Starting phenix.real_space_refine on Sun May 18 07:53:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iuz_35734/05_2025/8iuz_35734.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iuz_35734/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8iuz_35734/05_2025/8iuz_35734.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iuz_35734/05_2025/8iuz_35734.map" model { file = "/net/cci-nas-00/data/ceres_data/8iuz_35734/05_2025/8iuz_35734.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iuz_35734/05_2025/8iuz_35734.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.014 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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, F, I, E, H Time building chain proxies: 8.65, per 1000 atoms: 0.52 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: 3.96 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 2.67 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: 5.59 Time building geometry restraints manager: 4.61 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: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 36.110 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.850 ------------------------------------------------------------------------------- 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 : 8.63 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.45 (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 TRP 0.052 0.005 TRP G 143 HIS 0.013 0.004 HIS D 175 PHE 0.036 0.006 PHE G 335 TYR 0.052 0.004 TYR E 102 ARG 0.020 0.002 ARG D 450 Details of bonding type rmsd link_NAG-ASN : bond 0.00538 ( 9) link_NAG-ASN : angle 7.10285 ( 27) hydrogen bonds : bond 0.30501 ( 450) hydrogen bonds : angle 10.31721 ( 1305) SS BOND : bond 0.00512 ( 24) SS BOND : angle 2.01678 ( 48) covalent geometry : bond 0.01006 (17037) covalent geometry : angle 1.33708 (23079) Misc. bond : bond 0.45787 ( 3) *********************** 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 : 1.729 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: 1.0379 time to fit residues: 433.7173 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 : 1.920 ------------------------------------------------------------------------------- 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 174 optimal weight: 0.8980 chunk 156 optimal weight: 0.4980 chunk 87 optimal weight: 0.5980 chunk 53 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 162 optimal weight: 0.5980 chunk 62 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 187 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 HIS A 95 ASN A 124 ASN ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 HIS 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 155 GLN D 225 HIS D 353 GLN ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 150 ASN G 288 ASN G 373 GLN G 430 ASN G 455 ASN G 481 ASN G 485 HIS ** G 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4985 r_free = 0.4985 target = 0.195960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.160480 restraints weight = 28470.264| |-----------------------------------------------------------------------------| r_work (start): 0.4567 rms_B_bonded: 3.20 r_work: 0.4464 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.4464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6141 moved from start: 0.4850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 17073 Z= 0.230 Angle : 0.841 10.184 23154 Z= 0.437 Chirality : 0.049 0.213 2547 Planarity : 0.007 0.064 2994 Dihedral : 7.688 72.660 2489 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 3.62 % Allowed : 12.45 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (0.16), residues: 2103 helix: -1.48 (0.27), residues: 315 sheet: -2.16 (0.20), residues: 597 loop : -2.65 (0.16), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP G 340 HIS 0.007 0.002 HIS D 275 PHE 0.034 0.003 PHE D 116 TYR 0.019 0.002 TYR F 87 ARG 0.021 0.001 ARG G 104 Details of bonding type rmsd link_NAG-ASN : bond 0.01358 ( 9) link_NAG-ASN : angle 3.86663 ( 27) hydrogen bonds : bond 0.05818 ( 450) hydrogen bonds : angle 6.08145 ( 1305) SS BOND : bond 0.00555 ( 24) SS BOND : angle 1.91202 ( 48) covalent geometry : bond 0.00458 (17037) covalent geometry : angle 0.82771 (23079) Misc. bond : bond 0.00118 ( 3) *********************** 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 333 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 267 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASN cc_start: 0.7269 (p0) cc_final: 0.6623 (t0) REVERT: A 170 ILE cc_start: 0.7333 (OUTLIER) cc_final: 0.6834 (mp) REVERT: A 412 ASP cc_start: 0.6719 (t0) cc_final: 0.6457 (t0) REVERT: C 5 ASN cc_start: 0.6194 (m-40) cc_final: 0.5977 (m-40) REVERT: D 174 ILE cc_start: 0.6814 (OUTLIER) cc_final: 0.6055 (mm) REVERT: D 244 ILE cc_start: 0.6765 (OUTLIER) cc_final: 0.6340 (mp) REVERT: D 380 ARG cc_start: 0.6304 (OUTLIER) cc_final: 0.6058 (mmm-85) REVERT: D 412 ASP cc_start: 0.7050 (t70) cc_final: 0.6762 (t0) REVERT: D 454 GLU cc_start: 0.6381 (tm-30) cc_final: 0.6078 (tm-30) REVERT: D 493 MET cc_start: 0.6235 (OUTLIER) cc_final: 0.5822 (mtt) REVERT: E 1 MET cc_start: 0.1242 (tmt) cc_final: 0.0865 (tpp) REVERT: E 49 MET cc_start: 0.6448 (mmm) cc_final: 0.5688 (mmm) REVERT: E 68 MET cc_start: 0.6336 (tpp) cc_final: 0.6123 (mtm) REVERT: F 4 MET cc_start: 0.7022 (tpp) cc_final: 0.6639 (tpp) REVERT: G 62 THR cc_start: 0.7002 (OUTLIER) cc_final: 0.6753 (p) REVERT: G 201 TYR cc_start: 0.5745 (OUTLIER) cc_final: 0.4361 (t80) REVERT: G 252 LEU cc_start: 0.8072 (pp) cc_final: 0.7625 (mp) REVERT: G 386 ASN cc_start: 0.5903 (p0) cc_final: 0.5585 (p0) REVERT: G 475 MET cc_start: 0.4669 (tpp) cc_final: 0.4128 (mmt) REVERT: I 4 MET cc_start: 0.3584 (tpp) cc_final: 0.3178 (tpt) outliers start: 66 outliers final: 19 residues processed: 308 average time/residue: 0.9385 time to fit residues: 332.2301 Evaluate side-chains 197 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 time to evaluate : 1.880 ------------------------------------------------------------------------------- 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 C residue 23 CYS Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain D residue 4 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 244 ILE Chi-restraints excluded: chain D residue 380 ARG Chi-restraints excluded: chain D residue 420 TYR Chi-restraints excluded: chain D residue 493 MET Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 201 TYR Chi-restraints excluded: chain G residue 274 TYR 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 73 optimal weight: 0.6980 chunk 199 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 106 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 173 optimal weight: 0.6980 chunk 64 optimal weight: 9.9990 chunk 60 optimal weight: 20.0000 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 GLN D 69 GLN D 368 GLN ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 GLN F 92 GLN G 54 GLN G 214 GLN G 264 GLN G 430 ASN G 485 HIS G 495 ASN H 40 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4743 r_free = 0.4743 target = 0.173859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.136242 restraints weight = 28078.342| |-----------------------------------------------------------------------------| r_work (start): 0.4230 rms_B_bonded: 3.10 r_work: 0.4106 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6730 moved from start: 0.8003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 17073 Z= 0.201 Angle : 0.819 10.426 23154 Z= 0.422 Chirality : 0.049 0.211 2547 Planarity : 0.006 0.056 2994 Dihedral : 7.544 59.479 2488 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 4.00 % Allowed : 15.52 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.17), residues: 2103 helix: -1.07 (0.28), residues: 318 sheet: -1.82 (0.20), residues: 612 loop : -2.38 (0.17), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP D 143 HIS 0.005 0.001 HIS D 432 PHE 0.027 0.003 PHE G 239 TYR 0.074 0.003 TYR D 420 ARG 0.012 0.001 ARG G 486 Details of bonding type rmsd link_NAG-ASN : bond 0.00857 ( 9) link_NAG-ASN : angle 3.70499 ( 27) hydrogen bonds : bond 0.05419 ( 450) hydrogen bonds : angle 5.89377 ( 1305) SS BOND : bond 0.00390 ( 24) SS BOND : angle 1.52082 ( 48) covalent geometry : bond 0.00459 (17037) covalent geometry : angle 0.80712 (23079) Misc. bond : bond 0.00103 ( 3) *********************** 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 281 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 208 time to evaluate : 1.890 Fit side-chains revert: symmetry clash REVERT: A 22 GLU cc_start: 0.5902 (OUTLIER) cc_final: 0.4990 (mp0) REVERT: A 119 ASN cc_start: 0.7289 (p0) cc_final: 0.6555 (t0) REVERT: A 170 ILE cc_start: 0.7458 (OUTLIER) cc_final: 0.6814 (mp) REVERT: A 485 HIS cc_start: 0.7367 (p-80) cc_final: 0.6451 (p90) REVERT: C 4 MET cc_start: 0.6269 (mmm) cc_final: 0.5928 (mtm) REVERT: D 95 ASN cc_start: 0.8303 (t0) cc_final: 0.7985 (t0) REVERT: D 104 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.7336 (ttm170) REVERT: D 174 ILE cc_start: 0.7285 (OUTLIER) cc_final: 0.7024 (mm) REVERT: D 328 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.6807 (tt) REVERT: D 442 ASP cc_start: 0.7288 (t0) cc_final: 0.6523 (t0) REVERT: D 467 PHE cc_start: 0.6452 (m-80) cc_final: 0.6187 (m-80) REVERT: E 49 MET cc_start: 0.5853 (mmm) cc_final: 0.5277 (mmm) REVERT: F 49 TYR cc_start: 0.5036 (p90) cc_final: 0.4657 (p90) REVERT: F 97 THR cc_start: 0.4189 (p) cc_final: 0.3886 (p) REVERT: G 54 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7583 (tm-30) REVERT: G 119 ASN cc_start: 0.6359 (p0) cc_final: 0.5426 (p0) REVERT: G 137 PHE cc_start: 0.5477 (t80) cc_final: 0.5026 (t80) REVERT: G 201 TYR cc_start: 0.6732 (OUTLIER) cc_final: 0.6400 (m-80) REVERT: G 214 GLN cc_start: 0.6707 (OUTLIER) cc_final: 0.6485 (mm-40) REVERT: G 252 LEU cc_start: 0.8859 (pp) cc_final: 0.8436 (mt) REVERT: G 441 MET cc_start: 0.5783 (tpt) cc_final: 0.5527 (tpt) REVERT: G 442 ASP cc_start: 0.7488 (p0) cc_final: 0.7288 (p0) REVERT: G 454 GLU cc_start: 0.7442 (tm-30) cc_final: 