Starting phenix.real_space_refine on Mon Nov 18 15:01:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iuz_35734/11_2024/8iuz_35734.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iuz_35734/11_2024/8iuz_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iuz_35734/11_2024/8iuz_35734.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iuz_35734/11_2024/8iuz_35734.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iuz_35734/11_2024/8iuz_35734.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iuz_35734/11_2024/8iuz_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-5513/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: 10.65, per 1000 atoms: 0.64 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=8, 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 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 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 " Time building additional restraints: 4.41 Conformation dependent library (CDL) restraints added in 2.2 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: 2.55 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: 6.21 Time building geometry restraints manager: 5.08 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: 9254 16.02 - 32.05: 786 32.05 - 48.07: 146 48.07 - 64.09: 29 64.09 - 80.12: 15 Dihedral angle restraints: 10230 sinusoidal: 4164 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 10227 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: 6 1.99 - 2.71: 1278 2.71 - 3.44: 21763 3.44 - 4.17: 38588 4.17 - 4.90: 69014 Nonbonded interactions: 130649 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=" NE2 GLN A 202 " pdb=" CZ ARG G 212 " model vdw 1.888 3.350 nonbonded pdb=" CZ ARG A 212 " pdb=" NE2 GLN D 202 " model vdw 1.888 3.350 ... (remaining 130644 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.620 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: 0.700 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 40.700 Find NCS groups from input model: 0.540 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: 0.010 Load rotamer database and sin/cos tables:10.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.740 ------------------------------------------------------------------------------- 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 : 0.010 0.099 17037 Z= 0.673 Angle : 1.337 14.419 23079 Z= 0.744 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 *********************** 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 : 2.015 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: 1.0862 time to fit residues: 453.9342 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 : 1.841 ------------------------------------------------------------------------------- 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: 0.9990 chunk 98 optimal weight: 0.8980 chunk 120 optimal weight: 0.9990 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 A 225 HIS A 421 ASN A 430 ASN A 455 ASN A 468 HIS A 481 ASN 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 388 GLN ** D 430 ASN ** 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5994 moved from start: 0.4890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 17037 Z= 0.290 Angle : 0.818 9.665 23079 Z= 0.429 Chirality : 0.050 0.234 2547 Planarity : 0.007 0.076 2994 Dihedral : 7.707 72.610 2489 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 3.78 % Allowed : 12.23 % Favored : 83.99 % 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: -3.44 (0.16), residues: 2103 helix: -1.46 (0.27), residues: 315 sheet: -2.12 (0.20), residues: 597 loop : -2.67 (0.16), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 143 HIS 0.009 0.002 HIS G 275 PHE 0.029 0.003 PHE G 243 TYR 0.022 0.002 TYR D 488 ARG 0.010 0.001 ARG G 104 *********************** 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 338 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 269 time to evaluate : 1.