Starting phenix.real_space_refine on Sun Jun 15 00:23:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iuz_35734/06_2025/8iuz_35734.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iuz_35734/06_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_35734/06_2025/8iuz_35734.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iuz_35734/06_2025/8iuz_35734.map" model { file = "/net/cci-nas-00/data/ceres_data/8iuz_35734/06_2025/8iuz_35734.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iuz_35734/06_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-5710/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: 10.20, per 1000 atoms: 0.61 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 2.3 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: 2.73 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: 6.52 Time building geometry restraints manager: 4.73 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: 0.11 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: 4.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.670 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 40.920 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:13.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.990 ------------------------------------------------------------------------------- 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 : 1.669 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: 1.0557 time to fit residues: 440.0109 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 : 1.818 ------------------------------------------------------------------------------- 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 = 44)----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.160504 restraints weight = 28470.268| |-----------------------------------------------------------------------------| r_work (start): 0.4568 rms_B_bonded: 3.19 r_work: 0.4462 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.4462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6156 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 3.86662 ( 27) hydrogen bonds : bond 0.05818 ( 450) hydrogen bonds : angle 6.08145 ( 1305) SS BOND : bond 0.00555 ( 24) SS BOND : angle 1.91201 ( 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 : 2.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASN cc_start: 0.7241 (p0) cc_final: 0.6617 (t0) REVERT: A 170 ILE cc_start: 0.7341 (OUTLIER) cc_final: 0.6850 (mp) REVERT: A 412 ASP cc_start: 0.6646 (t0) cc_final: 0.6385 (t0) REVERT: C 5 ASN cc_start: 0.6350 (m-40) cc_final: 0.6131 (m-40) REVERT: D 174 ILE cc_start: 0.6800 (OUTLIER) cc_final: 0.6038 (mm) REVERT: D 244 ILE cc_start: 0.6772 (OUTLIER) cc_final: 0.6336 (mp) REVERT: D 380 ARG cc_start: 0.6308 (OUTLIER) cc_final: 0.6066 (mmm-85) REVERT: D 412 ASP cc_start: 0.7005 (t70) cc_final: 0.6733 (t0) REVERT: D 454 GLU cc_start: 0.6381 (tm-30) cc_final: 0.6107 (tm-30) REVERT: D 493 MET cc_start: 0.6190 (OUTLIER) cc_final: 0.5778 (mtt) REVERT: E 1 MET cc_start: 0.1231 (tmt) cc_final: 0.0853 (tpp) REVERT: E 49 MET cc_start: 0.6476 (mmm) cc_final: 0.5735 (mmm) REVERT: E 68 MET cc_start: 0.6314 (tpp) cc_final: 0.6103 (mtm) REVERT: F 4 MET cc_start: 0.7013 (tpp) cc_final: 0.6635 (tpp) REVERT: G 62 THR cc_start: 0.6963 (OUTLIER) cc_final: 0.6716 (p) REVERT: G 201 TYR cc_start: 0.5752 (OUTLIER) cc_final: 0.4382 (t80) REVERT: G 252 LEU cc_start: 0.8052 (pp) cc_final: 0.7620 (mp) REVERT: G 386 ASN cc_start: 0.5908 (p0) cc_final: 0.5593 (p0) REVERT: G 475 MET cc_start: 0.4690 (tpp) cc_final: 0.4165 (mmt) REVERT: I 4 MET cc_start: 0.3603 (tpp) cc_final: 0.3195 (tpt) outliers start: 66 outliers final: 19 residues processed: 308 average time/residue: 1.2998 time to fit residues: 459.7857 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 : 2.389 ------------------------------------------------------------------------------- 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: 1.9990 chunk 106 optimal weight: 4.9990 chunk 79 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 173 optimal weight: 0.6980 chunk 64 optimal weight: 8.9990 chunk 60 optimal weight: 20.0000 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 G 54 GLN G 214 GLN G 264 GLN G 430 ASN G 468 HIS G 495 ASN H 40 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.174172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.134697 restraints weight = 27266.537| |-----------------------------------------------------------------------------| r_work (start): 0.4245 rms_B_bonded: 3.13 r_work: 0.4138 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 0.7903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 17073 Z= 0.205 Angle : 0.817 10.333 23154 Z= 0.421 Chirality : 0.049 0.218 2547 Planarity : 0.006 0.058 2994 Dihedral : 7.523 59.935 2488 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 4.17 % Allowed : 15.62 % Favored : 80.21 % 