0.6750 (tm-30) REVERT: G 486 ARG cc_start: 0.7549 (mmm160) cc_final: 0.6822 (tpm170) outliers start: 73 outliers final: 19 residues processed: 267 average time/residue: 0.9616 time to fit residues: 294.3419 Evaluate side-chains 178 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 1.764 ------------------------------------------------------------------------------- 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 121 ILE Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain C residue 23 CYS Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 104 ARG 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 328 LEU Chi-restraints excluded: chain E residue 88 THR 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 170 ILE Chi-restraints excluded: chain G residue 201 TYR Chi-restraints excluded: chain G residue 214 GLN Chi-restraints excluded: chain G residue 495 ASN Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 63 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 142 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 26 optimal weight: 0.1980 chunk 2 optimal weight: 0.6980 chunk 150 optimal weight: 0.9990 chunk 169 optimal weight: 3.9990 chunk 141 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 GLN ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 ASN D 468 HIS G 54 GLN G 214 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4721 r_free = 0.4721 target = 0.174415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.133433 restraints weight = 26372.864| |-----------------------------------------------------------------------------| r_work (start): 0.4172 rms_B_bonded: 3.14 r_work: 0.4062 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 moved from start: 0.8470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 17073 Z= 0.137 Angle : 0.703 12.379 23154 Z= 0.359 Chirality : 0.046 0.269 2547 Planarity : 0.005 0.090 2994 Dihedral : 6.875 59.315 2487 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.95 % Allowed : 17.38 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.18), residues: 2103 helix: -0.45 (0.30), residues: 318 sheet: -1.46 (0.21), residues: 615 loop : -2.18 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP G 143 HIS 0.004 0.001 HIS B 104 PHE 0.019 0.002 PHE G 137 TYR 0.016 0.001 TYR D 445 ARG 0.020 0.001 ARG D 212 Details of bonding type rmsd link_NAG-ASN : bond 0.00413 ( 9) link_NAG-ASN : angle 3.36550 ( 27) hydrogen bonds : bond 0.04135 ( 450) hydrogen bonds : angle 5.30135 ( 1305) SS BOND : bond 0.00308 ( 24) SS BOND : angle 2.16207 ( 48) covalent geometry : bond 0.00314 (17037) covalent geometry : angle 0.68723 (23079) Misc. bond : bond 0.00319 ( 3) *********************** 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 246 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 174 time to evaluate : 1.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.5444 (OUTLIER) cc_final: 0.4645 (mp0) REVERT: A 119 ASN cc_start: 0.7516 (p0) cc_final: 0.6664 (t0) REVERT: A 170 ILE cc_start: 0.7401 (OUTLIER) cc_final: 0.6797 (mp) REVERT: A 299 ARG cc_start: 0.6750 (OUTLIER) cc_final: 0.5201 (mpp-170) REVERT: C 4 MET cc_start: 0.6447 (mmm) cc_final: 0.6225 (mtm) REVERT: D 95 ASN cc_start: 0.8220 (t0) cc_final: 0.7920 (t0) REVERT: D 114 MET cc_start: 0.7800 (ttm) cc_final: 0.7280 (ttm) REVERT: D 119 ASN cc_start: 0.6935 (p0) cc_final: 0.5962 (t0) REVERT: D 174 ILE cc_start: 0.7312 (OUTLIER) cc_final: 0.7096 (mm) REVERT: D 328 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.6851 (tt) REVERT: E 1 MET cc_start: 0.1559 (tmt) cc_final: 0.1302 (tpp) REVERT: F 49 TYR cc_start: 0.4695 (p90) cc_final: 0.4367 (p90) REVERT: G 54 GLN cc_start: 0.7578 (OUTLIER) cc_final: 0.7051 (tm-30) REVERT: G 119 ASN cc_start: 0.6584 (p0) cc_final: 0.5697 (p0) REVERT: G 201 TYR cc_start: 0.6799 (OUTLIER) cc_final: 0.6514 (m-80) REVERT: G 252 LEU cc_start: 0.8922 (pp) cc_final: 0.8641 (mp) REVERT: G 378 LEU cc_start: 0.7756 (mt) cc_final: 0.7513 (tm) REVERT: G 454 GLU cc_start: 0.7605 (tm-30) cc_final: 0.6848 (tm-30) REVERT: G 457 GLU cc_start: 0.6825 (mt-10) cc_final: 0.5492 (mp0) REVERT: G 463 CYS cc_start: 0.7917 (m) cc_final: 0.7554 (m) REVERT: G 486 ARG cc_start: 0.7622 (mmm160) cc_final: 0.7077 (tpm-80) REVERT: H 79 PHE cc_start: 0.5775 (OUTLIER) cc_final: 0.4660 (p90) outliers start: 72 outliers final: 21 residues processed: 233 average time/residue: 1.0156 time to fit residues: 271.8189 Evaluate side-chains 189 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 1.