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASN cc_start: 0.7259 (p0) cc_final: 0.6635 (t0) REVERT: A 170 ILE cc_start: 0.7302 (OUTLIER) cc_final: 0.6731 (mp) REVERT: A 412 ASP cc_start: 0.5864 (t0) cc_final: 0.5591 (t0) REVERT: C 5 ASN cc_start: 0.6212 (m-40) cc_final: 0.6002 (m-40) REVERT: D 141 MET cc_start: 0.5603 (mmt) cc_final: 0.4619 (mmm) REVERT: D 174 ILE cc_start: 0.6767 (OUTLIER) cc_final: 0.6009 (mm) REVERT: D 412 ASP cc_start: 0.6542 (t70) cc_final: 0.6306 (t0) REVERT: D 454 GLU cc_start: 0.6204 (tm-30) cc_final: 0.5989 (tm-30) REVERT: E 1 MET cc_start: 0.1095 (tmt) cc_final: 0.0673 (tpp) REVERT: E 49 MET cc_start: 0.6297 (mmm) cc_final: 0.5626 (mmm) REVERT: E 68 MET cc_start: 0.6294 (tpp) cc_final: 0.6083 (mtm) REVERT: F 4 MET cc_start: 0.6728 (OUTLIER) cc_final: 0.6438 (tpp) REVERT: G 62 THR cc_start: 0.6783 (OUTLIER) cc_final: 0.6516 (p) REVERT: G 87 VAL cc_start: 0.7878 (m) cc_final: 0.7631 (p) REVERT: G 201 TYR cc_start: 0.5443 (OUTLIER) cc_final: 0.4137 (t80) REVERT: G 252 LEU cc_start: 0.7745 (pp) cc_final: 0.7393 (mp) REVERT: G 386 ASN cc_start: 0.5668 (p0) cc_final: 0.5358 (p0) REVERT: I 4 MET cc_start: 0.3422 (tpp) cc_final: 0.3203 (mmm) outliers start: 69 outliers final: 17 residues processed: 311 average time/residue: 0.9842 time to fit residues: 352.1684 Evaluate side-chains 187 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain C residue 23 CYS Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain F residue 4 MET 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 201 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 104 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 156 optimal weight: 3.9990 chunk 128 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 188 optimal weight: 7.9990 chunk 203 optimal weight: 6.9990 chunk 167 optimal weight: 2.9990 chunk 186 optimal weight: 5.9990 chunk 64 optimal weight: 8.9990 chunk 151 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN A 264 GLN ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 GLN D 202 GLN D 264 GLN D 314 ASN D 368 GLN D 430 ASN ** D 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN F 92 GLN G 54 GLN G 202 GLN G 264 GLN G 430 ASN G 468 HIS G 495 ASN H 40 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6726 moved from start: 0.8997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 17037 Z= 0.483 Angle : 0.965 12.383 23079 Z= 0.502 Chirality : 0.055 0.339 2547 Planarity : 0.007 0.093 2994 Dihedral : 8.318 61.605 2488 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.41 % Favored : 88.59 % Rotamer: Outliers : 5.26 % Allowed : 15.57 % Favored : 79.17 % 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: -3.31 (0.17), residues: 2103 helix: -1.55 (0.26), residues: 318 sheet: -1.99 (0.20), residues: 597 loop : -2.54 (0.16), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP G 143 HIS 0.008 0.002 HIS G 8 PHE 0.037 0.004 PHE D 464 TYR 0.036 0.003 TYR D 445 ARG 0.013 0.001 ARG A 486 *********************** 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 310 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 214 time to evaluate : 2.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASN cc_start: 0.7320 (p0) cc_final: 0.6490 (t0) REVERT: A 387 GLN cc_start: 0.6910 (tp-100) cc_final: 0.6450 (tp-100) REVERT: A 485 HIS cc_start: 0.7606 (p90) cc_final: 0.6931 (p-80) REVERT: C 21 ILE cc_start: 0.6073 (OUTLIER) cc_final: 0.5788 (tp) REVERT: D 95 ASN cc_start: 0.7934 (t0) cc_final: 0.7609 (t0) REVERT: D 104 ARG cc_start: 0.7574 (OUTLIER) cc_final: 0.7230 (ttm170) REVERT: D 328 LEU cc_start: 0.7174 (OUTLIER) cc_final: 0.6436 (tt) REVERT: D 365 LYS cc_start: 0.5829 (pttp) cc_final: 0.5528 (ptpt) REVERT: D 442 ASP cc_start: 0.7250 (t0) cc_final: 0.6307 (t0) REVERT: D 467 PHE cc_start: 0.6504 (m-80) cc_final: 0.6172 (m-80) REVERT: E 1 MET cc_start: 0.1280 (tmt) cc_final: -0.0276 (ptm) REVERT: E 49 MET cc_start: 0.5223 (mmm) cc_final: 0.4822 (mmm) REVERT: F 23 CYS cc_start: 0.6212 (m) cc_final: 0.5572 (m) REVERT: F 49 TYR cc_start: 0.4968 (p90) cc_final: 0.4631 (p90) REVERT: G 54 GLN cc_start: 0.7682 (OUTLIER) cc_final: 0.7147 (tm-30) REVERT: G 201 TYR cc_start: 0.7144 (OUTLIER) cc_final: 0.6145 (t80) REVERT: G 402 GLN cc_start: 0.7582 (tt0) cc_final: 0.7254 (mp10) REVERT: G 442 ASP cc_start: 0.7584 (p0) cc_final: 0.7351 (p0) REVERT: G 452 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.6481 (pp) REVERT: G 486 ARG cc_start: 0.7439 (mmm160) cc_final: 0.6918 (tpm170) REVERT: I 50 LYS cc_start: 0.6883 (tmtt) cc_final: 0.6379 (mtpt) outliers start: 96 outliers final: 30 residues processed: 297 average time/residue: 1.0131 time to fit residues: 345.4226 Evaluate side-chains 195 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 159 time to evaluate : 1.