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: -1.06 (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 0.031 0.003 TRP D 143 HIS 0.004 0.001 HIS G 8 PHE 0.028 0.003 PHE G 93 TYR 0.076 0.003 TYR D 420 ARG 0.011 0.001 ARG G 486 Details of bonding type rmsd link_NAG-ASN : bond 0.00355 ( 9) link_NAG-ASN : angle 3.64879 ( 27) hydrogen bonds : bond 0.05370 ( 450) hydrogen bonds : angle 5.86567 ( 1305) SS BOND : bond 0.00370 ( 24) SS BOND : angle 1.52174 ( 48) covalent geometry : bond 0.00457 (17037) covalent geometry : angle 0.80555 (23079) Misc. bond : bond 0.00132 ( 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 290 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 214 time to evaluate : 1.708 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.5977 (OUTLIER) cc_final: 0.5093 (mp0) REVERT: A 119 ASN cc_start: 0.7265 (p0) cc_final: 0.6511 (t0) REVERT: A 170 ILE cc_start: 0.7488 (OUTLIER) cc_final: 0.6866 (mp) REVERT: A 485 HIS cc_start: 0.7407 (p-80) cc_final: 0.6555 (p90) REVERT: C 4 MET cc_start: 0.6348 (mmm) cc_final: 0.6058 (mtm) REVERT: D 95 ASN cc_start: 0.8316 (t0) cc_final: 0.8061 (t0) REVERT: D 104 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.7317 (ttm170) REVERT: D 174 ILE cc_start: 0.7263 (OUTLIER) cc_final: 0.6949 (mm) REVERT: D 307 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8104 (mm) REVERT: D 328 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.6764 (tt) REVERT: D 442 ASP cc_start: 0.7400 (t0) cc_final: 0.6606 (t0) REVERT: D 446 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6895 (pm20) REVERT: D 467 PHE cc_start: 0.6427 (m-80) cc_final: 0.6203 (m-80) REVERT: E 49 MET cc_start: 0.5934 (mmm) cc_final: 0.5419 (mmm) REVERT: F 49 TYR cc_start: 0.5134 (p90) cc_final: 0.4775 (p90) REVERT: G 54 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7489 (tm-30) REVERT: G 119 ASN cc_start: 0.6301 (p0) cc_final: 0.5364 (p0) REVERT: G 201 TYR cc_start: 0.6684 (OUTLIER) cc_final: 0.6219 (m-80) REVERT: G 252 LEU cc_start: 0.8857 (pp) cc_final: 0.8421 (mt) REVERT: G 306 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7527 (tp) REVERT: G 441 MET cc_start: 0.5730 (tpt) cc_final: 0.5525 (tpt) REVERT: G 454 GLU cc_start: 0.7288 (tm-30) cc_final: 0.6593 (tm-30) REVERT: G 486 ARG cc_start: 0.7455 (mmm160) cc_final: 0.6788 (tpm170) outliers start: 76 outliers final: 21 residues processed: 273 average time/residue: 0.9737 time to fit residues: 305.4649 Evaluate side-chains 181 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 150 time to evaluate : 1.705 ------------------------------------------------------------------------------- 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 B residue 69 SER Chi-restraints excluded: chain B residue 112 THR 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 307 LEU Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 446 GLU Chi-restraints excluded: chain D residue 461 THR 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 306 LEU Chi-restraints excluded: chain G residue 461 THR 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: 2.9990 chunk 45 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 150 optimal weight: 0.8980 chunk 169 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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** B 36 ASN D 275 HIS ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 ASN D 468 HIS G 54 GLN G 214 GLN G 485 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4751 r_free = 0.4751 target = 0.188858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.145757 restraints weight = 25766.997| |-----------------------------------------------------------------------------| r_work (start): 0.4164 rms_B_bonded: 3.50 r_work: 0.4051 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.4051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.8525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 17073 Z= 0.148 Angle : 0.709 11.022 23154 Z= 0.362 Chirality : 0.047 0.260 2547 Planarity : 0.005 0.055 2994 Dihedral : 6.875 59.284 2487 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 4.17 % Allowed : 17.38 % Favored : 78.45 % 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: -2.50 (0.18), residues: 2103 helix: -0.44 (0.30), residues: 318 sheet: -1.45 (0.21), residues: 615 loop : -2.16 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP G 143 HIS 0.008 0.001 HIS G 485 PHE 0.019 0.002 PHE G 137 TYR 0.020 0.002 TYR D 420 ARG 0.006 0.001 ARG D 248 Details of bonding type rmsd link_NAG-ASN : bond 0.00354 ( 9) link_NAG-ASN : angle 3.44733 ( 27) hydrogen bonds : bond 0.04119 ( 450) hydrogen bonds : angle 5.24169 ( 1305) SS BOND : bond 0.00515 ( 24) SS BOND : angle 1.97438 ( 48) covalent geometry : bond 0.00341 (17037) covalent geometry : angle 0.69468 (23079) Misc. bond : bond 0.00383 ( 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 253 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 177 time to evaluate : 1.