Starting phenix.real_space_refine on Mon Nov 18 19:31:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tpa_41471/11_2024/8tpa_41471.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tpa_41471/11_2024/8tpa_41471.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/8tpa_41471/11_2024/8tpa_41471.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tpa_41471/11_2024/8tpa_41471.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tpa_41471/11_2024/8tpa_41471.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tpa_41471/11_2024/8tpa_41471.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= 0.058 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 69 5.16 5 C 10875 2.51 5 N 2961 2.21 5 O 3381 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 105 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 17286 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2530 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 20, 'TRANS': 301} Chain: "B" Number of atoms: 1328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1328 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 1, 'TRANS': 161} Chain: "D" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 991 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "E" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 829 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Restraints were copied for chains: F, K, C, G, O, N, J, L, I, H Time building chain proxies: 8.77, per 1000 atoms: 0.51 Number of scatterers: 17286 At special positions: 0 Unit cell: (132.25, 127.65, 148.35, 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 69 16.00 O 3381 8.00 N 2961 7.00 C 10875 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.02 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.06 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.02 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 BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 401 " - " ASN A 132 " " NAG A 402 " - " ASN A 163 " " NAG A 403 " - " ASN A 289 " " NAG A 404 " - " ASN A 63 " " NAG C 401 " - " ASN C 132 " " NAG C 402 " - " ASN C 163 " " NAG C 403 " - " ASN C 289 " " NAG C 404 " - " ASN C 63 " " NAG G 401 " - " ASN G 132 " " NAG G 402 " - " ASN G 163 " " NAG G 403 " - " ASN G 289 " " NAG G 404 " - " ASN G 63 " " NAG M 1 " - " ASN A 95 " " NAG N 1 " - " ASN C 95 " " NAG O 1 " - " ASN G 95 " Time building additional restraints: 4.33 Conformation dependent library (CDL) restraints added in 2.3 seconds 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3960 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 51 sheets defined 21.4% alpha, 34.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.76 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 3.773A pdb=" N GLU A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N LEU A 78 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 125 through 130 removed outlier: 4.213A pdb=" N TRP A 130 " --> pdb=" O LYS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'B' and resid 37 through 58 Processing helix chain 'B' and resid 74 through 127 Processing helix chain 'B' and resid 145 through 155 Processing helix chain 'B' and resid 159 through 161 No H-bonds generated for 'chain 'B' and resid 159 through 161' Processing helix chain 'B' and resid 162 through 171 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 80 removed outlier: 3.772A pdb=" N GLU C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N LEU C 78 " --> pdb=" O GLU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 112 Processing helix chain 'C' and resid 125 through 130 removed outlier: 4.213A pdb=" N TRP C 130 " --> pdb=" O LYS C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'F' and resid 37 through 58 Processing helix chain 'F' and resid 74 through 127 Processing helix chain 'F' and resid 145 through 155 Processing helix chain 'F' and resid 159 through 161 No H-bonds generated for 'chain 'F' and resid 159 through 161' Processing helix chain 'F' and resid 162 through 171 Processing helix chain 'G' and resid 65 through 72 Processing helix chain 'G' and resid 73 through 80 removed outlier: 3.773A pdb=" N GLU G 77 " --> pdb=" O PRO G 74 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU G 78 " --> pdb=" O GLU G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 112 Processing helix chain 'G' and resid 125 through 130 removed outlier: 4.213A pdb=" N TRP G 130 " --> pdb=" O LYS G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 196 Processing helix chain 'I' and resid 73 through 75 No H-bonds generated for 'chain 'I' and resid 73 through 75' Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'J' and resid 79 through 83 Processing helix chain 'K' and resid 37 through 58 Processing helix chain 'K' and resid 74 through 127 Processing helix chain 'K' and resid 145 through 155 Processing helix chain 'K' and resid 159 through 161 No H-bonds generated for 'chain 'K' and resid 159 through 161' Processing helix chain 'K' and resid 162 through 171 Processing sheet with id=AA1, first strand: chain 'B' and resid 33 through 36 Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 26 removed outlier: 4.353A pdb=" N ASP A 24 