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 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 234 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 23 CYS Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain D residue 104 ARG 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 303 GLN Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 367 THR 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 170 ILE Chi-restraints excluded: chain G residue 201 TYR Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 461 THR 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 63 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 186 optimal weight: 5.9990 chunk 141 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 126 optimal weight: 6.9990 chunk 188 optimal weight: 8.9990 chunk 200 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 179 optimal weight: 0.7980 chunk 53 optimal weight: 8.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 275 HIS ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 421 ASN D 432 HIS D 468 HIS E 40 GLN F 6 GLN F 92 GLN G 54 GLN G 288 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6724 moved from start: 0.9271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 17037 Z= 0.303 Angle : 0.768 9.955 23079 Z= 0.396 Chirality : 0.049 0.286 2547 Planarity : 0.005 0.056 2994 Dihedral : 7.614 61.565 2487 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 4.11 % Allowed : 19.35 % Favored : 76.54 % 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: -2.86 (0.17), residues: 2103 helix: -1.02 (0.28), residues: 318 sheet: -1.67 (0.21), residues: 594 loop : -2.32 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 143 HIS 0.007 0.001 HIS B 104 PHE 0.031 0.003 PHE G 93 TYR 0.019 0.002 TYR D 300 ARG 0.007 0.001 ARG D 248 *********************** 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 249 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 174 time to evaluate : 1.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.5894 (OUTLIER) cc_final: 0.5236 (mp0) REVERT: A 119 ASN cc_start: 0.7242 (p0) cc_final: 0.6572 (t0) REVERT: A 170 ILE cc_start: 0.7379 (OUTLIER) cc_final: 0.6687 (mp) REVERT: A 299 ARG cc_start: 0.6863 (OUTLIER) cc_final: 0.6334 (mpp-170) REVERT: A 365 LYS cc_start: 0.7095 (OUTLIER) cc_final: 0.6329 (pttt) REVERT: A 485 HIS cc_start: 0.7363 (p90) cc_final: 0.6973 (p-80) REVERT: D 95 ASN cc_start: 0.7947 (t0) cc_final: 0.7581 (t0) REVERT: D 180 THR cc_start: 0.5809 (OUTLIER) cc_final: 0.5549 (t) REVERT: D 328 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.6822 (tt) REVERT: D 442 ASP cc_start: 0.6970 (t0) cc_final: 0.6261 (t0) REVERT: D 446 GLU cc_start: 0.6847 (OUTLIER) cc_final: 0.6475 (pm20) REVERT: D 463 CYS cc_start: 0.7670 (m) cc_final: 0.7084 (t) REVERT: E 1 MET cc_start: 0.1961 (tmt) cc_final: 0.0290 (ptm) REVERT: F 21 ILE cc_start: 0.6536 (mt) cc_final: 0.6091 (tt) REVERT: G 54 GLN cc_start: 0.7320 (OUTLIER) cc_final: 0.6962 (tm-30) REVERT: G 119 ASN cc_start: 0.6789 (OUTLIER) cc_final: 0.5646 (t0) REVERT: G 252 LEU cc_start: 0.8559 (pp) cc_final: 0.8278 (mp) REVERT: G 299 ARG cc_start: 0.6797 (OUTLIER) cc_final: 0.6596 (mpp-170) REVERT: G 452 LEU cc_start: 0.7384 (OUTLIER) cc_final: 0.7080 (pp) REVERT: G 454 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7278 (tm-30) REVERT: G 457 GLU cc_start: 0.6281 (mt-10) cc_final: 0.5481 (mp0) REVERT: I 21 ILE cc_start: 0.7197 (mt) cc_final: 0.6661 (tp) outliers start: 75 outliers final: 36 residues processed: 236 average time/residue: 0.9973 time to fit residues: 271.4858 Evaluate side-chains 206 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 159 time to evaluate : 1.979 ------------------------------------------------------------------------------- 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 299 ARG Chi-restraints excluded: chain A residue 365 LYS Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain C residue 23 CYS Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 180 THR 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 255 LYS Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 446 GLU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain G residue 15 THR 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 109 ILE Chi-restraints excluded: chain G residue 119 ASN Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 201 TYR Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 299 ARG Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 453 ARG Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 59 SER 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 166 optimal weight: 0.1980 chunk 113 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 148 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 170 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 102 optimal weight: 0.5980 chunk 179 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 495 ASN ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 