D residue 380 ARG Chi-restraints excluded: chain D residue 401 LYS Chi-restraints excluded: chain D residue 435 ASP Chi-restraints excluded: chain D residue 446 GLU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 201 TYR Chi-restraints excluded: chain G residue 454 GLU Chi-restraints excluded: chain H residue 79 PHE Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 63 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 138 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 204 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 130 optimal weight: 0.3980 chunk 61 optimal weight: 8.9990 chunk 49 optimal weight: 6.9990 chunk 203 optimal weight: 4.9990 chunk 123 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 109 optimal weight: 0.5980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN D 264 GLN D 314 ASN E 82 GLN ** F 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 288 ASN G 468 HIS ** I 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.171010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.130965 restraints weight = 26388.693| |-----------------------------------------------------------------------------| r_work (start): 0.4096 rms_B_bonded: 3.03 r_work: 0.3987 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work: 0.3878 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.9378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 17073 Z= 0.212 Angle : 0.796 11.882 23154 Z= 0.405 Chirality : 0.050 0.318 2547 Planarity : 0.005 0.049 2994 Dihedral : 7.217 59.559 2487 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 4.33 % Allowed : 18.53 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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 aren not related in a simple way. whole: -2.19 (0.18), residues: 2103 helix: -0.43 (0.29), residues: 318 sheet: -1.15 (0.21), residues: 639 loop : -1.95 (0.17), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 122 TYR 0.034 0.002 TYR D 445 PHE 0.027 0.003 PHE G 93 TRP 0.031 0.002 TRP G 143 HIS 0.005 0.002 HIS A 225 Details of bonding type rmsd covalent geometry : bond 0.00498 (17037) covalent geometry : angle 0.78251 (23079) SS BOND : bond 0.00451 ( 24) SS BOND : angle 1.65262 ( 48) hydrogen bonds : bond 0.04579 ( 450) hydrogen bonds : angle 5.20298 ( 1305) Misc. bond : bond 0.00060 ( 3) link_NAG-ASN : bond 0.00255 ( 9) link_NAG-ASN : angle 3.92123 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 164 time to evaluate : 0.659 Fit side-chains revert: symmetry clash REVERT: A 22 GLU cc_start: 0.5979 (OUTLIER) cc_final: 0.5211 (mp0) REVERT: A 45 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7515 (ttpp) REVERT: A 119 ASN cc_start: 0.7454 (p0) cc_final: 0.6899 (t0) REVERT: A 299 ARG cc_start: 0.6914 (OUTLIER) cc_final: 0.6072 (mpp-170) REVERT: A 454 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7633 (tm-30) REVERT: A 485 HIS cc_start: 0.7746 (p90) cc_final: 0.7029 (p-80) REVERT: D 9 HIS cc_start: 0.7655 (OUTLIER) cc_final: 0.6059 (p-80) REVERT: D 95 ASN cc_start: 0.8385 (t0) cc_final: 0.8024 (t0) REVERT: D 146 SER cc_start: 0.8645 (t) cc_final: 0.8392 (p) REVERT: D 174 ILE cc_start: 0.7493 (OUTLIER) cc_final: 0.7205 (mm) REVERT: D 380 ARG cc_start: 0.7105 (OUTLIER) cc_final: 0.6757 (ttp80) REVERT: D 435 ASP cc_start: 0.6854 (OUTLIER) cc_final: 0.6631 (p0) REVERT: D 442 ASP cc_start: 0.7513 (t0) cc_final: 0.7020 (t0) REVERT: D 446 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6998 (pm20) REVERT: E 1 MET cc_start: 0.2192 (tmt) cc_final: 0.0521 (mtt) REVERT: E 68 MET cc_start: 0.6795 (ptm) cc_final: 0.6178 (ptm) REVERT: G 105 GLU cc_start: 0.7461 (pm20) cc_final: 0.7201 (mt-10) REVERT: G 119 ASN cc_start: 0.7013 (p0) cc_final: 0.6023 (t0) REVERT: G 182 GLU cc_start: 0.6120 (tm-30) cc_final: 0.5444 (tp30) REVERT: G 255 LYS cc_start: 0.6549 (OUTLIER) cc_final: 0.6278 (ttpp) REVERT: G 402 GLN cc_start: 0.7570 (tt0) cc_final: 0.7119 (mp10) REVERT: G 435 ASP cc_start: 0.6625 (p0) cc_final: 0.6320 (p0) REVERT: G 454 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7563 (tm-30) REVERT: G 463 CYS cc_start: 0.8463 (m) cc_final: 0.8110 (m) REVERT: G 475 MET cc_start: 0.6185 (tpp) cc_final: 0.5971 (mmt) REVERT: G 486 ARG cc_start: 0.7858 (mmm160) cc_final: 0.7522 (tpm170) REVERT: I 4 MET cc_start: 0.6366 (mmm) cc_final: 0.5892 (mmm) REVERT: I 21 ILE cc_start: 0.7353 (mt) cc_final: 0.7013 (tt) REVERT: I 50 LYS cc_start: 0.6382 (tptp) cc_final: 0.5964 (mmmt) REVERT: I 85 SER cc_start: 0.6770 (OUTLIER) cc_final: 0.6419 (t) outliers start: 79 outliers final: 26 residues processed: 226 average time/residue: 0.4870 time to fit residues: 125.3422 Evaluate side-chains 184 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 146 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 299 ARG Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 23 CYS Chi-restraints excluded: chain D residue 9 HIS Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 380 ARG Chi-restraints excluded: chain D residue 435 ASP Chi-restraints excluded: chain D residue 446 GLU Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 9 HIS Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 109 ILE Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 255 LYS Chi-restraints excluded: chain G residue 454 GLU Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 85 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 86 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 125 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 172 optimal weight: 4.9990 chunk 120 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 GLN ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN D 147 ASN D 468 HIS E 82 GLN F 42 ASN F 55 HIS G 225 HIS ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 55 HIS I 90 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.165391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.125583 restraints weight = 26775.990| |-----------------------------------------------------------------------------| r_work (start): 0.4057 rms_B_bonded: 3.08 r_work: 0.3951 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.9855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 17073 Z= 0.248 Angle : 0.819 13.923 23154 Z= 0.417 Chirality : 0.051 0.323 2547 Planarity : 0.005 0.050 2994 Dihedral : 7.541 61.091 2487 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 3.84 % Allowed : 20.67 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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 aren not related in a simple way. whole: -2.32 (0.18), residues: 2103 helix: -0.56 (0.29), residues: 318 sheet: -1.27 (0.21), residues: 633 loop : -2.00 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 131 TYR 0.035 0.002 TYR D 445 PHE 0.023 0.003 PHE D 239 TRP 0.030 0.002 TRP A 409 HIS 0.007 0.002 HIS A 485 Details of bonding type rmsd covalent geometry : bond 0.00588 (17037) covalent geometry : angle 0.80270 (23079) SS BOND : bond 0.00503 ( 24) SS BOND : angle 1.90998 ( 48) hydrogen bonds : bond 0.04693 ( 450) hydrogen bonds : angle 5.27493 ( 1305) Misc. bond : bond 0.00079 ( 3) link_NAG-ASN : bond 0.00297 ( 9) link_NAG-ASN : angle 4.16305 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 153 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.5869 (OUTLIER) cc_final: 0.5012 (mp0) REVERT: A 119 ASN cc_start: 0.7385 (p0) cc_final: 0.6823 (t0) REVERT: A 299 ARG cc_start: 0.6854 (OUTLIER) cc_final: 0.6543 (mpp-170) REVERT: D 9 HIS cc_start: 0.7401 (OUTLIER) cc_final: 0.5711 (p-80) REVERT: D 95 ASN cc_start: 0.8281 (t0) cc_final: 0.7894 (t0) REVERT: D 380 ARG cc_start: 0.7176 (OUTLIER) cc_final: 0.6755 (ttp80) REVERT: D 387 GLN cc_start: 0.7351 (mm-40) cc_final: 0.7023 (mm-40) REVERT: D 442 ASP cc_start: 0.7347 (t0) cc_final: 0.6793 (t0) REVERT: D 446 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6855 (pm20) REVERT: D 493 MET cc_start: 0.7597 (mtt) cc_final: 0.6527 (ttt) REVERT: E 1 MET cc_start: 0.2239 (tmt) cc_final: 0.0419 (ptm) REVERT: E 67 ARG cc_start: 0.7061 (ptp-110) cc_final: 0.6604 (ttt180) REVERT: G 119 ASN cc_start: 0.7028 (p0) cc_final: 0.6190 (t0) REVERT: G 184 THR cc_start: 0.7197 (m) cc_final: 0.6991 (t) REVERT: G 201 TYR cc_start: 0.7114 (OUTLIER) cc_final: 0.5683 (t80) REVERT: G 389 PHE cc_start: 0.6595 (m-80) cc_final: 0.6348 (m-80) REVERT: G 395 GLU cc_start: 0.7546 (tt0) cc_final: 0.7270 (tt0) REVERT: G 402 GLN cc_start: 0.7423 (tt0) cc_final: 0.7135 (mp10) REVERT: G 454 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7347 (tm-30) REVERT: G 486 ARG cc_start: 0.7876 (mmm160) cc_final: 0.7656 (tpm170) REVERT: H 79 PHE cc_start: 0.6640 (OUTLIER) cc_final: 0.5399 (p90) REVERT: I 21 ILE cc_start: 0.7647 (mt) cc_final: 0.7420 (tt) REVERT: I 50 LYS cc_start: 0.6473 (tptp) cc_final: 0.5992 (mmmt) REVERT: I 85 SER cc_start: 0.6867 (OUTLIER) cc_final: 0.6505 (t) outliers start: 70 outliers final: 36 residues processed: 210 average time/residue: 0.4354 time to fit residues: 105.5860 Evaluate side-chains 190 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 145 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 299 ARG Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 23 CYS Chi-restraints excluded: chain D residue 9 HIS Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 312 MET Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 380 ARG Chi-restraints excluded: chain D residue 435 ASP Chi-restraints excluded: chain D residue 446 GLU Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 9 HIS Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 109 ILE Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 201 TYR Chi-restraints excluded: chain G residue 391 LEU Chi-restraints excluded: chain G residue 417 VAL Chi-restraints excluded: chain G residue 454 GLU Chi-restraints excluded: chain H residue 79 PHE Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 85 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 1 optimal weight: 0.8980 chunk 205 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 125 optimal weight: 0.3980 chunk 192 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 201 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN A 264 GLN A 314 ASN A 485 HIS A 495 ASN D 69 GLN D 275 HIS G 225 HIS ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.172097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.132654 restraints weight = 26591.877| |-----------------------------------------------------------------------------| r_work (start): 0.4119 rms_B_bonded: 3.05 r_work: 0.4012 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 1.0082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17073 Z= 0.133 Angle : 0.698 13.764 23154 Z= 0.354 Chirality : 0.046 0.296 2547 Planarity : 0.004 0.048 2994 Dihedral : 6.916 59.884 2487 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.30 % Allowed : 23.03 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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 aren not related in a simple way. whole: -2.01 (0.18), residues: 2103 helix: -0.24 (0.29), residues: 318 sheet: -1.06 (0.21), residues: 645 loop : -1.83 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 131 TYR 0.023 0.001 TYR D 445 PHE 0.018 0.002 PHE G 205 TRP 0.023 0.001 TRP A 409 HIS 0.004 0.001 HIS G 8 Details of bonding type rmsd covalent geometry : bond 0.00310 (17037) covalent geometry : angle 0.68540 (23079) SS BOND : bond 0.00385 ( 24) SS BOND : angle 1.45558 ( 48) hydrogen bonds : bond 0.03875 ( 450) hydrogen bonds : angle 4.88976 ( 1305) Misc. bond : bond 0.00024 ( 3) link_NAG-ASN : bond 0.00385 ( 9) link_NAG-ASN : angle 3.48929 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 158 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.5570 (OUTLIER) cc_final: 