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 removed outlier: 6.121A pdb=" N LEU A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N CYS A 277 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.632A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 115 through 122 removed outlier: 6.508A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU A 175 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 115 through 122 removed outlier: 6.508A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU A 175 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 136 through 141 removed outlier: 7.368A pdb=" N SER A 138 " --> pdb=" O LYS A 144 " (cutoff:3.500A) removed outlier: 10.094A pdb=" N LYS A 144 " --> pdb=" O SER A 138 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB2, first strand: chain 'A' and resid 286 through 287 Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.858A pdb=" N TYR H 35 " --> pdb=" O GLU H 95 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N TRP H 35A" --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N TYR H 50 " --> pdb=" O TRP H 35A" (cutoff:3.500A) removed outlier: 6.721A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AB6, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.411A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.411A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 33 through 36 Processing sheet with id=AC1, first strand: chain 'C' and resid 24 through 26 removed outlier: 4.354A pdb=" N ASP C 24 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AC3, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AC4, first strand: chain 'C' and resid 51 through 54 removed outlier: 6.121A pdb=" N LEU C 51 " --> pdb=" O ASP C 275 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N CYS C 277 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.632A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 115 through 122 removed outlier: 6.508A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU C 175 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N LEU C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 115 through 122 removed outlier: 6.508A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU C 175 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 136 through 141 removed outlier: 7.369A pdb=" N SER C 138 " --> pdb=" O LYS C 144 " (cutoff:3.500A) removed outlier: 10.093A pdb=" N LYS C 144 " --> pdb=" O SER C 138 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AD1, first strand: chain 'C' and resid 286 through 287 Processing sheet with id=AD2, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AD3, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.858A pdb=" N TYR D 35 " --> pdb=" O GLU D 95 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N TRP D 35A" --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N TYR D 50 " --> pdb=" O TRP D 35A" (cutoff:3.500A) removed outlier: 6.721A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 11 through 12 Processing sheet with id=AD5, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AD6, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.410A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA E 84 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.410A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA E 84 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 33 through 36 Processing sheet with id=AD9, first strand: chain 'G' and resid 24 through 26 removed outlier: 4.353A pdb=" N ASP G 24 " --> pdb=" O VAL G 36 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 39 through 41 Processing sheet with id=AE2, first strand: chain 'G' and resid 43 through 44 Processing sheet with id=AE3, first strand: chain 'G' and resid 51 through 54 removed outlier: 6.121A pdb=" N LEU G 51 " --> pdb=" O ASP G 275 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N CYS G 277 " --> pdb=" O LEU G 51 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 59 through 60 removed outlier: 6.632A pdb=" N LEU G 59 " --> pdb=" O VAL G 88 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 115 through 122 removed outlier: 6.509A pdb=" N TYR G 256 " --> pdb=" O LEU G 179 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N LEU G 179 " --> pdb=" O TYR G 256 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU G 175 " --> pdb=" O LEU G 260 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU G 179 " --> pdb=" O PRO G 254 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 115 through 122 removed outlier: 6.509A pdb=" N TYR G 256 " --> pdb=" O LEU G 179 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N LEU G 179 " --> pdb=" O TYR G 256 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU G 175 " --> pdb=" O LEU G 260 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 136 through 141 removed outlier: 7.368A pdb=" N SER G 138 " --> pdb=" O LYS G 144 " (cutoff:3.500A) removed outlier: 10.093A pdb=" N LYS G 144 " --> pdb=" O SER G 138 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 164 through 169 Processing sheet with id=AE9, first strand: chain 'G' and resid 286 through 287 Processing sheet with id=AF1, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AF2, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.858A