HIS G 54 GLN G 485 HIS I 90 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 moved from start: 0.9621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17037 Z= 0.278 Angle : 0.737 9.898 23079 Z= 0.380 Chirality : 0.048 0.232 2547 Planarity : 0.005 0.053 2994 Dihedral : 7.369 58.857 2487 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 4.93 % Allowed : 19.46 % Favored : 75.60 % 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 (0.17), residues: 2103 helix: -0.77 (0.29), residues: 318 sheet: -1.42 (0.21), residues: 600 loop : -2.25 (0.17), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 143 HIS 0.005 0.001 HIS D 176 PHE 0.017 0.002 PHE D 93 TYR 0.060 0.002 TYR E 102 ARG 0.006 0.001 ARG G 212 *********************** 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 244 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 154 time to evaluate : 1.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.5743 (OUTLIER) cc_final: 0.5124 (mp0) REVERT: A 45 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7240 (ttmt) REVERT: A 119 ASN cc_start: 0.7227 (p0) cc_final: 0.6581 (t0) REVERT: A 170 ILE cc_start: 0.7384 (OUTLIER) cc_final: 0.6674 (mp) REVERT: A 299 ARG cc_start: 0.6846 (OUTLIER) cc_final: 0.5967 (mpp-170) REVERT: A 485 HIS cc_start: 0.7496 (p90) cc_final: 0.7089 (p-80) REVERT: D 95 ASN cc_start: 0.7970 (t0) cc_final: 0.7628 (t0) REVERT: D 131 ARG cc_start: 0.6769 (mtt90) cc_final: 0.5496 (pmt-80) REVERT: D 463 CYS cc_start: 0.7756 (m) cc_final: 0.7208 (t) REVERT: E 1 MET cc_start: 0.2043 (tmt) cc_final: 0.0286 (ptm) REVERT: E 67 ARG cc_start: 0.6915 (ptp-110) cc_final: 0.6159 (ptm160) REVERT: F 21 ILE cc_start: 0.6653 (mt) cc_final: 0.6249 (tt) REVERT: G 54 GLN cc_start: 0.7056 (OUTLIER) cc_final: 0.6742 (tm-30) REVERT: G 119 ASN cc_start: 0.6870 (OUTLIER) cc_final: 0.5895 (t0) REVERT: G 141 MET cc_start: 0.7730 (OUTLIER) cc_final: 0.7215 (mmt) REVERT: G 201 TYR cc_start: 0.7224 (OUTLIER) cc_final: 0.6027 (t80) REVERT: G 252 LEU cc_start: 0.8539 (pp) cc_final: 0.8291 (mp) REVERT: G 452 LEU cc_start: 0.7177 (OUTLIER) cc_final: 0.6963 (pp) REVERT: G 457 GLU cc_start: 0.6512 (mt-10) cc_final: 0.5642 (mp0) REVERT: I 4 MET cc_start: 0.6513 (mmm) cc_final: 0.6182 (mtm) REVERT: I 21 ILE cc_start: 0.7280 (mt) cc_final: 0.6719 (tp) outliers start: 90 outliers final: 41 residues processed: 233 average time/residue: 0.9618 time to fit residues: 259.0039 Evaluate side-chains 191 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 141 time to evaluate : 1.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 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 403 ILE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 23 CYS Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 255 LYS Chi-restraints excluded: chain D residue 273 CYS Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 54 GLN Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 109 ILE Chi-restraints excluded: chain G residue 119 ASN 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 234 THR Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 453 ARG Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 112 THR 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 67 optimal weight: 6.9990 chunk 180 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 117 optimal weight: 3.9990 chunk 49 optimal weight: 9.9990 chunk 200 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 16 optimal weight: 0.0970 chunk 66 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN G 54 GLN ** G 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6705 moved from start: 0.9847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17037 Z= 0.219 Angle : 0.678 9.538 23079 Z= 0.349 Chirality : 0.046 0.223 2547 Planarity : 0.005 0.054 2994 Dihedral : 7.035 58.275 2487 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 4.11 % Allowed : 20.50 % Favored : 75.38 % 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: -2.40 (0.18), residues: 2103 helix: -0.51 (0.29), residues: 318 sheet: -1.26 (0.21), residues: 594 loop : -2.13 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 37 HIS 0.004 0.001 HIS D 176 PHE 0.016 0.002 PHE E 79 TYR 0.018 0.002 TYR A 445 ARG 0.006 0.001 ARG A 221 *********************** 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 242 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 167 time to evaluate : 2.