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 461 THR Chi-restraints excluded: chain C residue 23 CYS 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 235 VAL Chi-restraints excluded: chain D residue 255 LYS Chi-restraints excluded: chain D residue 328 LEU 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 117 THR Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 201 TYR Chi-restraints excluded: chain G residue 495 ASN Chi-restraints excluded: chain H residue 30 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 29 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 170 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 160 optimal weight: 1.9990 chunk 166 optimal weight: 0.4980 chunk 116 optimal weight: 4.9990 chunk 60 optimal weight: 20.0000 overall best weight: 2.2988 ------------------------------------------------------------------------------- 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 264 GLN D 275 HIS D 314 ASN F 55 HIS F 92 GLN G 214 GLN G 288 ASN G 468 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.169069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.131388 restraints weight = 28330.302| |-----------------------------------------------------------------------------| r_work (start): 0.4059 rms_B_bonded: 3.24 r_work: 0.3922 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.9389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 17073 Z= 0.270 Angle : 0.880 12.313 23154 Z= 0.450 Chirality : 0.052 0.277 2547 Planarity : 0.006 0.056 2994 Dihedral : 7.810 63.667 2487 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % Rotamer: Outliers : 4.28 % Allowed : 18.91 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.17), residues: 2103 helix: -0.82 (0.29), residues: 318 sheet: -1.59 (0.20), residues: 636 loop : -2.23 (0.17), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP G 143 HIS 0.006 0.002 HIS B 104 PHE 0.026 0.004 PHE G 93 TYR 0.030 0.003 TYR D 445 ARG 0.011 0.001 ARG A 486 Details of bonding type rmsd link_NAG-ASN : bond 0.00301 ( 9) link_NAG-ASN : angle 4.43004 ( 27) hydrogen bonds : bond 0.05071 ( 450) hydrogen bonds : angle 5.60989 ( 1305) SS BOND : bond 0.00399 ( 24) SS BOND : angle 2.32239 ( 48) covalent geometry : bond 0.00639 (17037) covalent geometry : angle 0.86200 (23079) Misc. bond : bond 0.00540 ( 3) *********************** 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 241 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 163 time to evaluate : 1.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.6021 (OUTLIER) cc_final: 0.5207 (mp0) REVERT: A 45 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7592 (ttmt) REVERT: A 119 ASN cc_start: 0.7497 (p0) cc_final: 0.6727 (t0) REVERT: A 337 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7268 (pm20) REVERT: A 467 PHE cc_start: 0.6995 (m-80) cc_final: 0.6736 (m-80) REVERT: A 485 HIS cc_start: 0.7573 (p90) cc_final: 0.6846 (p-80) REVERT: C 4 MET cc_start: 0.6443 (mmm) cc_final: 0.6195 (mtm) REVERT: D 95 ASN cc_start: 0.8321 (t0) cc_final: 0.7945 (t0) REVERT: D 104 ARG cc_start: 0.7578 (OUTLIER) cc_final: 0.7373 (ttm170) REVERT: D 174 ILE cc_start: 0.7505 (OUTLIER) cc_final: 0.7266 (mm) REVERT: D 328 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.6740 (tt) REVERT: E 1 MET cc_start: 0.1977 (tmt) cc_final: 0.0675 (mtt) REVERT: F 4 MET cc_start: 0.5236 (tpp) cc_final: 0.4635 (tpt) REVERT: G 105 GLU cc_start: 0.7431 (pm20) cc_final: 0.7166 (mt-10) REVERT: G 119 ASN cc_start: 0.7215 (p0) cc_final: 0.6213 (t0) REVERT: G 122 ARG cc_start: 0.6588 (tmm-80) cc_final: 0.6317 (tmm-80) REVERT: G 201 TYR cc_start: 0.7221 (OUTLIER) cc_final: 0.5755 (t80) REVERT: G 402 GLN cc_start: 0.7578 (tt0) cc_final: 0.7037 (mp10) REVERT: G 486 ARG cc_start: 0.7707 (mmm160) cc_final: 0.7263 (tpm170) REVERT: I 4 MET cc_start: 0.6546 (mmm) cc_final: 0.5966 (mmm) REVERT: I 21 ILE cc_start: 0.6467 (OUTLIER) cc_final: 0.6188 (tp) REVERT: I 50 LYS cc_start: 0.6605 (tptp) cc_final: 0.6177 (mmmt) outliers start: 78 outliers final: 36 residues processed: 230 average time/residue: 0.9871 time to fit residues: 260.0077 Evaluate side-chains 186 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 142 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 337 GLU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain C residue 23 CYS Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 104 ARG 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 234 THR Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 255 LYS Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 435 ASP Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 201 TYR Chi-restraints excluded: chain G residue 401 LYS Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 21 ILE 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 18 optimal weight: 0.0010 chunk 190 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 16 optimal weight: 0.0170 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 0.1980 overall best weight: 0.3224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN A 495 ASN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 214 GLN ** G 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4689 r_free = 0.4689 target = 0.173828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.135472 restraints weight = 27333.136| |-----------------------------------------------------------------------------| r_work (start): 0.4148 rms_B_bonded: 3.21 r_work: 0.4043 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 moved from start: 0.9635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17073 