Starting phenix.real_space_refine on Thu Mar 5 11:39:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t3d_25655/03_2026/7t3d_25655.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t3d_25655/03_2026/7t3d_25655.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7t3d_25655/03_2026/7t3d_25655.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t3d_25655/03_2026/7t3d_25655.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7t3d_25655/03_2026/7t3d_25655.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t3d_25655/03_2026/7t3d_25655.map" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.042 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 93 5.16 5 C 13923 2.51 5 N 3744 2.21 5 O 4362 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 111 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22122 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2529 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 19, 'TRANS': 304} Chain: "B" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1326 Classifications: {'peptide': 163} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 1, 'TRANS': 161} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "D" 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': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "C" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 900 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "H" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 872 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 3, 'TRANS': 106} Chain: "L" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 820 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain: "S" 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 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: E, F, G, I, M, N, J, K, O, P, Q, R, T, U Time building chain proxies: 3.90, per 1000 atoms: 0.18 Number of scatterers: 22122 At special positions: 0 Unit cell: (142.6, 152.95, 161, 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 93 16.00 O 4362 8.00 N 3744 7.00 C 13923 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 137 " distance=2.03 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.02 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 Simple disulfide: pdb=" SG CYS E 14 " - pdb=" SG CYS G 137 " distance=2.03 Simple disulfide: pdb=" SG CYS F 14 " - pdb=" SG CYS I 137 " distance=2.03 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 277 " distance=2.04 Simple disulfide: pdb=" SG CYS F 52 " - pdb=" SG CYS F 277 " distance=2.04 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 76 " distance=2.02 Simple disulfide: pdb=" SG CYS F 64 " - pdb=" SG CYS F 76 " distance=2.02 Simple disulfide: pdb=" SG CYS E 97 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS F 97 " - pdb=" SG CYS F 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 305 " distance=2.02 Simple disulfide: pdb=" SG CYS F 281 " - pdb=" SG CYS F 305 " distance=2.02 Simple disulfide: pdb=" SG CYS G 144 " - pdb=" SG CYS G 148 " distance=2.03 Simple disulfide: pdb=" SG CYS I 144 " - pdb=" SG CYS I 148 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.02 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.02 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.02 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.02 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " 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 S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A 401 " - " ASN A 21 " " NAG A 402 " - " ASN A 33 " " NAG A 403 " - " ASN A 278 " " NAG A 404 " - " ASN A 289 " " NAG B 201 " - " ASN B 154 " " NAG E 401 " - " ASN E 21 " " NAG E 402 " - " ASN E 33 " " NAG E 403 " - " ASN E 278 " " NAG E 404 " - " ASN E 289 " " NAG F 401 " - " ASN F 21 " " NAG F 402 " - " ASN F 33 " " NAG F 403 " - " ASN F 278 " " NAG F 404 " - " ASN F 289 " " NAG G 201 " - " ASN G 154 " " NAG I 201 " - " ASN I 154 " " NAG S 1 " - " ASN A 94 " " NAG T 1 " - " ASN E 94 " " NAG U 1 " - " ASN F 94 " Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 1.2 seconds 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5118 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 66 sheets defined 16.2% alpha, 36.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 187 through 195 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 154 Processing helix chain 'B' and resid 158 through 169 removed outlier: 4.071A pdb=" N TYR B 162 " --> pdb=" O ASP B 158 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLU B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N GLU B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.564A pdb=" N ILE D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'H' and resid 61 through 64 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 'E' and resid 65 through 72 Processing helix chain 'E' and resid 104 through 112 Processing helix chain 'E' and resid 187 through 195 Processing helix chain 'G' and resid 37 through 58 Processing helix chain 'G' and resid 74 through 127 Processing helix chain 'G' and resid 145 through 154 Processing helix chain 'G' and resid 158 through 169 removed outlier: 4.071A pdb=" N TYR G 162 " --> pdb=" O ASP G 158 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLU G 164 " --> pdb=" O PRO G 160 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N GLU G 165 " --> pdb=" O LYS G 161 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.565A pdb=" N ILE M 83 " --> pdb=" O PRO M 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'O' and resid 61 through 64 Processing helix chain 'O' and resid 73 through 75 No H-bonds generated for 'chain 'O' and resid 73 through 75' Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'F' and resid 65 through 72 Processing helix chain 'F' and resid 104 through 112 Processing helix chain 'F' and resid 187 through 195 Processing helix chain 'I' and resid 37 through 58 Processing helix chain 'I' and resid 74 through 127 Processing helix chain 'I' and resid 145 through 154 Processing helix