pdb=" N TYR I 35 " --> pdb=" O GLU I 95 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N TRP I 35A" --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N TYR I 50 " --> pdb=" O TRP I 35A" (cutoff:3.500A) removed outlier: 6.722A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 11 through 12 Processing sheet with id=AF4, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AF5, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.409A pdb=" N LEU J 11 " --> pdb=" O GLU J 105 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA J 84 " --> pdb=" O LEU J 104 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.409A pdb=" N LEU J 11 " --> pdb=" O GLU J 105 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA J 84 " --> pdb=" O LEU J 104 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR J 97 " --> pdb=" O GLN J 90 " (cutoff:3.500A) 777 hydrogen bonds defined for protein. 2070 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: 6.67 Time building geometry restraints manager: 4.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 5199 1.33 - 1.47: 5392 1.47 - 1.61: 7013 1.61 - 1.75: 12 1.75 - 1.89: 81 Bond restraints: 17697 Sorted by residual: bond pdb=" CB ILE I 37 " pdb=" CG1 ILE I 37 " ideal model delta sigma weight residual 1.530 1.425 0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" CB ILE D 37 " pdb=" CG1 ILE D 37 " ideal model delta sigma weight residual 1.530 1.425 0.105 2.00e-02 2.50e+03 2.73e+01 bond pdb=" CB ILE H 37 " pdb=" CG1 ILE H 37 " ideal model delta sigma weight residual 1.530 1.426 0.104 2.00e-02 2.50e+03 2.70e+01 bond pdb=" CB ASN G 48 " pdb=" CG ASN G 48 " ideal model delta sigma weight residual 1.516 1.391 0.125 2.50e-02 1.60e+03 2.49e+01 bond pdb=" CB ASN C 48 " pdb=" CG ASN C 48 " ideal model delta sigma weight residual 1.516 1.392 0.124 2.50e-02 1.60e+03 2.46e+01 ... (remaining 17692 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.57: 23985 7.57 - 15.14: 36 15.14 - 22.71: 0 22.71 - 30.28: 0 30.28 - 37.85: 6 Bond angle restraints: 24027 Sorted by residual: angle pdb=" C2 NAG C 402 " pdb=" N2 NAG C 402 " pdb=" C7 NAG C 402 " ideal model delta sigma weight residual 124.56 162.41 -37.85 3.00e+00 1.11e-01 1.59e+02 angle pdb=" C2 NAG G 402 " pdb=" N2 NAG G 402 " pdb=" C7 NAG G 402 " ideal model delta sigma weight residual 124.56 162.34 -37.78 3.00e+00 1.11e-01 1.59e+02 angle pdb=" C2 NAG A 402 " pdb=" N2 NAG A 402 " pdb=" C7 NAG A 402 " ideal model delta sigma weight residual 124.56 162.31 -37.75 3.00e+00 1.11e-01 1.58e+02 angle pdb=" C2 NAG C 403 " pdb=" N2 NAG C 403 " pdb=" C7 NAG C 403 " ideal model delta sigma weight residual 124.56 160.05 -35.49 3.00e+00 1.11e-01 1.40e+02 angle pdb=" C2 NAG A 403 " pdb=" N2 NAG A 403 " pdb=" C7 NAG A 403 " ideal model delta sigma weight residual 124.56 160.01 -35.45 3.00e+00 1.11e-01 1.40e+02 ... (remaining 24022 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 10302 17.80 - 35.61: 260 35.61 - 53.41: 92 53.41 - 71.22: 35 71.22 - 89.02: 9 Dihedral angle restraints: 10698 sinusoidal: 4479 harmonic: 6219 Sorted by residual: dihedral pdb=" CB CYS A 64 " pdb=" SG CYS A 64 " pdb=" SG CYS A 76 " pdb=" CB CYS A 76 " ideal model delta sinusoidal sigma weight residual -86.00 -117.98 31.98 1 1.00e+01 1.00e-02 1.46e+01 dihedral pdb=" C LEU A 164 " pdb=" N LEU A 164 " pdb=" CA LEU A 164 " pdb=" CB LEU A 164 " ideal model delta harmonic sigma weight residual -122.60 -113.67 -8.93 0 2.50e+00 1.60e-01 1.28e+01 dihedral pdb=" C LEU C 164 " pdb=" N LEU C 164 " pdb=" CA LEU C 164 " pdb=" CB LEU C 164 " ideal model delta harmonic sigma weight residual -122.60 -113.70 -8.90 0 2.50e+00 1.60e-01 1.27e+01 ... (remaining 10695 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1731 0.089 - 0.178: 663 0.178 - 0.267: 150 0.267 - 0.356: 60 0.356 - 0.445: 21 Chirality restraints: 2625 Sorted by residual: chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.03e+02 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.93e+01 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.79e+01 ... (remaining 2622 not shown) Planarity restraints: 3114 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 113 " 0.034 2.00e-02 2.50e+03 6.99e-02 4.89e+01 pdb=" C SER D 113 " -0.121 2.00e-02 2.50e+03 pdb=" O SER D 113 " 0.043 2.00e-02 2.50e+03 pdb=" OXT SER D 113 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER I 113 " 0.034 2.00e-02 2.50e+03 6.96e-02 4.84e+01 pdb=" C SER I 113 " -0.120 2.00e-02 2.50e+03 pdb=" O SER I 113 " 0.043 2.00e-02 2.50e+03 pdb=" OXT SER I 113 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER H 113 " -0.034 2.00e-02 2.50e+03 6.96e-02 4.84e+01 pdb=" C SER H 113 " 0.120 2.00e-02 2.50e+03 pdb=" O SER H 113 " -0.043 2.00e-02 2.50e+03 pdb=" OXT SER H 113 " -0.043 2.00e-02 2.50e+03 ... (remaining 3111 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 113 2.59 - 3.17: 14279 3.17 - 3.75: 26553 3.75 - 4.32: 39580 4.32 - 4.90: 64067 Nonbonded interactions: 144592 Sorted by model distance: nonbonded pdb=" SG CYS G 64 " pdb=" SG CYS G 76 " model vdw 2.017 3.760 nonbonded pdb=" SG CYS C 64 " pdb=" SG CYS C 76 " model vdw 2.018 3.760 nonbonded pdb=" SG CYS C 281 " pdb=" SG CYS C 305 " model vdw 2.020 3.760 nonbonded pdb=" SG CYS G 281 " pdb=" SG CYS G 305 " model vdw 2.020 3.760 nonbonded pdb=" SG CYS E 23 " pdb=" SG CYS E 88 " model vdw 2.022 3.760 ... (remaining 144587 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 'C' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } 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: 2.