0.4847 (mp0) REVERT: A 119 ASN cc_start: 0.7363 (p0) cc_final: 0.6853 (t0) REVERT: A 170 ILE cc_start: 0.7393 (OUTLIER) cc_final: 0.6852 (mp) REVERT: A 299 ARG cc_start: 0.6668 (OUTLIER) cc_final: 0.5180 (mpp-170) REVERT: C 4 MET cc_start: 0.5875 (OUTLIER) cc_final: 0.5613 (mtp) REVERT: D 95 ASN cc_start: 0.8213 (t0) cc_final: 0.7830 (t0) REVERT: D 114 MET cc_start: 0.7644 (ttm) cc_final: 0.7338 (ttm) REVERT: D 131 ARG cc_start: 0.6391 (mtp85) cc_final: 0.5120 (pmt-80) REVERT: D 380 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.6763 (ttp80) REVERT: D 387 GLN cc_start: 0.7155 (mm-40) cc_final: 0.6854 (mm-40) REVERT: D 446 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6830 (pm20) REVERT: D 493 MET cc_start: 0.7470 (mtt) cc_final: 0.6281 (ttt) REVERT: E 1 MET cc_start: 0.2133 (tmt) cc_final: 0.0300 (ptm) REVERT: E 67 ARG cc_start: 0.7068 (ptp-110) cc_final: 0.6577 (ttt180) REVERT: G 119 ASN cc_start: 0.7218 (p0) cc_final: 0.6496 (t0) REVERT: G 184 THR cc_start: 0.7139 (m) cc_final: 0.6938 (t) REVERT: G 402 GLN cc_start: 0.7401 (tt0) cc_final: 0.7101 (mp10) REVERT: G 454 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.6995 (tm-30) REVERT: G 493 MET cc_start: 0.7823 (tpp) cc_final: 0.6170 (ttt) REVERT: I 4 MET cc_start: 0.6167 (mtm) cc_final: 0.5569 (mtp) outliers start: 42 outliers final: 21 residues processed: 192 average time/residue: 0.4557 time to fit residues: 100.6694 Evaluate side-chains 181 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 299 ARG Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 23 CYS Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 380 ARG Chi-restraints excluded: chain D residue 446 GLU Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 435 ASP Chi-restraints excluded: chain G residue 454 GLU Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 63 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 149 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 144 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 171 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 485 HIS A 495 ASN D 69 GLN H 61 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.171000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.131423 restraints weight = 26534.986| |-----------------------------------------------------------------------------| r_work (start): 0.4106 rms_B_bonded: 3.06 r_work: 0.3998 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 moved from start: 1.0211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17073 Z= 0.147 Angle : 0.723 13.812 23154 Z= 0.363 Chirality : 0.046 0.272 2547 Planarity : 0.004 0.048 2994 Dihedral : 6.863 58.065 2487 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 2.41 % Allowed : 23.46 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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 aren not related in a simple way. whole: -1.94 (0.18), residues: 2103 helix: -0.22 (0.29), residues: 318 sheet: -0.96 (0.21), residues: 633 loop : -1.81 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 131 TYR 0.024 0.002 TYR G 420 PHE 0.017 0.002 PHE G 205 TRP 0.039 0.002 TRP B 37 HIS 0.004 0.001 HIS G 8 Details of bonding type rmsd covalent geometry : bond 0.00347 (17037) covalent geometry : angle 0.71031 (23079) SS BOND : bond 0.00388 ( 24) SS BOND : angle 1.49516 ( 48) hydrogen bonds : bond 0.03962 ( 450) hydrogen bonds : angle 4.91633 ( 1305) Misc. bond : bond 0.00019 ( 3) link_NAG-ASN : bond 0.00318 ( 9) link_NAG-ASN : angle 3.63045 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 155 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.5655 (OUTLIER) cc_final: 0.4906 (mp0) REVERT: A 119 ASN cc_start: 0.7446 (p0) cc_final: 0.6984 (t0) REVERT: A 170 ILE cc_start: 0.7484 (OUTLIER) cc_final: 0.6803 (mp) REVERT: A 201 TYR cc_start: 0.6991 (OUTLIER) cc_final: 0.5878 (t80) REVERT: A 299 ARG cc_start: 0.6734 (OUTLIER) cc_final: 0.5211 (mpp-170) REVERT: A 485 HIS cc_start: 0.7302 (p-80) cc_final: 0.6863 (p90) REVERT: C 4 MET cc_start: 0.5872 (OUTLIER) cc_final: 0.5600 (mtp) REVERT: D 95 ASN cc_start: 0.8280 (t0) cc_final: 0.7910 (t0) REVERT: D 131 ARG cc_start: 0.6520 (mtp85) cc_final: 0.5262 (pmt-80) REVERT: D 380 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.6766 (ttp80) REVERT: D 387 GLN cc_start: 0.7164 (mm-40) cc_final: 0.6838 (mm-40) REVERT: D 493 MET cc_start: 0.7438 (mtt) cc_final: 0.6294 (ttt) REVERT: E 1 MET cc_start: 0.2393 (tmt) cc_final: 0.0554 (ptm) REVERT: E 67 ARG cc_start: 0.7149 (ptp-110) cc_final: 0.6518 (ttt180) REVERT: F 21 ILE cc_start: 0.5922 (tt) cc_final: 0.5584 (tp) REVERT: G 119 ASN cc_start: 0.7338 (p0) cc_final: 0.6675 (t0) REVERT: G 201 TYR cc_start: 0.6948 (OUTLIER) cc_final: 0.5565 (t80) REVERT: G 435 ASP cc_start: 0.6765 (OUTLIER) cc_final: 0.6502 (p0) REVERT: G 454 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.6912 (tm-30) REVERT: G 493 MET cc_start: 0.7821 (tpp) cc_final: 0.6164 (ttt) REVERT: I 4 MET cc_start: 0.6120 (mtm) cc_final: 0.5569 (mtp) REVERT: I 50 LYS cc_start: 0.6060 (tptp) cc_final: 0.5683 (mmmt) outliers start: 44 outliers final: 25 residues processed: 188 average time/residue: 0.4653 time to fit residues: 100.8846 Evaluate side-chains 181 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 147 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 299 ARG Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 23 CYS Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 312 MET Chi-restraints excluded: chain D residue 380 ARG Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 109 ILE Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 201 TYR Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 435 ASP Chi-restraints excluded: chain G residue 454 GLU Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 63 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 38 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 70 optimal weight: 0.4980 chunk 76 optimal weight: 3.9990 chunk 174 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 198 optimal weight: 8.9990 chunk 4 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 ASN D 69 GLN H 61 ASN I 90 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.168066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.128665 restraints weight = 26690.432| |-----------------------------------------------------------------------------| r_work (start): 0.4073 rms_B_bonded: 3.03 r_work: 0.3964 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 1.0306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 17073 Z= 0.202 Angle : 0.766 13.749 23154 Z= 0.387 Chirality : 0.048 0.282 2547 Planarity : 0.005 0.048 2994 Dihedral : 7.209 61.713 2487 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 2.74 % Allowed : 23.46 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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 aren not related in a simple way. whole: -2.04 (0.18), residues: 2103 helix: -0.40 (0.29), residues: 318 sheet: -0.98 (0.21), residues: 615 loop : -1.85 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 131 TYR 0.023 0.002 TYR D 445 PHE 0.023 0.003 PHE D 239 TRP 0.042 0.002 TRP A 409 HIS 0.005 0.002 HIS D 485 Details of bonding type rmsd covalent geometry : bond 0.00481 (17037) covalent geometry : angle 0.75173 (23079) SS BOND : bond 0.00400 ( 24) SS BOND : angle 1.64071 ( 48) hydrogen bonds : bond 0.04287 ( 450) hydrogen bonds : angle 5.07878 ( 1305) Misc. bond : bond 0.00063 ( 3) link_NAG-ASN : bond 0.00270 ( 9) link_NAG-ASN : angle 3.98849 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 143 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.5822 (OUTLIER) cc_final: 0.5079 (mp0) REVERT: A 119 ASN cc_start: 0.7386 (p0) cc_final: 0.6984 (t0) REVERT: A 201 TYR cc_start: 0.7086 (OUTLIER) cc_final: 0.5966 (t80) REVERT: A 299 ARG cc_start: 0.6844 (OUTLIER) cc_final: 0.5498 (mpp-170) REVERT: C 4 MET cc_start: 0.5818 (OUTLIER) cc_final: 0.5514 (mtp) REVERT: D 95 ASN cc_start: 0.8271 (t0) cc_final: 0.7900 (t0) REVERT: D 114 MET cc_start: 0.7660 (ttm) cc_final: 0.7448 (ttm) REVERT: D 131 ARG cc_start: 0.6579 (mtp85) cc_final: 0.5224 (pmt-80) REVERT: D 380 ARG cc_start: 0.7187 (OUTLIER) cc_final: 0.6718 (ttp80) REVERT: D 387 GLN cc_start: 0.7154 (mm-40) cc_final: 0.6825 (mm-40) REVERT: D 493 MET cc_start: 0.7341 (mtt) cc_final: 0.6166 (ttt) REVERT: E 1 MET cc_start: 0.2580 (tmt) cc_final: 0.1210 (ptm) REVERT: E 67 ARG cc_start: 0.7149 (ptp-110) cc_final: 0.6534 (ttt180) REVERT: F 4 MET cc_start: 0.5785 (mmm) cc_final: 0.5455 (mtm) REVERT: G 119 ASN cc_start: 0.7212 (p0) cc_final: 0.6652 (t0) REVERT: G 201 TYR cc_start: 0.7036 (OUTLIER) cc_final: 0.5648 (t80) REVERT: G 395 GLU cc_start: 0.7559 (tt0) cc_final: 0.7199 (tt0) REVERT: G 435 ASP cc_start: 0.6819 (p0) cc_final: 0.6604 (p0) REVERT: G 454 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.6778 (tm-30) REVERT: G 493 MET cc_start: 0.7632 (tpp) cc_final: 0.6112 (ttt) REVERT: I 4 MET cc_start: 0.6177 (mtm) cc_final: 0.5566 (mtp) REVERT: I 90 GLN cc_start: 0.5643 (OUTLIER) cc_final: 0.5419 (pt0) outliers start: 50 outliers final: 28 residues processed: 184 average time/residue: 0.4395 time to fit residues: 93.0476 Evaluate side-chains 174 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 138 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 299 ARG Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 23 CYS Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 312 MET Chi-restraints excluded: chain D residue 380 ARG Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 109 ILE Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 201 TYR Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 417 VAL Chi-restraints excluded: chain G residue 454 GLU Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 90 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 83 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 133 optimal weight: 7.9990 chunk 173 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 114 optimal weight: 0.0170 chunk 169 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 overall best weight: 1.1822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN H 61 ASN I 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.168003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.128621 restraints weight = 26665.177| |-----------------------------------------------------------------------------| r_work (start): 0.4086 rms_B_bonded: 3.02 r_work: 0.3980 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work: 0.3864 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 1.0363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17073 Z= 0.169 Angle : 0.738 13.712 23154 Z= 0.373 Chirality : 0.047 0.271 2547 Planarity : 0.004 0.048 2994 Dihedral : 7.119 61.312 2487 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 2.52 % Allowed : 23.96 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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 aren not related in a simple way. whole: -2.04 (0.18), residues: 2103 helix: -0.39 (0.28), residues: 318 sheet: -1.01 (0.22), residues: 609 loop : -1.84 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 486 TYR 0.022 0.002 TYR G 420 PHE 0.018 0.002 PHE G 205 TRP 0.057 0.002 TRP B 37 HIS 0.012 0.001 HIS A 485 Details of bonding type rmsd covalent geometry : bond 0.00403 (17037) covalent geometry : angle 0.72440 (23079) SS BOND : bond 0.00385 ( 24) SS BOND : angle 1.51917 ( 48) hydrogen bonds : bond 0.04169 ( 450) hydrogen bonds : angle 5.04629 ( 1305) Misc. bond : bond 0.00028 ( 3) link_NAG-ASN : bond 0.00299 ( 9) link_NAG-ASN : angle 3.87500 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6802.56 seconds wall clock time: 116 minutes 36.95 seconds (6996.95 seconds total)