Z= 0.116 Angle : 0.646 9.903 23154 Z= 0.332 Chirality : 0.045 0.213 2547 Planarity : 0.004 0.043 2994 Dihedral : 6.792 58.267 2487 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.91 % Allowed : 20.61 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.18), residues: 2103 helix: -0.20 (0.30), residues: 318 sheet: -1.18 (0.21), residues: 639 loop : -2.01 (0.17), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 37 HIS 0.005 0.001 HIS A 485 PHE 0.014 0.001 PHE D 239 TYR 0.013 0.001 TYR A 420 ARG 0.005 0.000 ARG A 486 Details of bonding type rmsd link_NAG-ASN : bond 0.00409 ( 9) link_NAG-ASN : angle 3.35018 ( 27) hydrogen bonds : bond 0.03736 ( 450) hydrogen bonds : angle 4.98082 ( 1305) SS BOND : bond 0.00379 ( 24) SS BOND : angle 1.71884 ( 48) covalent geometry : bond 0.00255 (17037) covalent geometry : angle 0.63207 (23079) Misc. bond : bond 0.00096 ( 3) *********************** 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 217 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 164 time to evaluate : 1.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.5359 (OUTLIER) cc_final: 0.4590 (mp0) REVERT: A 119 ASN cc_start: 0.7467 (p0) cc_final: 0.6757 (t0) REVERT: A 170 ILE cc_start: 0.7398 (OUTLIER) cc_final: 0.6856 (mp) REVERT: A 467 PHE cc_start: 0.7073 (m-80) cc_final: 0.6836 (m-80) REVERT: A 485 HIS cc_start: 0.7101 (p90) cc_final: 0.6850 (p-80) REVERT: D 95 ASN cc_start: 0.8388 (t0) cc_final: 0.7960 (t0) REVERT: D 119 ASN cc_start: 0.7079 (p0) cc_final: 0.6476 (t0) REVERT: D 131 ARG cc_start: 0.6598 (mtp85) cc_final: 0.5277 (pmt-80) REVERT: E 1 MET cc_start: 0.2471 (tmt) cc_final: 0.0835 (mtt) REVERT: E 67 ARG cc_start: 0.6883 (ptp-110) cc_final: 0.6178 (ptm160) REVERT: E 68 MET cc_start: 0.6317 (ptm) cc_final: 0.6068 (ptp) REVERT: G 119 ASN cc_start: 0.7008 (p0) cc_final: 0.6184 (t0) REVERT: G 247 ASP cc_start: 0.6599 (OUTLIER) cc_final: 0.6368 (m-30) REVERT: G 252 LEU cc_start: 0.8828 (pp) cc_final: 0.8593 (mp) REVERT: G 365 LYS cc_start: 0.6772 (OUTLIER) cc_final: 0.6528 (pttt) REVERT: G 454 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7401 (tm-30) REVERT: G 486 ARG cc_start: 0.7773 (mmm160) cc_final: 0.7198 (tpm170) REVERT: H 49 MET cc_start: 0.5865 (mmm) cc_final: 0.5600 (mmt) REVERT: I 4 MET cc_start: 0.6380 (mmm) cc_final: 0.5974 (mmm) outliers start: 53 outliers final: 17 residues processed: 202 average time/residue: 0.8278 time to fit residues: 196.8686 Evaluate side-chains 172 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 1.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 23 CYS Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain G residue 201 TYR Chi-restraints excluded: chain G residue 228 ILE Chi-restraints excluded: chain G residue 247 ASP Chi-restraints excluded: chain G residue 365 LYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 38 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 21 optimal weight: 0.0030 chunk 206 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 133 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 128 optimal weight: 6.9990 chunk 111 optimal weight: 0.9980 overall best weight: 1.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.167057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.128686 restraints weight = 27395.543| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 3.07 r_work: 0.3998 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6724 moved from start: 0.9844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17073 Z= 0.164 Angle : 0.712 10.347 23154 Z= 0.362 Chirality : 0.046 0.204 2547 Planarity : 0.005 0.046 2994 Dihedral : 6.961 59.124 2487 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 3.23 % Allowed : 21.44 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.18), residues: 2103 helix: -0.16 (0.30), residues: 318 sheet: -1.09 (0.22), residues: 606 loop : -1.99 (0.17), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 409 HIS 0.004 0.001 HIS A 275 PHE 0.017 0.002 PHE B 79 TYR 0.028 0.002 TYR D 445 ARG 0.007 0.001 ARG D 486 Details of bonding type rmsd link_NAG-ASN : bond 0.00332 ( 9) link_NAG-ASN : angle 3.67193 ( 27) hydrogen bonds : bond 0.04128 ( 450) hydrogen bonds : angle 4.99792 ( 1305) SS BOND : bond 0.00363 ( 24) SS BOND : angle 1.87847 ( 48) covalent geometry : bond 0.00387 (17037) covalent geometry : angle 0.69651 (23079) Misc. bond : bond 0.00184 ( 3) *********************** 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 211 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 152 time to evaluate : 1.