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.680 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 39.620 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.060 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:12.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 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 : 0.022 0.152 17697 Z= 1.421 Angle : 1.807 37.848 24027 Z= 1.159 Chirality : 0.106 0.445 2625 Planarity : 0.009 0.070 3099 Dihedral : 10.431 89.023 6726 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.17), residues: 2130 helix: 1.50 (0.24), residues: 357 sheet: 0.96 (0.20), residues: 528 loop : 0.54 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.009 TRP C 84 HIS 0.014 0.003 HIS B 142 PHE 0.033 0.006 PHE C 118 TYR 0.086 0.009 TYR I 50 ARG 0.007 0.001 ARG G 192 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 400 time to evaluate : 1.897 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 42 GLN cc_start: 0.7525 (mm-40) cc_final: 0.7298 (mm110) REVERT: B 162 TYR cc_start: 0.7328 (m-80) cc_final: 0.6700 (m-80) REVERT: C 60 GLN cc_start: 0.8554 (mt0) cc_final: 0.8319 (mt0) REVERT: G 274 MET cc_start: 0.7003 (tpt) cc_final: 0.6397 (tpt) outliers start: 0 outliers final: 3 residues processed: 400 average time/residue: 1.5270 time to fit residues: 671.4671 Evaluate side-chains 198 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 195 time to evaluate : 1.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain G residue 323 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.9990 chunk 159 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 164 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 190 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN L 28 ASN B 26 HIS B 46 ASN B 154 ASN C 33 ASN D 3 GLN F 26 HIS F 42 GLN F 46 ASN G 33 ASN G 73 ASN G 295 GLN I 60 ASN ** J 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 26 HIS K 46 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17697 Z= 0.253 Angle : 0.702 11.956 24027 Z= 0.366 Chirality : 0.049 0.360 2625 Planarity : 0.005 0.042 3099 Dihedral : 6.435 78.665 2745 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.89 % Allowed : 8.37 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.18), residues: 2130 helix: 2.49 (0.25), residues: 360 sheet: 0.68 (0.20), residues: 579 loop : 0.33 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 47 HIS 0.007 0.001 HIS A 47 PHE 0.035 0.002 PHE A 118 TYR 0.033 0.002 TYR H 50 ARG 0.007 0.001 ARG I 81 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 263 time to evaluate : 1.998 Fit side-chains REVERT: A 173 GLU cc_start: 0.6512 (tp30) cc_final: 0.6191 (tp30) REVERT: C 285 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7879 (tt0) REVERT: D 16 GLN cc_start: 0.8765 (mt0) cc_final: 0.8561 (mt0) REVERT: D 63 LEU cc_start: 0.7946 (mt) cc_final: 0.7588 (mt) REVERT: F 69 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7750 (mm-30) REVERT: G 145 SER cc_start: 0.8424 (m) cc_final: 0.8075 (p) REVERT: G 274 MET cc_start: 0.7092 (tpt) cc_final: 0.6460 (tpt) REVERT: K 72 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8316 (mttt) outliers start: 73 outliers final: 22 residues processed: 305 average time/residue: 1.3553 time to fit residues: 459.7080 Evaluate side-chains 213 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 189 time to evaluate : 2.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain C residue 97 CYS Chi-restraints excluded: chain C residue 285 GLN Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 77 GLU Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain K residue 72 LYS Chi-restraints excluded: chain K residue 145 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 158 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 191 optimal weight: 3.9990 chunk 206 optimal weight: 10.0000 chunk 170 optimal weight: 0.0980 chunk 189 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 153 optimal weight: 0.7980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN B 26 HIS ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 ASN D 3 GLN D 76 ASN F 26 HIS G 33 ASN G 199 ASN G 295 GLN I 76 ASN J 28 ASN K 26 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 17697 Z= 0.264 Angle : 0.638 9.517 24027 Z= 0.330 Chirality : 0.048 0.284 2625 Planarity : 0.004 0.035 3099 Dihedral : 5.972 75.058 2739 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 4.69 % Allowed : 10.56 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.69 (0.18), residues: 2130 helix: 2.14 (0.26), residues: 363 sheet: 0.44 (0.21), residues: 579 loop : 0.01 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 47 HIS 0.008 0.001 HIS C 47 PHE 0.027 0.002 PHE C 118 TYR 0.032 0.002 TYR H 50 ARG 0.008 0.001 ARG H 81 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 