chain 'I' and resid 158 through 169 removed outlier: 4.071A pdb=" N TYR I 162 " --> pdb=" O ASP I 158 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLU I 164 " --> pdb=" O PRO I 160 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N GLU I 165 " --> pdb=" O LYS I 161 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.565A pdb=" N ILE N 83 " --> pdb=" O PRO N 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'P' and resid 61 through 64 Processing helix chain 'P' and resid 73 through 75 No H-bonds generated for 'chain 'P' and resid 73 through 75' Processing helix chain 'P' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 36 removed outlier: 6.645A pdb=" N CYS B 137 " --> pdb=" O ILE B 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 26 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: 5.984A pdb=" N LEU A 51 " --> pdb=" O HIS A 275 " (cutoff:3.500A) removed outlier: 5.645A 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: 6.268A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE A 87 " --> pdb=" O ILE A 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 115 through 122 removed outlier: 6.947A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 7.761A 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: 6.947A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 136 through 141 removed outlier: 4.936A pdb=" N CYS A 139 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER A 146 " --> pdb=" O CYS A 139 " (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 288 removed outlier: 4.141A pdb=" N CYS A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 5 through 7 removed outlier: 5.593A pdb=" N VAL D 19 " --> pdb=" O ILE D 75 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 10 through 14 removed outlier: 6.422A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 10 through 14 removed outlier: 3.530A pdb=" N THR D 97 " --> pdb=" O HIS D 90 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 3 through 7 removed outlier: 6.319A pdb=" N SER C 17 " --> pdb=" O SER C 82A" (cutoff:3.500A) removed outlier: 6.763A pdb=" N SER C 82A" --> pdb=" O SER C 17 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N SER C 19 " --> pdb=" O GLN C 81 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLN C 81 " --> pdb=" O SER C 19 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N SER C 21 " --> pdb=" O TYR C 79 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N TYR C 79 " --> pdb=" O SER C 21 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ALA C 23 " --> pdb=" O THR C 77 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N THR C 77 " --> pdb=" O ALA C 23 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 10 through 12 removed outlier: 7.017A pdb=" N MET C 34 " --> pdb=" O MET C 50 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N MET C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 10 through 12 Processing sheet with id=AB9, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AC1, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.597A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AC3, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.687A pdb=" N TRP L 35 " --> pdb=" O ILE L 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 10 through 13 removed outlier: 4.166A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 31 through 36 removed outlier: 6.645A pdb=" N CYS G 137 " --> pdb=" O ILE G 133 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 25 through 26 Processing sheet with id=AC7, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AC8, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AC9, first strand: chain 'E' and resid 51 through 54 removed outlier: 5.984A pdb=" N LEU E 51 " --> pdb=" O HIS E 275 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N CYS E 277 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 59 through 60 removed outlier: 6.268A pdb=" N LEU E 59 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE E 87 " --> pdb=" O ILE E 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'E' and resid 115 through 122 removed outlier: 6.948A pdb=" N TYR E 256 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N LEU E 179 " --> pdb=" O TYR E 256 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N LEU E 179 " --> pdb=" O PRO E 254 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 115 through 122 removed outlier: 6.948A pdb=" N TYR E 256 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N LEU E 179 " --> pdb=" O TYR E 256 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 136 through 141 removed outlier: 4.937A pdb=" N CYS E 139 " --> pdb=" O SER E 146 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER E 146 " --> pdb=" O CYS E 139 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 164 through 169 Processing sheet with id=AD6, first strand: chain 'E' and resid 286 through 288 removed outlier: 4.141A pdb=" N CYS E 281 " --> pdb=" O ILE E 288 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 5 through 7 removed outlier: 5.593A pdb=" N VAL M 19 " --> pdb=" O ILE M 75 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'M' and resid 10 through 14 removed outlier: 6.421A pdb=" N LEU M 33 " --> pdb=" O TYR M 49 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N TYR M 49 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'M' and resid 10 through 14 removed outlier: 3.530A pdb=" N THR M 97 " --> pdb=" O HIS M 90 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 3 through 7 removed outlier: 6.319A pdb=" N SER J 17 " --> pdb=" O SER J 82A" (cutoff:3.500A) removed outlier: 6.763A pdb=" N SER J 82A" --> pdb=" O SER J 17 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N SER J 19 " --> pdb=" O GLN J 81 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLN J 81 " --> pdb=" O SER J 19 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N SER J 21 " --> pdb=" O TYR J 79 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N TYR J 79 " --> pdb=" O SER J 21 