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.5535 (OUTLIER) cc_final: 0.4694 (mp0) REVERT: A 45 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7525 (ttpp) REVERT: A 119 ASN cc_start: 0.7445 (p0) cc_final: 0.6855 (t0) REVERT: A 159 SER cc_start: 0.8448 (OUTLIER) cc_final: 0.8009 (t) REVERT: A 170 ILE cc_start: 0.7468 (OUTLIER) cc_final: 0.6807 (mp) REVERT: A 201 TYR cc_start: 0.6945 (OUTLIER) cc_final: 0.5855 (t80) REVERT: A 467 PHE cc_start: 0.7052 (m-80) cc_final: 0.6773 (m-80) REVERT: A 485 HIS cc_start: 0.7485 (p90) cc_final: 0.7152 (p90) REVERT: B 67 ARG cc_start: 0.6364 (ptp-110) cc_final: 0.6153 (ttt180) REVERT: C 21 ILE cc_start: 0.5854 (tt) cc_final: 0.5573 (tp) REVERT: D 22 GLU cc_start: 0.5696 (OUTLIER) cc_final: 0.5422 (mp0) REVERT: D 95 ASN cc_start: 0.8441 (t0) cc_final: 0.8047 (t0) REVERT: D 442 ASP cc_start: 0.7482 (t0) cc_final: 0.6997 (t0) REVERT: E 1 MET cc_start: 0.1954 (tmt) cc_final: 0.0077 (ptm) REVERT: E 67 ARG cc_start: 0.6963 (ptp-110) cc_final: 0.6664 (ttt180) REVERT: F 4 MET cc_start: 0.5806 (mmm) cc_final: 0.5384 (mmm) REVERT: G 119 ASN cc_start: 0.7124 (p0) cc_final: 0.6389 (t0) REVERT: G 122 ARG cc_start: 0.6502 (tmm-80) cc_final: 0.6021 (tmt90) REVERT: G 201 TYR cc_start: 0.7015 (OUTLIER) cc_final: 0.5710 (t80) REVERT: G 252 LEU cc_start: 0.8863 (pp) cc_final: 0.8627 (mp) REVERT: G 402 GLN cc_start: 0.7329 (tt0) cc_final: 0.6877 (pm20) REVERT: G 486 ARG cc_start: 0.7753 (mmm160) cc_final: 0.7543 (tpm-80) REVERT: H 49 MET cc_start: 0.5854 (mmm) cc_final: 0.5622 (mmt) REVERT: I 4 MET cc_start: 0.6444 (mmm) cc_final: 0.5931 (mpm) REVERT: I 50 LYS cc_start: 0.6482 (tptp) cc_final: 0.6084 (mmmt) outliers start: 59 outliers final: 23 residues processed: 195 average time/residue: 0.9217 time to fit residues: 207.0108 Evaluate side-chains 177 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 201 TYR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain C residue 23 CYS Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 109 ILE Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 201 TYR Chi-restraints excluded: chain G residue 446 GLU Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 38 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 37 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 193 optimal weight: 10.0000 chunk 180 optimal weight: 0.5980 chunk 83 optimal weight: 4.9990 chunk 138 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 485 HIS ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.170303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.131130 restraints weight = 26878.741| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 3.08 r_work: 0.3967 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 moved from start: 1.0106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 17073 Z= 0.208 Angle : 0.773 12.127 23154 Z= 0.392 Chirality : 0.048 0.202 2547 Planarity : 0.005 0.048 2994 Dihedral : 7.314 63.152 2487 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 3.29 % Allowed : 21.44 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.18), residues: 2103 helix: -0.37 (0.29), residues: 318 sheet: -1.30 (0.21), residues: 636 loop : -2.03 (0.17), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 409 HIS 0.011 0.001 HIS G 485 PHE 0.016 0.003 PHE A 93 TYR 0.029 0.002 TYR D 445 ARG 0.005 0.001 ARG G 453 Details of bonding type rmsd link_NAG-ASN : bond 0.00281 ( 9) link_NAG-ASN : angle 3.98982 ( 27) hydrogen bonds : bond 0.04384 ( 450) hydrogen bonds : angle 5.16379 ( 1305) SS BOND : bond 0.00292 ( 24) SS BOND : angle 1.59751 ( 48) covalent geometry : bond 0.00494 (17037) covalent geometry : angle 0.75900 (23079) Misc. bond : bond 0.00173 ( 3) *********************** 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 218 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 158 time to evaluate : 1.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.5717 (OUTLIER) cc_final: 0.4983 (mp0) REVERT: A 45 LYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7483 (ttmt) REVERT: A 119 ASN cc_start: 0.7405 (p0) cc_final: 0.6838 (t0) REVERT: A 201 TYR cc_start: 0.7061 (OUTLIER) cc_final: 0.5949 (t80) REVERT: A 467 PHE cc_start: 0.7065 (m-80) cc_final: 0.6805 (m-80) REVERT: A 485 HIS cc_start: 0.7535 (p90) cc_final: 0.6716 (p90) REVERT: C 21 ILE cc_start: 0.5953 (tt) cc_final: 0.5660 (tp) REVERT: D 22 GLU cc_start: 0.5761 (OUTLIER) cc_final: 0.5373 (mp0) REVERT: D 95 ASN cc_start: 0.8465 (t0) cc_final: 0.8029 (t0) REVERT: D 131 ARG cc_start: 0.6551 (mtp85) cc_final: 0.5106 (pmt-80) REVERT: D 328 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.6797 (tt) REVERT: E 1 MET cc_start: 0.2637 (tmt) cc_final: 0.0827 (ptm) REVERT: E 67 ARG cc_start: 0.7077 (ptp-110) cc_final: 0.6740 (ttt180) REVERT: G 119 ASN cc_start: 0.7278 (p0) cc_final: 0.6740 (t0) REVERT: G 184 THR cc_start: 0.7153 (m) cc_final: 0.6953 (t) REVERT: G 201 TYR cc_start: 0.7125 (OUTLIER) cc_final: 0.5765 (t80) REVERT: G 252 LEU cc_start: 0.8904 (pp) cc_final: 0.8578 (mp) REVERT: G 402 GLN cc_start: 0.7426 (tt0) cc_final: 0.7135 (mp10) REVERT: I 4 MET cc_start: 0.6779 (mmm) cc_final: 0.6232 (mpm) outliers start: 60 outliers final: 37 residues processed: 206 average time/residue: 0.9173 time to fit residues: 219.5337 Evaluate side-chains 189 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 146 time to evaluate : 1.