220 time to evaluate : 1.882 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7492 (tp30) REVERT: A 274 MET cc_start: 0.7796 (tpt) cc_final: 0.7592 (tpt) REVERT: C 127 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.6624 (pt0) REVERT: D 16 GLN cc_start: 0.8683 (mt0) cc_final: 0.8467 (mt0) REVERT: D 53 TYR cc_start: 0.5587 (m-80) cc_final: 0.5337 (m-10) REVERT: E 68 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7370 (mtp85) REVERT: F 69 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7841 (mm-30) REVERT: G 145 SER cc_start: 0.8410 (m) cc_final: 0.8150 (p) REVERT: G 274 MET cc_start: 0.7203 (tpt) cc_final: 0.6521 (tpt) REVERT: J 68 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.8266 (mtp85) REVERT: K 72 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8330 (mttt) outliers start: 88 outliers final: 36 residues processed: 283 average time/residue: 1.3605 time to fit residues: 429.5587 Evaluate side-chains 231 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 190 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 97 CYS Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 261 SER Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 50 TYR Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 68 ARG Chi-restraints excluded: chain K residue 72 LYS Chi-restraints excluded: chain K residue 144 CYS Chi-restraints excluded: chain K residue 145 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 0.9980 chunk 143 optimal weight: 0.0870 chunk 99 optimal weight: 0.5980 chunk 21 optimal weight: 0.0770 chunk 91 optimal weight: 0.9990 chunk 128 optimal weight: 0.9990 chunk 191 optimal weight: 0.6980 chunk 202 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 181 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN H 76 ASN B 26 HIS C 33 ASN C 199 ASN D 3 GLN D 60 ASN D 76 ASN F 26 HIS G 199 ASN I 76 ASN J 31 ASN K 26 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 17697 Z= 0.172 Angle : 0.570 9.546 24027 Z= 0.293 Chirality : 0.045 0.309 2625 Planarity : 0.004 0.033 3099 Dihedral : 5.623 67.386 2739 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 3.20 % Allowed : 13.76 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.63 (0.18), residues: 2130 helix: 2.26 (0.25), residues: 363 sheet: 0.30 (0.22), residues: 504 loop : -0.01 (0.17), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 47 HIS 0.005 0.001 HIS K 26 PHE 0.017 0.001 PHE A 118 TYR 0.025 0.001 TYR D 50 ARG 0.007 0.000 ARG H 81 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 215 time to evaluate : 1.877 Fit side-chains REVERT: C 127 GLU cc_start: 0.6906 (OUTLIER) cc_final: 0.6629 (pt0) REVERT: D 16 GLN cc_start: 0.8710 (mt0) cc_final: 0.8434 (mt0) REVERT: D 53 TYR cc_start: 0.5575 (m-80) cc_final: 0.5366 (m-10) REVERT: E 68 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7230 (mtp85) REVERT: G 32 LYS cc_start: 0.8223 (ttmm) cc_final: 0.7939 (ttpp) REVERT: G 145 SER cc_start: 0.8390 (m) cc_final: 0.8153 (p) REVERT: G 219 LYS cc_start: 0.8132 (tptt) cc_final: 0.7881 (tptt) REVERT: G 274 MET cc_start: 0.7085 (tpt) cc_final: 0.6398 (tpt) outliers start: 60 outliers final: 33 residues processed: 261 average time/residue: 1.3449 time to fit residues: 391.1136 Evaluate side-chains 223 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 188 time to evaluate : 2.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 97 CYS Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 105 GLN Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 76 ASN Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain K residue 121 LYS Chi-restraints excluded: chain K residue 144 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 0.9990 chunk 115 optimal weight: 0.0980 chunk 2 optimal weight: 2.9990 chunk 151 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 173 optimal weight: 9.9990 chunk 140 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 182 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 60 ASN H 76 ASN B 26 HIS ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 ASN D 3 GLN D 60 ASN D 76 ASN F 26 HIS ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 199 ASN I 76 ASN J 28 ASN K 26 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 17697 Z= 0.309 Angle : 0.622 9.615 24027 Z= 0.318 Chirality : 0.047 0.341 2625 Planarity : 0.004 0.029 3099 Dihedral : 5.717 65.872 2739 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.95 % Allowed : 14.03 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.49 (0.17), residues: 2130 helix: 2.10 (0.26), residues: 363 sheet: 0.32 (0.21), residues: 561 loop : -0.17 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 35A HIS 0.006 0.001 HIS C 47 PHE 0.025 0.002 PHE C 118 TYR 0.031 0.002 TYR I 50 ARG 0.007 0.001 ARG H 81 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 206 time to evaluate : 1.907 Fit side-chains REVERT: B 154 ASN cc_start: 0.6746 (OUTLIER) cc_final: 0.6417 (p0) REVERT: C 127 GLU cc_start: 0.6945 (OUTLIER) cc_final: 0.6650 (pt0) REVERT: D 12 VAL cc_start: 0.8280 (t) cc_final: 0.8070 (t) REVERT: D 16 GLN cc_start: 0.8676 (mt0) cc_final: 0.8383 (mt0) REVERT: D 53 TYR cc_start: 0.5626 (m-80) cc_final: 0.5352 (m-80) REVERT: E 68 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.7352 (mtp85) REVERT: G 32 LYS cc_start: 0.8240 (ttmm) cc_final: 0.7973 (ttpp) REVERT: G 219 LYS cc_start: 0.8179 (tptt) cc_final: 0.7925 (tptt) REVERT: G 274 MET cc_start: 0.7284 (tpt) cc_final: 0.6414 (tpt) REVERT: I 75 LYS cc_start: 0.7580 (mtmm) cc_final: 0.7314 (mtmm) outliers start: 74 outliers final: 40 residues processed: 260 average time/residue: 1.4167 time to fit residues: 409.5414 Evaluate side-chains 233 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 190 time to evaluate : 2.