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.5461 (OUTLIER) cc_final: 0.4777 (mp0) REVERT: A 45 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7482 (ttpp) REVERT: A 119 ASN cc_start: 0.7173 (p0) cc_final: 0.6612 (t0) REVERT: A 170 ILE cc_start: 0.7324 (OUTLIER) cc_final: 0.6677 (mp) REVERT: A 299 ARG cc_start: 0.6720 (OUTLIER) cc_final: 0.5131 (mpp-170) REVERT: D 22 GLU cc_start: 0.5605 (OUTLIER) cc_final: 0.5272 (mp0) REVERT: D 95 ASN cc_start: 0.7983 (t0) cc_final: 0.7642 (t0) REVERT: D 104 ARG cc_start: 0.7462 (OUTLIER) cc_final: 0.7154 (ttm170) REVERT: D 328 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.6841 (tt) REVERT: D 337 GLU cc_start: 0.7306 (pm20) cc_final: 0.6798 (pm20) REVERT: D 392 ILE cc_start: 0.6946 (OUTLIER) cc_final: 0.6707 (mt) REVERT: D 463 CYS cc_start: 0.7771 (m) cc_final: 0.7343 (t) REVERT: E 1 MET cc_start: 0.2265 (tmt) cc_final: 0.0534 (ptm) REVERT: E 67 ARG cc_start: 0.7008 (ptp-110) cc_final: 0.6192 (ptm160) REVERT: G 54 GLN cc_start: 0.6995 (OUTLIER) cc_final: 0.6752 (tm-30) REVERT: G 119 ASN cc_start: 0.6869 (p0) cc_final: 0.6072 (t0) REVERT: G 141 MET cc_start: 0.7633 (OUTLIER) cc_final: 0.7117 (mmt) REVERT: G 457 GLU cc_start: 0.6436 (mt-10) cc_final: 0.5694 (mp0) REVERT: G 485 HIS cc_start: 0.6915 (p-80) cc_final: 0.6575 (p-80) REVERT: I 21 ILE cc_start: 0.7301 (mt) cc_final: 0.6777 (tp) outliers start: 75 outliers final: 36 residues processed: 225 average time/residue: 1.0807 time to fit residues: 278.5892 Evaluate side-chains 191 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 145 time to evaluate : 1.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 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 417 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 23 CYS Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 104 ARG Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 255 LYS Chi-restraints excluded: chain D residue 273 CYS Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 392 ILE Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 9 HIS Chi-restraints excluded: chain G residue 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 234 THR Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 453 ARG Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 63 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 193 optimal weight: 7.9990 chunk 22 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 168 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 199 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 121 optimal weight: 0.0570 chunk 92 optimal weight: 0.8980 overall best weight: 0.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 485 HIS A 495 ASN ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 54 GLN ** G 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 1.0045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17037 Z= 0.202 Angle : 0.677 12.233 23079 Z= 0.344 Chirality : 0.045 0.212 2547 Planarity : 0.004 0.053 2994 Dihedral : 6.826 57.575 2487 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.84 % Allowed : 21.93 % Favored : 74.23 % 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: -2.23 (0.18), residues: 2103 helix: -0.26 (0.30), residues: 318 sheet: -1.16 (0.21), residues: 621 loop : -2.05 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 37 HIS 0.006 0.001 HIS A 485 PHE 0.016 0.002 PHE E 79 TYR 0.025 0.001 TYR G 420 ARG 0.005 0.000 ARG A 221 *********************** 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 225 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 155 time to evaluate : 1.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.5460 (OUTLIER) cc_final: 0.4773 (mp0) REVERT: A 119 ASN cc_start: 0.7156 (p0) cc_final: 0.6631 (t0) REVERT: A 170 ILE cc_start: 0.7305 (OUTLIER) cc_final: 0.6664 (mp) REVERT: A 299 ARG cc_start: 0.6748 (OUTLIER) cc_final: 0.5194 (mpp-170) REVERT: A 485 HIS cc_start: 0.7565 (p90) cc_final: 0.7320 (p-80) REVERT: D 22 GLU cc_start: 0.5685 (OUTLIER) cc_final: 0.5278 (mp0) REVERT: D 95 ASN cc_start: 0.7962 (t0) cc_final: 0.7635 (t0) REVERT: D 104 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.7244 (ttm170) REVERT: D 131 ARG cc_start: 0.6620 (mtt90) cc_final: 0.5482 (pmt-80) REVERT: D 328 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.6609 (tt) REVERT: D 337 GLU cc_start: 0.7236 (pm20) cc_final: 0.6897 (pm20) REVERT: D 392 ILE cc_start: 0.6950 (OUTLIER) cc_final: 0.6749 (mt) REVERT: D 463 CYS cc_start: 0.7521 (m) cc_final: 0.7218 (t) REVERT: E 1 MET cc_start: 0.2469 (tmt) cc_final: 0.0907 (ptm) REVERT: E 67 ARG cc_start: 0.6984 (ptp-110) cc_final: 0.6153 (ptm160) REVERT: F 21 ILE cc_start: 0.6464 (mm) cc_final: 0.6122 (tt) REVERT: G 54 GLN cc_start: 0.6977 (OUTLIER) cc_final: 