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.5377 (OUTLIER) cc_final: 0.4577 (mp0) REVERT: A 119 ASN cc_start: 0.7554 (p0) cc_final: 0.6681 (t0) REVERT: A 170 ILE cc_start: 0.7403 (OUTLIER) cc_final: 0.6777 (mp) REVERT: A 299 ARG cc_start: 0.6653 (OUTLIER) cc_final: 0.5109 (mpp-170) REVERT: D 95 ASN cc_start: 0.8298 (t0) cc_final: 0.7974 (t0) REVERT: D 119 ASN cc_start: 0.7000 (p0) cc_final: 0.6025 (t0) REVERT: D 127 THR cc_start: 0.8571 (p) cc_final: 0.8267 (t) REVERT: D 131 ARG cc_start: 0.6422 (ttm-80) cc_final: 0.6194 (mtt90) REVERT: D 174 ILE cc_start: 0.7317 (OUTLIER) cc_final: 0.7089 (mm) REVERT: D 328 LEU cc_start: 0.7177 (OUTLIER) cc_final: 0.6744 (tt) REVERT: D 442 ASP cc_start: 0.7370 (t0) cc_final: 0.6366 (t0) REVERT: D 446 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6797 (pm20) REVERT: D 463 CYS cc_start: 0.7351 (m) cc_final: 0.6902 (m) REVERT: E 1 MET cc_start: 0.1201 (tmt) cc_final: -0.0171 (mtt) REVERT: F 49 TYR cc_start: 0.4400 (p90) cc_final: 0.4072 (p90) REVERT: G 54 GLN cc_start: 0.7428 (OUTLIER) cc_final: 0.7026 (tm-30) REVERT: G 111 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7646 (mmtm) REVERT: G 119 ASN cc_start: 0.6696 (p0) cc_final: 0.5797 (p0) REVERT: G 201 TYR cc_start: 0.6533 (OUTLIER) cc_final: 0.6183 (m-80) REVERT: G 252 LEU cc_start: 0.8936 (pp) cc_final: 0.8644 (mp) REVERT: G 378 LEU cc_start: 0.7816 (mt) cc_final: 0.7613 (tm) REVERT: G 454 GLU cc_start: 0.7564 (tm-30) cc_final: 0.6868 (tm-30) REVERT: G 463 CYS cc_start: 0.7891 (m) cc_final: 0.7573 (m) REVERT: G 486 ARG cc_start: 0.7736 (mmm160) cc_final: 0.7144 (tpm-80) REVERT: I 4 MET cc_start: 0.5553 (OUTLIER) cc_final: 0.5282 (mpp) outliers start: 76 outliers final: 22 residues processed: 238 average time/residue: 1.1025 time to fit residues: 302.9363 Evaluate side-chains 186 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 154 time to evaluate : 3.403 ------------------------------------------------------------------------------- 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 D residue 446 GLU Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain G residue 25 VAL 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 111 LYS 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 I residue 4 MET 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: 2.9990 chunk 119 optimal weight: 9.9990 chunk 170 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 160 optimal weight: 0.6980 chunk 166 optimal weight: 0.0000 chunk 116 optimal weight: 3.9990 chunk 60 optimal weight: 20.0000 overall best weight: 2.1390 ------------------------------------------------------------------------------- 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 264 GLN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 ASN F 55 HIS G 54 GLN G 214 GLN G 288 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.168166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.129637 restraints weight = 28006.407| |-----------------------------------------------------------------------------| r_work (start): 0.4058 rms_B_bonded: 3.13 r_work: 0.3937 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.9442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 17073 Z= 0.259 Angle : 0.868 12.634 23154 Z= 0.442 Chirality : 0.051 0.268 2547 Planarity : 0.006 0.058 2994 Dihedral : 7.735 62.688 2487 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.13 % Favored : 89.87 % Rotamer: Outliers : 4.66 % Allowed : 18.97 % Favored : 76.37 % 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: -2.63 (0.18), residues: 2103 helix: -0.74 (0.29), residues: 318 sheet: -1.54 (0.21), residues: 636 loop : -2.18 (0.17), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP G 143 HIS 0.006 0.002 HIS B 104 PHE 0.026 0.003 PHE G 93 TYR 0.030 0.003 TYR D 445 ARG 0.007 0.001 ARG G 453 Details of bonding type rmsd link_NAG-ASN : bond 0.00279 ( 9) link_NAG-ASN : angle 4.47118 ( 27) hydrogen bonds : bond 0.04981 ( 450) hydrogen bonds : angle 5.54859 ( 1305) SS BOND : bond 0.00710 ( 24) SS BOND : angle 2.10835 ( 48) covalent geometry : bond 0.00613 (17037) covalent geometry : angle 0.85024 (23079) Misc. bond : bond 0.00241 ( 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 242 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 157 time to evaluate : 1.751 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.5953 (OUTLIER) cc_final: 0.5149 (mp0) REVERT: A 119 ASN cc_start: 0.7426 (p0) cc_final: 0.6681 (t0) REVERT: A 299 ARG cc_start: 0.6970 (OUTLIER) cc_final: 0.6746 (mpp-170) REVERT: A 485 HIS cc_start: 0.7492 (p90) cc_final: 0.6773 (p-80) REVERT: D 22 GLU cc_start: 0.6149 (OUTLIER) cc_final: 0.5931 (mp0) REVERT: D 95 ASN cc_start: 0.8303 (t0) cc_final: 0.7918 (t0) REVERT: D 174 ILE cc_start: 0.7502 (OUTLIER) cc_final: 0.7280 (mm) REVERT: D 328 LEU