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 97 CYS Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 105 GLN Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain G residue 77 GLU Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 261 SER Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 13 LYS Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 50 TYR Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain K residue 144 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 0.8980 chunk 182 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 50 optimal weight: 8.9990 chunk 203 optimal weight: 5.9990 chunk 168 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN H 60 ASN H 76 ASN B 26 HIS ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 ASN C 199 ASN D 3 GLN D 76 ASN F 26 HIS F 142 HIS G 199 ASN I 76 ASN J 28 ASN K 26 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17697 Z= 0.216 Angle : 0.581 9.583 24027 Z= 0.296 Chirality : 0.045 0.292 2625 Planarity : 0.004 0.029 3099 Dihedral : 5.598 66.365 2739 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.68 % Allowed : 15.31 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.42 (0.18), residues: 2130 helix: 2.18 (0.26), residues: 363 sheet: 0.16 (0.23), residues: 492 loop : -0.19 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 103 HIS 0.005 0.001 HIS K 26 PHE 0.018 0.002 PHE C 118 TYR 0.027 0.002 TYR I 50 ARG 0.007 0.000 ARG I 81 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 204 time to evaluate : 1.757 Fit side-chains REVERT: B 154 ASN cc_start: 0.6717 (OUTLIER) cc_final: 0.6365 (p0) REVERT: C 127 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6720 (pt0) REVERT: D 16 GLN cc_start: 0.8676 (mt0) cc_final: 0.8380 (mt0) REVERT: E 68 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.7396 (mtp85) REVERT: F 149 MET cc_start: 0.7155 (mmt) cc_final: 0.6937 (mmt) REVERT: G 32 LYS cc_start: 0.8141 (ttmm) cc_final: 0.7837 (ttpp) REVERT: G 219 LYS cc_start: 0.8111 (tptt) cc_final: 0.7851 (tppp) REVERT: G 274 MET cc_start: 0.7230 (tpt) cc_final: 0.6476 (tpt) outliers start: 69 outliers final: 31 residues processed: 251 average time/residue: 1.3471 time to fit residues: 376.8981 Evaluate side-chains 223 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 189 time to evaluate : 2.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 97 CYS Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 219 LYS Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 261 SER Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain K residue 121 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 chunk 148 optimal weight: 0.8980 chunk 114 optimal weight: 0.8980 chunk 171 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 202 optimal weight: 3.9990 chunk 126 optimal weight: 9.9990 chunk 123 optimal weight: 1.9990 chunk 93 optimal weight: 0.3980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN H 60 ASN H 76 ASN ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 HIS ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 ASN D 76 ASN F 26 HIS F 142 HIS I 76 ASN I 77 GLN J 28 ASN K 26 HIS K 142 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 17697 Z= 0.202 Angle : 0.578 10.097 24027 Z= 0.295 Chirality : 0.045 0.325 2625 Planarity : 0.004 0.031 3099 Dihedral : 5.543 67.085 2739 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.95 % Allowed : 15.25 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.42 (0.18), residues: 2130 helix: 2.26 (0.26), residues: 363 sheet: 0.15 (0.22), residues: 492 loop : -0.21 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 103 HIS 0.005 0.001 HIS K 26 PHE 0.017 0.001 PHE C 118 TYR 0.028 0.002 TYR I 50 ARG 0.008 0.000 ARG H 81 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 206 time to evaluate : 1.983 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 18 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8321 (tp) REVERT: B 39 LYS cc_start: 0.6932 (OUTLIER) cc_final: 0.6708 (pttt) REVERT: B 154 ASN cc_start: 0.6695 (OUTLIER) cc_final: 0.6339 (p0) REVERT: C 127 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6686 (pt0) REVERT: D 16 GLN cc_start: 0.8674 (mt0) cc_final: 0.8373 (mt0) REVERT: D 53 TYR cc_start: 0.6345 (p90) cc_final: 0.5951 (p90) REVERT: E 68 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.7397 (mtp85) REVERT: F 149 MET cc_start: 0.7073 (mmt) cc_final: 0.6864 (mmt) REVERT: G 32 LYS cc_start: 0.8170 (ttmm) cc_final: 0.7929 (ttpp) REVERT: G 219 LYS cc_start: 0.8011 (tptt) cc_final: 0.7737 (tppp) REVERT: G 274 MET cc_start: 0.7235 (tpt) cc_final: 0.6375 (tpt) REVERT: J 68 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8185 (mtp85) outliers start: 74 outliers final: 43 residues processed: 258 average time/residue: 1.2905 time to fit residues: 372.5842 Evaluate side-chains 237 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 188 time to evaluate : 2.