0.6719 (tm-30) REVERT: G 119 ASN cc_start: 0.7134 (p0) cc_final: 0.6396 (t0) REVERT: G 141 MET cc_start: 0.7613 (OUTLIER) cc_final: 0.7040 (mmt) REVERT: G 270 GLU cc_start: 0.6533 (tm-30) cc_final: 0.6297 (tt0) REVERT: G 463 CYS cc_start: 0.7913 (m) cc_final: 0.7267 (t) REVERT: G 485 HIS cc_start: 0.7035 (p-80) cc_final: 0.6716 (p90) REVERT: H 105 ILE cc_start: 0.4832 (OUTLIER) cc_final: 0.4306 (mp) REVERT: I 21 ILE cc_start: 0.7411 (mt) cc_final: 0.6886 (tp) outliers start: 70 outliers final: 35 residues processed: 214 average time/residue: 0.9798 time to fit residues: 242.2846 Evaluate side-chains 189 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 144 time to evaluate : 1.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 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 299 ARG Chi-restraints excluded: chain A residue 429 GLU 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 104 ARG Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 273 CYS Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 392 ILE Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 54 GLN Chi-restraints excluded: chain G residue 141 MET Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 228 ILE Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 435 ASP Chi-restraints excluded: chain G residue 453 ARG Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 90 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 123 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 119 optimal weight: 8.9990 chunk 60 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 126 optimal weight: 9.9990 chunk 135 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 156 optimal weight: 5.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 485 HIS D 495 ASN E 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 1.0151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 17037 Z= 0.413 Angle : 0.826 15.448 23079 Z= 0.420 Chirality : 0.051 0.212 2547 Planarity : 0.005 0.057 2994 Dihedral : 7.621 66.449 2487 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.13 % Favored : 89.87 % Rotamer: Outliers : 4.22 % Allowed : 22.09 % Favored : 73.68 % 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: -2.54 (0.17), residues: 2103 helix: -0.62 (0.29), residues: 318 sheet: -1.31 (0.21), residues: 615 loop : -2.26 (0.16), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP E 37 HIS 0.007 0.002 HIS D 275 PHE 0.020 0.003 PHE D 239 TYR 0.024 0.003 TYR G 420 ARG 0.007 0.001 ARG D 453 *********************** 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 219 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 142 time to evaluate : 1.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.5860 (OUTLIER) cc_final: 0.5153 (mp0) REVERT: A 119 ASN cc_start: 0.7196 (p0) cc_final: 0.6766 (t0) REVERT: A 299 ARG cc_start: 0.6911 (OUTLIER) cc_final: 0.6565 (mpp-170) REVERT: D 22 GLU cc_start: 0.5785 (OUTLIER) cc_final: 0.5382 (mp0) REVERT: D 69 GLN cc_start: 0.7215 (tm-30) cc_final: 0.6981 (tm-30) REVERT: D 95 ASN cc_start: 0.8100 (t0) cc_final: 0.7709 (t0) REVERT: D 104 ARG cc_start: 0.7636 (OUTLIER) cc_final: 0.7431 (ttm170) REVERT: D 328 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.6960 (tt) REVERT: D 463 CYS cc_start: 0.7532 (m) cc_final: 0.7256 (t) REVERT: E 1 MET cc_start: 0.2322 (tmt) cc_final: 0.0950 (ptm) REVERT: E 67 ARG cc_start: 0.7037 (ptp-110) cc_final: 0.6201 (ptm160) REVERT: F 21 ILE cc_start: 0.6523 (mm) cc_final: 0.6128 (tt) REVERT: G 119 ASN cc_start: 0.7093 (OUTLIER) cc_final: 0.6276 (t0) REVERT: G 184 THR cc_start: 0.7356 (m) cc_final: 0.7108 (t) REVERT: G 270 GLU cc_start: 0.6789 (tm-30) cc_final: 0.6529 (tt0) REVERT: G 395 GLU cc_start: 0.7392 (tt0) cc_final: 0.7088 (tt0) REVERT: I 21 ILE cc_start: 0.7415 (mt) cc_final: 0.6855 (tp) outliers start: 77 outliers final: 48 residues processed: 209 average time/residue: 0.9635 time to fit residues: 232.5154 Evaluate side-chains 195 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 141 time to evaluate : 1.