cc_start: 0.7247 (OUTLIER) cc_final: 0.6694 (tt) REVERT: E 1 MET cc_start: 0.1639 (tmt) cc_final: 0.0387 (mtt) REVERT: F 4 MET cc_start: 0.5371 (tpp) cc_final: 0.4791 (tpt) REVERT: G 54 GLN cc_start: 0.7273 (OUTLIER) cc_final: 0.6696 (tm-30) REVERT: G 119 ASN cc_start: 0.7141 (p0) cc_final: 0.6178 (t0) REVERT: G 141 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.8040 (mmt) REVERT: G 201 TYR cc_start: 0.7011 (OUTLIER) cc_final: 0.5563 (t80) REVERT: G 402 GLN cc_start: 0.7574 (tt0) cc_final: 0.6987 (mp10) REVERT: G 463 CYS cc_start: 0.7940 (m) cc_final: 0.7510 (m) REVERT: G 486 ARG cc_start: 0.7719 (mmm160) cc_final: 0.7339 (tpm170) REVERT: H 79 PHE cc_start: 0.6682 (OUTLIER) cc_final: 0.5403 (p90) REVERT: I 4 MET cc_start: 0.6234 (OUTLIER) cc_final: 0.5775 (mpp) REVERT: I 21 ILE cc_start: 0.6639 (OUTLIER) cc_final: 0.6333 (tp) REVERT: I 50 LYS cc_start: 0.6300 (tptp) cc_final: 0.6035 (mmmt) outliers start: 85 outliers final: 35 residues processed: 225 average time/residue: 0.9420 time to fit residues: 244.7069 Evaluate side-chains 187 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 141 time to evaluate : 1.717 ------------------------------------------------------------------------------- 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 159 SER Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 299 ARG Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 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 22 GLU Chi-restraints excluded: chain D residue 49 THR 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 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 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 54 GLN Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 141 MET 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 79 PHE Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain I residue 4 MET 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: 0.0870 chunk 190 optimal weight: 0.6980 chunk 66 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 97 optimal weight: 0.0870 chunk 74 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 0.0970 overall best weight: 0.3936 ------------------------------------------------------------------------------- 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** D 485 HIS ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 54 GLN G 214 GLN G 451 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.179437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.140601 restraints weight = 26952.030| |-----------------------------------------------------------------------------| r_work (start): 0.4152 rms_B_bonded: 3.36 r_work: 0.4037 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6650 moved from start: 0.9692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17073 Z= 0.114 Angle : 0.656 11.557 23154 Z= 0.336 Chirality : 0.045 0.213 2547 Planarity : 0.004 0.045 2994 Dihedral : 6.838 58.420 2487 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.56 % Allowed : 20.72 % Favored : 75.71 % 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: -2.16 (0.18), residues: 2103 helix: -0.26 (0.30), residues: 318 sheet: -1.18 (0.21), residues: 621 loop : -1.94 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 37 HIS 0.004 0.001 HIS G 432 PHE 0.015 0.001 PHE H 79 TYR 0.015 0.001 TYR D 445 ARG 0.005 0.000 ARG G 453 Details of bonding type rmsd link_NAG-ASN : bond 0.00410 ( 9) link_NAG-ASN : angle 3.42953 ( 27) hydrogen bonds : bond 0.03798 ( 450) hydrogen bonds : angle 4.98745 ( 1305) SS BOND : bond 0.00332 ( 24) SS BOND : angle 1.72315 ( 48) covalent geometry : bond 0.00252 (17037) covalent geometry : angle 0.64162 (23079) Misc. bond : bond 0.00135 ( 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 229 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 164 time to evaluate : 1.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.5359 (OUTLIER) cc_final: 0.4613 (mp0) REVERT: A 119 ASN cc_start: 0.7380 (p0) cc_final: 0.6737 (t0) REVERT: A 170 ILE cc_start: 0.7355 (OUTLIER) cc_final: 0.6849 (mp) REVERT: A 299 ARG cc_start: 0.6662 (OUTLIER) cc_final: 0.5235 (mpp-170) REVERT: A 337 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7196 (pm20) REVERT: A 457 GLU cc_start: 0.6975 (tt0) cc_final: 0.6774 (tt0) REVERT: A 467 PHE cc_start: 0.6929 (m-80) cc_final: 0.6723 (m-80) REVERT: A 485 HIS cc_start: 0.7164 (p90) cc_final: 0.6925 (p-80) REVERT: D 22 GLU cc_start: 0.5818 (OUTLIER) cc_final: 0.5365 (mp0) REVERT: D 95 ASN cc_start: 0.8387 (t0) cc_final: 0.7959 (t0) REVERT: E 1 MET cc_start: 0.2242 (tmt) cc_final: 0.0750 (mtt) REVERT: G 54 GLN cc_start: 0.7187 (OUTLIER) cc_final: 0.6651 (tm-30) REVERT: G 119 ASN cc_start: 0.6880 (p0) cc_final: 0.6168 (t0) REVERT: G 201 TYR cc_start: 0.6769 (OUTLIER) cc_final: 0.6546 (t80) REVERT: G 252 LEU cc_start: 0.8848 (pp) cc_final: 0.8605 (mp) REVERT: G 402 GLN cc_start: 