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 97 CYS Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 219 LYS Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 77 GLU Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 261 SER Chi-restraints excluded: chain G residue 304 GLU Chi-restraints excluded: chain I residue 6 GLU Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 13 LYS Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 76 ASN Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 68 ARG Chi-restraints excluded: chain K residue 121 LYS Chi-restraints excluded: chain K residue 142 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 120 optimal weight: 9.9990 chunk 60 optimal weight: 0.2980 chunk 39 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 184 optimal weight: 4.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 60 ASN H 76 ASN ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 HIS ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 ASN D 76 ASN E 79 GLN F 26 HIS I 76 ASN J 28 ASN K 26 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 17697 Z= 0.440 Angle : 0.714 17.457 24027 Z= 0.360 Chirality : 0.050 0.423 2625 Planarity : 0.005 0.037 3099 Dihedral : 6.027 66.732 2739 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.32 % Allowed : 15.31 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.20 (0.17), residues: 2130 helix: 2.03 (0.26), residues: 363 sheet: 0.19 (0.21), residues: 561 loop : -0.46 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 103 HIS 0.025 0.002 HIS K 142 PHE 0.028 0.002 PHE C 118 TYR 0.043 0.003 TYR L 49 ARG 0.006 0.001 ARG H 81 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 205 time to evaluate : 2.135 Fit side-chains REVERT: L 22 THR cc_start: 0.8490 (m) cc_final: 0.8248 (m) REVERT: B 39 LYS cc_start: 0.7043 (OUTLIER) cc_final: 0.6813 (pttt) REVERT: B 154 ASN cc_start: 0.6753 (OUTLIER) cc_final: 0.6396 (p0) REVERT: C 127 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6807 (pt0) REVERT: D 16 GLN cc_start: 0.8698 (mt0) cc_final: 0.8393 (mt0) REVERT: D 105 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.7314 (pm20) REVERT: E 24 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7278 (ttt90) REVERT: E 68 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.7513 (mtp85) REVERT: G 32 LYS cc_start: 0.8166 (ttmm) cc_final: 0.7920 (ttpp) REVERT: G 219 LYS cc_start: 0.8192 (tptt) cc_final: 0.7916 (tppp) REVERT: G 274 MET cc_start: 0.7494 (tpt) cc_final: 0.6589 (tpt) REVERT: J 68 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.8134 (mtp85) REVERT: K 72 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8336 (mttt) outliers start: 81 outliers final: 42 residues processed: 265 average time/residue: 1.3550 time to fit residues: 400.6987 Evaluate side-chains 244 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 194 time to evaluate : 1.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 97 CYS Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 105 GLN Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 24 ARG Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 77 GLU Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 145 SER Chi-restraints excluded: chain G residue 261 SER Chi-restraints excluded: chain G residue 304 GLU Chi-restraints excluded: chain I residue 6 GLU Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 68 ARG Chi-restraints excluded: chain K residue 72 LYS Chi-restraints excluded: chain K residue 121 LYS Chi-restraints excluded: chain K residue 142 HIS Chi-restraints excluded: chain K residue 144 CYS Chi-restraints excluded: chain K residue 148 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 0.9980 chunk 176 optimal weight: 0.7980 chunk 188 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 82 optimal weight: 0.3980 chunk 148 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 170 optimal weight: 0.9990 chunk 178 optimal weight: 0.6980 chunk 187 optimal weight: 0.9980 chunk 123 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 54 ASN H 76 ASN ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 HIS ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 ASN C 199 ASN D 3 GLN D 76 ASN F 26 HIS ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 ASN J 28 ASN K 26 HIS ** K 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17697 Z= 0.201 Angle : 0.593 14.807 24027 Z= 0.301 Chirality : 0.045 0.269 2625 Planarity : 0.004 0.031 3099 Dihedral : 5.713 68.442 2739 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.99 % Allowed : 16.75 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.21 (0.17), residues: 2130 helix: 2.15 (0.26), residues: 363 sheet: 0.06 (0.23), residues: 492 loop : -0.40 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 103 HIS 0.005 0.001 HIS K 142 PHE 0.016 0.001 PHE C 118 TYR 0.036 0.002 TYR L 49 ARG 0.009 0.000 ARG D 81 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 