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 222 ILE 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 417 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 495 ASN Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain C residue 23 CYS Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 104 ARG Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 273 CYS Chi-restraints excluded: chain D residue 312 MET Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 119 ASN Chi-restraints excluded: chain G residue 122 ARG Chi-restraints excluded: chain G residue 159 SER Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 228 ILE Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 453 ARG Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 63 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 181 optimal weight: 0.6980 chunk 191 optimal weight: 0.0170 chunk 174 optimal weight: 0.5980 chunk 185 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 145 optimal weight: 0.5980 chunk 57 optimal weight: 8.9990 chunk 168 optimal weight: 0.9980 chunk 175 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 ASN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 495 ASN ** G 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 61 ASN I 90 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 moved from start: 1.0353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17037 Z= 0.182 Angle : 0.673 13.951 23079 Z= 0.340 Chirality : 0.045 0.186 2547 Planarity : 0.004 0.051 2994 Dihedral : 6.818 59.624 2487 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.69 % Allowed : 23.96 % Favored : 73.36 % 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: -2.23 (0.18), residues: 2103 helix: -0.27 (0.29), residues: 318 sheet: -1.18 (0.20), residues: 645 loop : -2.05 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 37 HIS 0.005 0.001 HIS D 485 PHE 0.017 0.001 PHE E 79 TYR 0.024 0.001 TYR G 420 ARG 0.005 0.000 ARG A 221 *********************** 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 207 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 158 time to evaluate : 1.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.5455 (OUTLIER) cc_final: 0.4783 (mp0) REVERT: A 119 ASN cc_start: 0.7237 (p0) cc_final: 0.6816 (t0) REVERT: A 170 ILE cc_start: 0.7289 (OUTLIER) cc_final: 0.6683 (mp) REVERT: A 299 ARG cc_start: 0.6678 (OUTLIER) cc_final: 0.5090 (mpp-170) REVERT: A 485 HIS cc_start: 0.7552 (p90) cc_final: 0.7241 (p-80) REVERT: B 67 ARG cc_start: 0.6284 (ptp-110) cc_final: 0.5740 (ttt180) REVERT: D 22 GLU cc_start: 0.5493 (OUTLIER) cc_final: 0.5160 (mp0) REVERT: D 95 ASN cc_start: 0.8128 (t0) cc_final: 0.7735 (t0) REVERT: D 104 ARG cc_start: 0.7490 (OUTLIER) cc_final: 0.7213 (ttm170) REVERT: D 131 ARG cc_start: 0.6583 (mtt90) cc_final: 0.5343 (pmt-80) REVERT: D 328 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.6567 (tt) REVERT: D 442 ASP cc_start: 0.6908 (t0) cc_final: 0.6286 (t0) REVERT: D 446 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.6629 (pm20) REVERT: D 463 CYS cc_start: 0.7550 (m) cc_final: 0.7241 (t) REVERT: E 1 MET cc_start: 0.2906 (tmt) cc_final: 0.1302 (ptm) REVERT: E 67 ARG cc_start: 0.7082 (ptp-110) cc_final: 0.6062 (ptm160) REVERT: F 21 ILE cc_start: 0.6464 (mm) cc_final: 0.6146 (tt) REVERT: G 119 ASN cc_start: 0.7146 (p0) cc_final: 0.6535 (t0) REVERT: G 184 THR cc_start: 0.7158 (m) cc_final: 0.6945 (t) REVERT: G 201 TYR cc_start: 0.6926 (OUTLIER) cc_final: 0.6465 (t80) REVERT: G 463 CYS cc_start: 0.7620 (m) cc_final: 0.7358 (t) REVERT: G 493 MET cc_start: 0.7064 (tpp) cc_final: 0.5842 (ttt) REVERT: I 21 ILE cc_start: 0.7358 (mt) cc_final: 0.6866 (tp) outliers start: 49 outliers final: 29 residues processed: 204 average time/residue: 1.0078 time to fit residues: 237.0285 Evaluate side-chains 182 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 145 time to evaluate : 2.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 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 417 VAL Chi-restraints excluded: chain C residue 23 CYS Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 104 ARG Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 273 CYS Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 446 GLU Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain G residue 9 HIS Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 201 TYR Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 446 GLU Chi-restraints excluded: chain G residue 453 ARG Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 46 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 196 optimal weight: 0.0770 chunk 119 optimal weight: 0.0000 chunk 93 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 206 optimal weight: 1.9990 chunk 189 optimal weight: 0.7980 chunk 164 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 130 optimal weight: 7.9990 overall best weight: 0.