0.7284 (tt0) cc_final: 0.6914 (mp10) REVERT: G 446 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.6740 (pm20) REVERT: G 454 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7420 (tm-30) REVERT: G 486 ARG cc_start: 0.7723 (mmm160) cc_final: 0.7202 (tpm170) REVERT: I 50 LYS cc_start: 0.5785 (OUTLIER) cc_final: 0.5307 (mmmt) outliers start: 65 outliers final: 18 residues processed: 212 average time/residue: 0.9077 time to fit residues: 223.1625 Evaluate side-chains 177 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 1.664 ------------------------------------------------------------------------------- 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 337 GLU 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 228 ILE Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain G residue 54 GLN 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 H residue 30 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 50 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 21 optimal weight: 1.9990 chunk 206 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 133 optimal weight: 10.0000 chunk 94 optimal weight: 0.9990 chunk 153 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 485 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.166528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.126723 restraints weight = 26647.331| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 3.07 r_work: 0.3957 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.9897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 17073 Z= 0.194 Angle : 0.762 10.291 23154 Z= 0.387 Chirality : 0.048 0.212 2547 Planarity : 0.005 0.048 2994 Dihedral : 7.202 59.718 2487 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 3.51 % Allowed : 21.71 % Favored : 74.78 % 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: -2.28 (0.18), residues: 2103 helix: -0.38 (0.30), residues: 318 sheet: -1.22 (0.21), residues: 615 loop : -2.04 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 409 HIS 0.008 0.001 HIS G 485 PHE 0.017 0.003 PHE D 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 0.00276 ( 9) link_NAG-ASN : angle 4.01340 ( 27) hydrogen bonds : bond 0.04357 ( 450) hydrogen bonds : angle 5.14481 ( 1305) SS BOND : bond 0.00348 ( 24) SS BOND : angle 2.01544 ( 48) covalent geometry : bond 0.00459 (17037) covalent geometry : angle 0.74491 (23079) Misc. bond : bond 0.00165 ( 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 223 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 159 time to evaluate : 1.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.5781 (OUTLIER) cc_final: 0.5001 (mp0) REVERT: A 45 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7261 (ttmt) REVERT: A 119 ASN cc_start: 0.7416 (p0) cc_final: 0.6806 (t0) REVERT: A 201 TYR cc_start: 0.7062 (OUTLIER) cc_final: 0.5953 (t80) REVERT: A 299 ARG cc_start: 0.6837 (OUTLIER) cc_final: 0.5624 (mpp-170) REVERT: A 337 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7314 (pm20) REVERT: A 485 HIS cc_start: 0.7500 (p90) cc_final: 0.7156 (p90) REVERT: C 38 LEU cc_start: 0.5386 (OUTLIER) cc_final: 0.4463 (mp) REVERT: D 22 GLU cc_start: 0.5882 (OUTLIER) cc_final: 0.5613 (mp0) REVERT: D 45 LYS cc_start: 0.7962 (ttmp) cc_final: 0.7012 (tppt) REVERT: D 95 ASN cc_start: 0.8404 (t0) cc_final: 0.8021 (t0) REVERT: E 1 MET cc_start: 0.2261 (tmt) cc_final: 0.0407 (ptm) REVERT: E 67 ARG cc_start: 0.7098 (ptp-110) cc_final: 0.6691 (ttt180) REVERT: G 119 ASN cc_start: 0.7144 (p0) cc_final: 0.6452 (t0) REVERT: G 122 ARG cc_start: 0.6249 (tmm-80) cc_final: 0.6026 (tpt-90) REVERT: G 184 THR cc_start: 0.7101 (m) cc_final: 0.6865 (t) REVERT: G 201 TYR cc_start: 0.7015 (OUTLIER) cc_final: 0.5706 (t80) REVERT: G 252 LEU cc_start: 0.8861 (pp) cc_final: 0.8597 (mp) REVERT: G 402 GLN cc_start: 0.7348 (tt0) cc_final: 0.7071 (mp10) REVERT: G 446 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.7036 (pm20) REVERT: I 4 MET cc_start: 0.6404 (mmm) cc_final: 0.5895 (mtt) REVERT: I 50 LYS cc_start: 0.6316 (OUTLIER) cc_final: 0.5885 (mmmt) outliers start: 64 outliers final: 29 residues processed: 205 average time/residue: 0.9710 time to fit residues: 227.8054 Evaluate side-chains 188 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 149 time to evaluate : 1.791 ------------------------------------------------------------------------------- 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 299 ARG Chi-restraints excluded: chain A residue 337 GLU 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 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 312 MET 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 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 435 ASP 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 38 LEU Chi-restraints excluded: chain I residue 50 LYS Chi-restraints excluded: chain I residue 63 