209 time to evaluate : 1.971 Fit side-chains REVERT: L 4 MET cc_start: 0.7909 (mmm) cc_final: 0.7696 (mmm) REVERT: L 22 THR cc_start: 0.8349 (m) cc_final: 0.8120 (m) REVERT: B 154 ASN cc_start: 0.6683 (OUTLIER) cc_final: 0.6303 (p0) REVERT: C 127 GLU cc_start: 0.6961 (OUTLIER) cc_final: 0.6640 (pt0) REVERT: D 16 GLN cc_start: 0.8653 (mt0) cc_final: 0.8349 (mt0) REVERT: E 68 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.7434 (mtp85) REVERT: G 32 LYS cc_start: 0.8136 (ttmm) cc_final: 0.7912 (ttpp) REVERT: G 219 LYS cc_start: 0.8041 (tptt) cc_final: 0.7769 (tppp) REVERT: G 274 MET cc_start: 0.7336 (tpt) cc_final: 0.6427 (tpt) outliers start: 56 outliers final: 32 residues processed: 252 average time/residue: 1.2791 time to fit residues: 362.0433 Evaluate side-chains 230 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 195 time to evaluate : 2.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 97 CYS Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 261 SER Chi-restraints excluded: chain I residue 6 GLU Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain K residue 144 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 6.9990 chunk 121 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 209 optimal weight: 10.0000 chunk 192 optimal weight: 4.9990 chunk 166 optimal weight: 0.0980 chunk 17 optimal weight: 0.8980 chunk 128 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 60 ASN H 76 ASN H 77 GLN B 26 HIS ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 ASN D 3 GLN D 60 ASN D 76 ASN ** D 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 HIS ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 199 ASN I 60 ASN I 76 ASN J 28 ASN K 26 HIS ** K 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 129 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 17697 Z= 0.376 Angle : 0.677 14.037 24027 Z= 0.344 Chirality : 0.049 0.351 2625 Planarity : 0.005 0.038 3099 Dihedral : 5.935 68.683 2739 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.51 % Allowed : 17.33 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.13 (0.17), residues: 2130 helix: 2.12 (0.26), residues: 360 sheet: 0.25 (0.23), residues: 462 loop : -0.56 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 103 HIS 0.006 0.001 HIS K 26 PHE 0.024 0.002 PHE C 118 TYR 0.044 0.002 TYR D 100G ARG 0.010 0.001 ARG I 81 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 200 time to evaluate : 1.941 Fit side-chains revert: symmetry clash REVERT: A 122 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7611 (tp30) REVERT: L 22 THR cc_start: 0.8455 (m) cc_final: 0.8226 (m) REVERT: B 154 ASN cc_start: 0.6716 (OUTLIER) cc_final: 0.6381 (p0) REVERT: C 127 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6744 (pt0) REVERT: D 16 GLN cc_start: 0.8660 (mt0) cc_final: 0.8342 (mt0) REVERT: E 24 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7273 (ttt90) REVERT: E 68 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.7463 (mtp85) REVERT: G 219 LYS cc_start: 0.8212 (tptt) cc_final: 0.7951 (tppp) REVERT: G 274 MET cc_start: 0.7486 (tpt) cc_final: 0.6549 (tpt) REVERT: J 18 ARG cc_start: 0.7841 (mtp180) cc_final: 0.7618 (mtp180) outliers start: 47 outliers final: 34 residues processed: 234 average time/residue: 1.2956 time to fit residues: 339.7087 Evaluate side-chains 232 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 193 time to evaluate : 2.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 97 CYS Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 24 ARG Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 261 SER Chi-restraints excluded: chain G residue 304 GLU Chi-restraints excluded: chain I residue 6 GLU Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 76 ASN Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain K residue 144 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 153 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 171 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 146 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 54 ASN H 60 ASN B 26 HIS ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 ASN C 199 ASN D 3 GLN D 76 ASN F 26 HIS ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 ASN J 28 ASN K 26 HIS ** K 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.152279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.126649 restraints weight = 23887.242| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.00 r_work: 0.3341 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17697 Z= 0.203 Angle : 0.598 13.387 24027 Z= 0.304 Chirality : 0.046 0.371 2625 Planarity : 0.004 0.040 3099 Dihedral : 5.771 69.777 2739 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.56 % Allowed : 17.44 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.19 (0.17), residues: 2130 helix: 2.16 (0.26), residues: 363 sheet: 0.29 (0.24), residues: 462 loop : -0.51 (0.16), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 103 HIS 0.009 0.001 HIS F 142 PHE 0.016 0.001 PHE C 118 TYR 0.031 0.002 TYR D 100G ARG 0.010 0.000 ARG I 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6667.25 seconds wall clock time: 120 minutes 30.91 seconds (7230.91 seconds total)