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 ASN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 485 HIS D 495 ASN ** G 288 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 1.0429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17037 Z= 0.204 Angle : 0.680 13.590 23079 Z= 0.345 Chirality : 0.045 0.185 2547 Planarity : 0.004 0.051 2994 Dihedral : 6.755 58.946 2487 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 2.47 % Allowed : 24.51 % Favored : 73.03 % 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: -2.12 (0.18), residues: 2103 helix: -0.16 (0.29), residues: 318 sheet: -1.10 (0.21), residues: 639 loop : -1.98 (0.17), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP E 37 HIS 0.005 0.001 HIS G 485 PHE 0.019 0.002 PHE E 79 TYR 0.015 0.001 TYR E 95 ARG 0.006 0.000 ARG G 212 ********************** 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 197 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 152 time to evaluate : 1.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.5546 (OUTLIER) cc_final: 0.4844 (mp0) REVERT: A 119 ASN cc_start: 0.7247 (p0) cc_final: 0.6897 (t0) REVERT: A 170 ILE cc_start: 0.7344 (OUTLIER) cc_final: 0.6692 (mp) REVERT: A 299 ARG cc_start: 0.6666 (OUTLIER) cc_final: 0.5018 (mpp-170) REVERT: B 67 ARG cc_start: 0.6139 (ptp-110) cc_final: 0.5809 (ttt180) REVERT: D 22 GLU cc_start: 0.5595 (OUTLIER) cc_final: 0.5189 (mp0) REVERT: D 95 ASN cc_start: 0.8126 (t0) cc_final: 0.7731 (t0) REVERT: D 104 ARG cc_start: 0.7505 (OUTLIER) cc_final: 0.7203 (ttm170) REVERT: D 131 ARG cc_start: 0.6529 (mtt90) cc_final: 0.5358 (pmt-80) REVERT: D 442 ASP cc_start: 0.6905 (t0) cc_final: 0.6356 (t0) REVERT: D 446 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.6574 (pm20) REVERT: D 463 CYS cc_start: 0.7557 (m) cc_final: 0.7203 (t) REVERT: E 1 MET cc_start: 0.2924 (tmt) cc_final: 0.1303 (ptm) REVERT: E 67 ARG cc_start: 0.7125 (ptp-110) cc_final: 0.6095 (ptm160) REVERT: F 21 ILE cc_start: 0.6447 (mm) cc_final: 0.6185 (tt) REVERT: G 119 ASN cc_start: 0.7142 (p0) cc_final: 0.6526 (t0) REVERT: G 184 THR cc_start: 0.7183 (m) cc_final: 0.6979 (t) REVERT: G 201 TYR cc_start: 0.6990 (OUTLIER) cc_final: 0.5657 (t80) REVERT: G 463 CYS cc_start: 0.7757 (m) cc_final: 0.7294 (t) REVERT: G 493 MET cc_start: 0.7051 (tpp) cc_final: 0.5832 (ttt) REVERT: I 21 ILE cc_start: 0.7368 (mt) cc_final: 0.6882 (tp) outliers start: 45 outliers final: 30 residues processed: 191 average time/residue: 0.9813 time to fit residues: 216.3098 Evaluate side-chains 182 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 145 time to evaluate : 1.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 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 417 VAL Chi-restraints excluded: chain C residue 23 CYS Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 104 ARG Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 273 CYS Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 446 GLU Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 201 TYR Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 446 GLU Chi-restraints excluded: chain G residue 453 ARG Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 63 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 151 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 164 optimal weight: 0.2980 chunk 68 optimal weight: 4.9990 chunk 168 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 30 optimal weight: 0.4980 chunk 144 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN ** A 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 ASN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 288 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 = 0.4668 r_free = 0.4668 target = 0.172023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.133626 restraints weight = 27130.735| |-----------------------------------------------------------------------------| r_work (start): 0.4137 rms_B_bonded: 3.13 r_work: 0.4024 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 1.0547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17037 Z= 0.192 Angle : 0.670 13.625 23079 Z= 0.339 Chirality : 0.045 0.184 2547 Planarity : 0.004 0.051 2994 Dihedral : 6.613 57.122 2487 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.30 % Allowed : 24.51 % Favored : 73.19 % 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: -2.00 (0.18), residues: 2103 helix: -0.10 (0.29), residues: 318 sheet: -1.01 (0.21), residues: 633 loop : -1.89 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP E 37 HIS 0.006 0.001 HIS A 468 PHE 0.020 0.002 PHE E 79 TYR 0.027 0.001 TYR G 420 ARG 0.007 0.000 ARG G 212 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5640.10 seconds wall clock time: 102 minutes 21.20 seconds (6141.20 seconds total)