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 37 optimal weight: 0.9990 chunk 114 optimal weight: 0.8980 chunk 73 optimal weight: 0.0980 chunk 94 optimal weight: 0.9990 chunk 193 optimal weight: 9.9990 chunk 180 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 152 optimal weight: 0.0270 chunk 50 optimal weight: 0.6980 overall best weight: 0.5038 ------------------------------------------------------------------------------- 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** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 54 GLN ** G 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 485 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.177661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.138960 restraints weight = 27296.888| |-----------------------------------------------------------------------------| r_work (start): 0.4139 rms_B_bonded: 3.12 r_work: 0.4034 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 1.0109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17073 Z= 0.118 Angle : 0.667 10.725 23154 Z= 0.339 Chirality : 0.044 0.194 2547 Planarity : 0.004 0.084 2994 Dihedral : 6.648 56.894 2487 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.96 % Allowed : 22.42 % Favored : 74.62 % 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: -2.00 (0.18), residues: 2103 helix: -0.11 (0.30), residues: 318 sheet: -1.03 (0.21), residues: 627 loop : -1.88 (0.17), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 37 HIS 0.015 0.001 HIS G 485 PHE 0.015 0.001 PHE B 79 TYR 0.017 0.001 TYR E 95 ARG 0.006 0.000 ARG A 486 Details of bonding type rmsd link_NAG-ASN : bond 0.00388 ( 9) link_NAG-ASN : angle 3.47947 ( 27) hydrogen bonds : bond 0.03703 ( 450) hydrogen bonds : angle 4.83497 ( 1305) SS BOND : bond 0.00284 ( 24) SS BOND : angle 1.62217 ( 48) covalent geometry : bond 0.00269 (17037) covalent geometry : angle 0.65365 (23079) Misc. bond : bond 0.00143 ( 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 213 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 159 time to evaluate : 1.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.5390 (OUTLIER) cc_final: 0.4634 (mp0) REVERT: A 45 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7447 (ttpp) REVERT: A 119 ASN cc_start: 0.7535 (p0) cc_final: 0.6873 (t0) REVERT: A 170 ILE cc_start: 0.7391 (OUTLIER) cc_final: 0.6794 (mp) REVERT: A 299 ARG cc_start: 0.6629 (OUTLIER) cc_final: 0.5059 (mpp-170) REVERT: A 485 HIS cc_start: 0.7348 (p90) cc_final: 0.6912 (p-80) REVERT: A 493 MET cc_start: 0.7079 (mtt) cc_final: 0.6459 (mmt) REVERT: D 22 GLU cc_start: 0.5782 (OUTLIER) cc_final: 0.5398 (mp0) REVERT: D 95 ASN cc_start: 0.8387 (t0) cc_final: 0.7967 (t0) REVERT: D 328 LEU cc_start: 0.7007 (OUTLIER) cc_final: 0.6378 (tt) REVERT: E 1 MET cc_start: 0.2202 (tmt) cc_final: 0.0364 (ptm) REVERT: E 67 ARG cc_start: 0.7139 (ptp-110) cc_final: 0.6708 (ttt180) REVERT: F 4 MET cc_start: 0.6176 (mmm) cc_final: 0.5861 (mmm) REVERT: F 21 ILE cc_start: 0.5408 (tt) cc_final: 0.5167 (tp) REVERT: G 54 GLN cc_start: 0.7405 (OUTLIER) cc_final: 0.6901 (tm-30) REVERT: G 119 ASN cc_start: 0.7229 (p0) cc_final: 0.6512 (t0) REVERT: G 122 ARG cc_start: 0.6042 (tmm-80) cc_final: 0.5679 (tpt-90) REVERT: G 184 THR cc_start: 0.7065 (m) cc_final: 0.6843 (t) REVERT: I 4 MET cc_start: 0.6409 (mmm) cc_final: 0.6128 (mtm) REVERT: I 38 LEU cc_start: 0.7116 (OUTLIER) cc_final: 0.6784 (mp) REVERT: I 50 LYS cc_start: 0.5675 (OUTLIER) cc_final: 0.5206 (mmmt) outliers start: 54 outliers final: 23 residues processed: 198 average time/residue: 0.9115 time to fit residues: 210.6768 Evaluate side-chains 180 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 1.889 ------------------------------------------------------------------------------- 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 299 ARG 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 49 THR Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 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 54 GLN Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 50 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 108 optimal weight: 0.6980 chunk 23 optimal weight: 0.2980 chunk 40 optimal weight: 3.9990 chunk 4 optimal weight: 0.0980 chunk 24 optimal weight: 1.9990 chunk 175 optimal weight: 6.9990 chunk 61 optimal weight: 8.9990 chunk 181 optimal weight: 0.9990 chunk 166 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 81 optimal weight: 0.0570 overall best weight: 0.4300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 495 ASN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 54 GLN ** G 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 485 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.174341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.135500 restraints weight = 27103.671| |-----------------------------------------------------------------------------| r_work (start): 