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 37 THR 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 201 TYR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain C residue 23 CYS Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 446 GLU 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 401 LYS Chi-restraints excluded: chain G residue 446 GLU Chi-restraints excluded: chain G residue 485 HIS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 33 LEU 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 108 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 24 optimal weight: 0.1980 chunk 175 optimal weight: 2.9990 chunk 61 optimal weight: 0.0570 chunk 181 optimal weight: 0.6980 chunk 166 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 81 optimal weight: 0.0370 overall best weight: 0.3176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN A 495 ASN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 485 HIS H 61 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.173231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.134722 restraints weight = 27183.698| |-----------------------------------------------------------------------------| r_work (start): 0.4153 rms_B_bonded: 3.14 r_work: 0.4026 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 moved from start: 1.0270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 17073 Z= 0.109 Angle : 0.648 14.148 23154 Z= 0.329 Chirality : 0.044 0.190 2547 Planarity : 0.004 0.077 2994 Dihedral : 6.617 58.130 2487 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.97 % Allowed : 23.19 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.18), residues: 2103 helix: -0.01 (0.30), residues: 318 sheet: -0.98 (0.21), residues: 627 loop : -1.81 (0.17), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 37 HIS 0.018 0.001 HIS G 485 PHE 0.014 0.001 PHE H 79 TYR 0.027 0.001 TYR G 420 ARG 0.016 0.001 ARG G 486 Details of bonding type rmsd link_NAG-ASN : bond 0.00465 ( 9) link_NAG-ASN : angle 3.14923 ( 27) hydrogen bonds : bond 0.03617 ( 450) hydrogen bonds : angle 4.76556 ( 1305) SS BOND : bond 0.00297 ( 24) SS BOND : angle 1.09781 ( 48) covalent geometry : bond 0.00243 (17037) covalent geometry : angle 0.63855 (23079) Misc. bond : bond 0.00176 ( 3) *********************** 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 192 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 156 time to evaluate : 1.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.5460 (OUTLIER) cc_final: 0.4701 (mp0) REVERT: A 45 LYS cc_start: 0.7830 (OUTLIER) cc_final: 0.7388 (ttpp) REVERT: A 119 ASN cc_start: 0.7520 (p0) cc_final: 0.6930 (t0) REVERT: A 170 ILE cc_start: 0.7416 (OUTLIER) cc_final: 0.6879 (mp) REVERT: A 467 PHE cc_start: 0.7087 (m-80) cc_final: 0.6851 (m-80) REVERT: A 493 MET cc_start: 0.7409 (mtt) cc_final: 0.7172 (mmt) REVERT: B 67 ARG cc_start: 0.6115 (ptp-110) cc_final: 0.5866 (ttt-90) REVERT: C 21 ILE cc_start: 0.6021 (tt) cc_final: 0.5774 (tp) REVERT: D 22 GLU cc_start: 0.5630 (OUTLIER) cc_final: 0.5248 (mp0) REVERT: D 95 ASN cc_start: 0.8396 (t0) cc_final: 0.7950 (t0) REVERT: D 119 ASN cc_start: 0.7049 (p0) cc_final: 0.6593 (t0) REVERT: D 131 ARG cc_start: 0.6132 (mtp85) cc_final: 0.5078 (pmt-80) REVERT: D 328 LEU cc_start: 0.7093 (OUTLIER) cc_final: 0.6415 (tt) REVERT: E 1 MET cc_start: 0.2519 (tmt) cc_final: 0.0760 (ptm) REVERT: E 67 ARG cc_start: 0.7072 (ptp-110) cc_final: 0.6586 (ttt180) REVERT: F 21 ILE cc_start: 0.5802 (tt) cc_final: 0.5600 (tp) REVERT: G 119 ASN cc_start: 0.7316 (p0) cc_final: 0.6847 (t0) REVERT: G 122 ARG cc_start: 0.6271 (tmm-80) cc_final: 0.5776 (tmt90) REVERT: G 201 TYR cc_start: 0.6815 (OUTLIER) cc_final: 0.5334 (t80) REVERT: G 485 HIS cc_start: 0.7075 (OUTLIER) cc_final: 0.6590 (p90) REVERT: I 4 MET cc_start: 0.6514 (mmm) cc_final: 0.5922 (mpm) REVERT: I 38 LEU cc_start: 0.7073 (OUTLIER) cc_final: 0.6701 (mp) outliers start: 36 outliers final: 14 residues processed: 182 average time/residue: 0.9502 time to fit residues: 199.8223 Evaluate side-chains 168 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 45 LYS 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 429 GLU Chi-restraints excluded: chain C residue 23 CYS Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 446 GLU Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 201 TYR Chi-restraints excluded: chain G residue 485 HIS Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 38 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 171 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 203 optimal weight: 20.0000 chunk 142 optimal weight: 2.9990 chunk 175 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 181 optimal weight: 0.7980 chunk 125 optimal weight: 2.9990 chunk 9 optimal weight: 0.1980 chunk 156 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN A 485 HIS A 495 ASN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 485 HIS G 494 GLN H 61 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.171238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.132768 restraints weight = 27421.951| |-----------------------------------------------------------------------------| r_work (start): 0.4113 rms_B_bonded: 3.11 r_work: 0.4003 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 moved from start: 1.0318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17073 Z= 0.158 Angle : 0.711 15.042 23154 Z= 0.358 Chirality : 0.046 0.186 2547 Planarity : 0.005 0.060 2994 Dihedral : 6.843 58.426 2487 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 2.03 % Allowed : 23.52 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.18), residues: 2103 helix: -0.14 (0.30), residues: 318 sheet: -1.01 (0.21), residues: 627 loop : -1.87 (0.17), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 409 HIS 0.012 0.001 HIS G 485 PHE 0.019 0.002 PHE E 79 TYR 0.035 0.002 TYR D 445 ARG 0.006 0.001 ARG A 221 Details of bonding type rmsd link_NAG-ASN : bond 0.00302 ( 9) link_NAG-ASN : angle 3.64921 ( 27) hydrogen bonds : bond 0.03924 ( 450) hydrogen bonds : angle 4.86695 ( 1305) SS BOND : bond 0.00318 ( 24) SS BOND : angle 1.29549 ( 48) covalent geometry : bond 0.00375 (17037) covalent geometry : angle 0.69850 (23079) Misc. bond : bond 0.00161 ( 3) ********************** 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 178 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 141 time to evaluate : 1.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.5521 (OUTLIER) cc_final: 0.4703 (mp0) REVERT: A 45 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7470 (ttpp) REVERT: A 119 ASN cc_start: 0.7500 (p0) cc_final: 0.6999 (t0) REVERT: A 170 ILE cc_start: 0.7436 (OUTLIER) cc_final: 0.6754 (mp) REVERT: A 467 PHE cc_start: 0.7043 (m-80) cc_final: 0.6766 (m-80) REVERT: C 21 ILE cc_start: 0.6063 (tt) cc_final: 0.5783 (tp) REVERT: D 22 GLU cc_start: 0.5690 (OUTLIER) cc_final: 0.5324 (mp0) REVERT: D 95 ASN cc_start: 0.8439 (t0) cc_final: 0.8000 (t0) REVERT: D 131 ARG cc_start: 0.6654 (mtp85) cc_final: 0.5114 (pmt-80) REVERT: D 328 LEU cc_start: 0.7026 (OUTLIER) cc_final: 0.6521 (tt) REVERT: D 387 GLN cc_start: 0.7231 (mm-40) cc_final: 0.6763 (mm-40) REVERT: E 1 MET cc_start: 0.2670 (tmt) cc_final: 0.1163 (ptm) REVERT: E 67 ARG cc_start: 0.7122 (ptp-110) cc_final: 0.6562 (ttt180) REVERT: G 119 ASN cc_start: 0.7349 (p0) cc_final: 0.6863 (t0) REVERT: G 122 ARG cc_start: 0.6335 (tmm-80) cc_final: 0.5766 (tmt90) REVERT: G 201 TYR cc_start: 0.6982 (OUTLIER) cc_final: 0.5657 (t80) REVERT: G 402 GLN cc_start: 0.7286 (tt0) cc_final: 0.6863 (mp10) REVERT: I 4 MET cc_start: 0.6659 (mmm) cc_final: 0.6080 (mpm) REVERT: I 38 LEU cc_start: 0.6899 (OUTLIER) cc_final: 0.6480 (mp) outliers start: 37 outliers final: 21 residues processed: 171 average time/residue: 0.9323 time to fit residues: 184.8023 Evaluate side-chains 168 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 1.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 170 ILE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain C residue 23 CYS Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 446 GLU Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 201 TYR Chi-restraints excluded: chain G residue 485 HIS Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 38 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 51 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 63 optimal weight: 4.9990 chunk 154 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 186 optimal weight: 20.0000 chunk 76 optimal weight: 2.9990 chunk 147 optimal weight: 0.2980 chunk 74 optimal weight: 0.7980 chunk 131 optimal weight: 0.0370 chunk 164 optimal weight: 0.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN A 485 HIS A 495 ASN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 485 HIS H 61 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.172848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.134389 restraints weight = 27069.105| |-----------------------------------------------------------------------------| r_work (start): 0.4152 rms_B_bonded: 3.13 r_work: 0.4029 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 1.0433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17073 Z= 0.113 Angle : 0.657 14.292 23154 Z= 0.331 Chirality : 0.044 0.223 2547 Planarity : 0.004 0.046 2994 Dihedral : 6.517 56.709 2487 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.70 % Allowed : 24.07 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.18), residues: 2103 helix: -0.01 (0.30), residues: 318 sheet: -0.81 (0.21), residues: 627 loop : -1.75 (0.17), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP E 37 HIS 0.013 0.001 HIS A 485 PHE 0.018 0.001 PHE E 79 TYR 0.025 0.001 TYR G 420 ARG 0.006 0.000 ARG A 221 Details of bonding type rmsd link_NAG-ASN : bond 0.00396 ( 9) link_NAG-ASN : angle 3.31452 ( 27) hydrogen bonds : bond 0.03592 ( 450) hydrogen bonds : angle 4.71787 ( 1305) SS BOND : bond 0.00309 ( 24) SS BOND : angle 1.06803 ( 48) covalent geometry : bond 0.00258 (17037) covalent geometry : angle 0.64595 (23079) Misc. bond : bond 0.00156 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12745.33 seconds wall clock time: 220 minutes 14.32 seconds (13214.32 seconds total)