0.4157 rms_B_bonded: 3.15 r_work: 0.4055 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6642 moved from start: 1.0202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17073 Z= 0.108 Angle : 0.646 14.042 23154 Z= 0.324 Chirality : 0.044 0.183 2547 Planarity : 0.004 0.082 2994 Dihedral : 6.408 56.139 2487 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.36 % Allowed : 22.92 % Favored : 74.73 % 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: -1.84 (0.18), residues: 2103 helix: -0.01 (0.30), residues: 318 sheet: -0.85 (0.21), residues: 642 loop : -1.82 (0.17), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 37 HIS 0.006 0.001 HIS G 485 PHE 0.016 0.001 PHE B 79 TYR 0.026 0.001 TYR G 420 ARG 0.018 0.000 ARG G 486 Details of bonding type rmsd link_NAG-ASN : bond 0.00372 ( 9) link_NAG-ASN : angle 3.25046 ( 27) hydrogen bonds : bond 0.03552 ( 450) hydrogen bonds : angle 4.67080 ( 1305) SS BOND : bond 0.00296 ( 24) SS BOND : angle 1.49689 ( 48) covalent geometry : bond 0.00242 (17037) covalent geometry : angle 0.63343 (23079) Misc. bond : bond 0.00140 ( 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 205 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 162 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.5335 (OUTLIER) cc_final: 0.4527 (mp0) REVERT: A 119 ASN cc_start: 0.7537 (p0) cc_final: 0.6937 (t0) REVERT: A 170 ILE cc_start: 0.7376 (OUTLIER) cc_final: 0.6767 (mp) REVERT: A 201 TYR cc_start: 0.6659 (OUTLIER) cc_final: 0.5548 (t80) REVERT: A 299 ARG cc_start: 0.6579 (OUTLIER) cc_final: 0.4942 (mpp-170) REVERT: A 337 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7201 (pm20) REVERT: A 493 MET cc_start: 0.7142 (mtt) cc_final: 0.6430 (mmt) REVERT: D 22 GLU cc_start: 0.5695 (OUTLIER) cc_final: 0.5296 (mp0) REVERT: D 95 ASN cc_start: 0.8397 (t0) cc_final: 0.7982 (t0) REVERT: D 131 ARG cc_start: 0.6424 (mtp85) cc_final: 0.5217 (pmt-80) REVERT: D 328 LEU cc_start: 0.6944 (OUTLIER) cc_final: 0.6246 (tt) REVERT: E 1 MET cc_start: 0.2326 (tmt) cc_final: 0.0422 (ptm) REVERT: E 54 TYR cc_start: 0.5168 (p90) cc_final: 0.4820 (p90) REVERT: E 67 ARG cc_start: 0.7093 (ptp-110) cc_final: 0.6672 (ttt180) REVERT: F 4 MET cc_start: 0.6225 (mmm) cc_final: 0.5819 (mmm) REVERT: G 22 GLU cc_start: 0.6020 (mt-10) cc_final: 0.5603 (mp0) REVERT: G 54 GLN cc_start: 0.7164 (OUTLIER) cc_final: 0.6625 (tm-30) REVERT: G 119 ASN cc_start: 0.7431 (p0) cc_final: 0.6733 (t0) REVERT: G 486 ARG cc_start: 0.7765 (mmm160) cc_final: 0.7483 (tpm170) REVERT: I 4 MET cc_start: 0.6392 (mmm) cc_final: 0.5723 (mtm) REVERT: I 38 LEU cc_start: 0.7159 (OUTLIER) cc_final: 0.6815 (mp) REVERT: I 50 LYS cc_start: 0.5673 (tptp) cc_final: 0.5224 (mmmt) outliers start: 43 outliers final: 26 residues processed: 194 average time/residue: 0.9979 time to fit residues: 222.0754 Evaluate side-chains 183 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 148 time to evaluate : 1.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU 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 201 TYR 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 299 ARG Chi-restraints excluded: chain A residue 337 GLU 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 49 THR Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain D residue 446 GLU Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 54 GLN Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 228 ILE Chi-restraints excluded: chain G residue 401 LYS Chi-restraints excluded: chain G residue 412 ASP 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 171 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 203 optimal weight: 20.0000 chunk 142 optimal weight: 3.9990 chunk 175 optimal weight: 6.9990 chunk 54 optimal weight: 0.2980 chunk 181 optimal weight: 1.9990 chunk 125 optimal weight: 9.9990 chunk 9 optimal weight: 0.8980 chunk 156 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 485 HIS ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 485 HIS ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 485 HIS H 61 ASN I 90 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.172144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.133468 restraints weight = 27459.299| |-----------------------------------------------------------------------------| r_work (start): 0.4125 rms_B_bonded: 3.12 r_work: 0.4018 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6706 moved from start: 1.0261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17073 Z= 0.167 Angle : 0.714 14.841 23154 Z= 0.359 Chirality : 0.046 0.234 2547 Planarity : 0.005 0.076 2994 Dihedral : 6.676 57.361 2487 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 2.30 % Allowed : 23.85 % Favored : 73.85 % 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: -1.91 (0.18), residues: 2103 helix: -0.15 (0.30), residues: 318 sheet: -0.90 (0.21), residues: 624 loop : -1.82 (0.17), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP E 37 HIS 0.007 0.001 HIS G 485 PHE 0.017 0.002 PHE E 79 TYR 0.033 0.002 TYR D 445 ARG 0.018 0.001 ARG G 486 Details of bonding type rmsd link_NAG-ASN : bond 0.00548 ( 9) link_NAG-ASN : angle 3.63262 ( 27) hydrogen bonds : bond 0.03880 ( 450) hydrogen bonds : angle 4.81473 ( 1305) SS BOND : bond 0.00291 ( 24) SS BOND : angle 1.64035 ( 48) covalent geometry : bond 0.00392 (17037) covalent geometry : angle 0.69988 (23079) Misc. bond : bond 0.00136 ( 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 188 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 146 time to evaluate : 1.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.5501 (OUTLIER) cc_final: 0.4664 (mp0) REVERT: A 119 ASN cc_start: 0.7497 (p0) cc_final: 0.6944 (t0) REVERT: A 170 ILE cc_start: 0.7428 (OUTLIER) cc_final: 0.6733 (mp) REVERT: A 201 TYR cc_start: 0.6901 (OUTLIER) cc_final: 0.5712 (t80) REVERT: A 299 ARG cc_start: 0.6724 (OUTLIER) cc_final: 0.5177 (mpp-170) REVERT: A 485 HIS cc_start: 0.7493 (p-80) cc_final: 0.7099 (p-80) REVERT: A 493 MET cc_start: 0.7367 (mtt) cc_final: 0.6895 (mmt) REVERT: D 22 GLU cc_start: 0.5797 (OUTLIER) cc_final: 0.5395 (mp0) REVERT: D 95 ASN cc_start: 0.8450 (t0) cc_final: 0.7997 (t0) REVERT: D 131 ARG cc_start: 0.6410 (mtp85) cc_final: 0.5154 (pmt-80) REVERT: D 255 LYS cc_start: 0.7440 (OUTLIER) cc_final: 0.7166 (ptmm) REVERT: D 328 LEU cc_start: 0.7026 (OUTLIER) cc_final: 0.6321 (tt) REVERT: D 387 GLN cc_start: 0.7236 (mm-40) cc_final: 0.6777 (mm-40) REVERT: E 1 MET cc_start: 0.2445 (tmt) cc_final: 0.0627 (ptm) REVERT: E 67 ARG cc_start: 0.7154 (ptp-110) cc_final: 0.6707 (ttt180) REVERT: F 4 MET cc_start: 0.6220 (mmm) cc_final: 0.5986 (mmm) REVERT: G 119 ASN cc_start: 0.7494 (p0) cc_final: 0.6824 (t0) REVERT: I 38 LEU cc_start: 0.6999 (OUTLIER) cc_final: 0.6613 (mp) REVERT: I 50 LYS cc_start: 0.5937 (OUTLIER) cc_final: 0.5510 (mmmt) outliers start: 42 outliers final: 26 residues processed: 178 average time/residue: 0.9461 time to fit residues: 194.0208 Evaluate side-chains 176 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 141 time to evaluate : 1.746 ------------------------------------------------------------------------------- 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 201 TYR 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 299 ARG 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 49 THR Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 255 LYS Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain D residue 446 GLU Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 401 LYS 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 Chi-restraints excluded: chain I residue 50 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 51 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 154 optimal weight: 0.7980 chunk 21 optimal weight: 6.9990 chunk 186 optimal weight: 20.0000 chunk 76 optimal weight: 2.9990 chunk 147 optimal weight: 0.0570 chunk 74 optimal weight: 1.9990 chunk 131 optimal weight: 20.0000 chunk 164 optimal weight: 0.9990 overall best weight: 0.9704 ------------------------------------------------------------------------------- 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 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 432 HIS ** G 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 485 HIS H 61 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.172762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.134292 restraints weight = 27131.602| |-----------------------------------------------------------------------------| r_work (start): 0.4127 rms_B_bonded: 3.11 r_work: 0.3998 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6703 moved from start: 1.0339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 17073 Z= 0.145 Angle : 0.704 14.206 23154 Z= 0.355 Chirality : 0.045 0.186 2547 Planarity : 0.004 0.094 2994 Dihedral : 6.665 57.585 2487 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.30 % Allowed : 23.90 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (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: -1.88 (0.18), residues: 2103 helix: -0.11 (0.29), residues: 318 sheet: -0.88 (0.21), residues: 624 loop : -1.81 (0.17), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP E 37 HIS 0.004 0.001 HIS G 485 PHE 0.018 0.002 PHE E 79 TYR 0.032 0.002 TYR D 445 ARG 0.012 0.001 ARG G 486 Details of bonding type rmsd link_NAG-ASN : bond 0.00332 ( 9) link_NAG-ASN : angle 3.55727 ( 27) hydrogen bonds : bond 0.03765 ( 450) hydrogen bonds : angle 4.79124 ( 1305) SS BOND : bond 0.00293 ( 24) SS BOND : angle 1.53172 ( 48) covalent geometry : bond 0.00342 (17037) covalent geometry : angle 0.69132 (23079) Misc. bond : bond 0.00131 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13765.67 seconds wall clock time: 238 minutes 39.61 seconds (14319.61 seconds total)