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ALA J 23 " --> pdb=" O THR J 77 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N THR J 77 " --> pdb=" O ALA J 23 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 10 through 12 removed outlier: 7.016A pdb=" N MET J 34 " --> pdb=" O MET J 50 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N MET J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 10 through 12 Processing sheet with id=AE4, first strand: chain 'O' and resid 4 through 7 Processing sheet with id=AE5, first strand: chain 'O' and resid 57 through 59 removed outlier: 6.598A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N TYR O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N MET O 34 " --> pdb=" O TYR O 50 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Q' and resid 4 through 5 Processing sheet with id=AE7, first strand: chain 'Q' and resid 10 through 13 removed outlier: 6.687A pdb=" N TRP Q 35 " --> pdb=" O ILE Q 47 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Q' and resid 10 through 13 removed outlier: 4.167A pdb=" N THR Q 97 " --> pdb=" O GLN Q 90 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 31 through 36 removed outlier: 6.645A pdb=" N CYS I 137 " --> pdb=" O ILE I 133 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 25 through 26 Processing sheet with id=AF2, first strand: chain 'F' and resid 39 through 41 Processing sheet with id=AF3, first strand: chain 'F' and resid 43 through 44 Processing sheet with id=AF4, first strand: chain 'F' and resid 51 through 54 removed outlier: 5.984A pdb=" N LEU F 51 " --> pdb=" O HIS F 275 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N CYS F 277 " --> pdb=" O LEU F 51 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 59 through 60 removed outlier: 6.268A pdb=" N LEU F 59 " --> pdb=" O VAL F 88 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE F 87 " --> pdb=" O ILE F 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'F' and resid 115 through 122 removed outlier: 6.948A pdb=" N TYR F 256 " --> pdb=" O LEU F 179 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N LEU F 179 " --> pdb=" O TYR F 256 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N LEU F 179 " --> pdb=" O PRO F 254 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 115 through 122 removed outlier: 6.948A pdb=" N TYR F 256 " --> pdb=" O LEU F 179 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N LEU F 179 " --> pdb=" O TYR F 256 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 136 through 141 removed outlier: 4.937A pdb=" N CYS F 139 " --> pdb=" O SER F 146 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER F 146 " --> pdb=" O CYS F 139 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 164 through 169 Processing sheet with id=AG1, first strand: chain 'F' and resid 286 through 288 removed outlier: 4.141A pdb=" N CYS F 281 " --> pdb=" O ILE F 288 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'N' and resid 5 through 7 removed outlier: 5.593A pdb=" N VAL N 19 " --> pdb=" O ILE N 75 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'N' and resid 10 through 14 removed outlier: 6.422A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'N' and resid 10 through 14 removed outlier: 3.530A pdb=" N THR N 97 " --> pdb=" O HIS N 90 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'K' and resid 3 through 7 removed outlier: 6.318A pdb=" N SER K 17 " --> pdb=" O SER K 82A" (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER K 82A" --> pdb=" O SER K 17 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N SER K 19 " --> pdb=" O GLN K 81 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLN K 81 " --> pdb=" O SER K 19 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N SER K 21 " --> pdb=" O TYR K 79 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N TYR K 79 " --> pdb=" O SER K 21 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ALA K 23 " --> pdb=" O THR K 77 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N THR K 77 " --> pdb=" O ALA K 23 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 10 through 12 removed outlier: 7.017A pdb=" N MET K 34 " --> pdb=" O MET K 50 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N MET K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'K' and resid 10 through 12 Processing sheet with id=AG8, first strand: chain 'P' and resid 4 through 7 Processing sheet with id=AG9, first strand: chain 'P' and resid 57 through 59 removed outlier: 6.598A pdb=" N TRP P 36 " --> pdb=" O VAL P 48 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N TYR P 50 " --> pdb=" O MET P 34 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N MET P 34 " --> pdb=" O TYR P 50 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'R' and resid 4 through 5 Processing sheet with id=AH2, first strand: chain 'R' and resid 10 through 13 removed outlier: 6.687A pdb=" N TRP R 35 " --> pdb=" O ILE R 47 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'R' and resid 10 through 13 removed outlier: 4.166A pdb=" N THR R 97 " --> pdb=" O GLN R 90 " (cutoff:3.500A) 990 hydrogen bonds defined for protein. 2529 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: 4.25 Time building geometry restraints manager: 2.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 5426 1.32 - 1.47: 7825 1.47 - 1.61: 9252 1.61 - 1.75: 21 1.75 - 1.89: 111 Bond restraints: 22635 Sorted by residual: bond pdb=" NE1 TRP J 103 " pdb=" CE2 TRP J 103 " ideal model delta sigma weight residual 1.370 1.299 0.071 1.10e-02 8.26e+03 4.16e+01 bond pdb=" NE1 TRP K 103 " pdb=" CE2 TRP K 103 " ideal model delta sigma weight residual 1.370 1.299 0.071 1.10e-02 8.26e+03 4.14e+01 bond pdb=" NE1 TRP C 103 " pdb=" CE2 TRP C 103 " ideal model delta sigma weight residual 1.370 1.299 0.071 1.10e-02 8.26e+03 4.14e+01 bond pdb=" CD2 TRP O 103 " pdb=" CE3 TRP O 103 " ideal model delta sigma weight residual 1.398 1.501 -0.103 1.60e-02 3.91e+03 4.13e+01 bond pdb=" CD2 TRP H 103 " pdb=" CE3 TRP H 103 " ideal model delta sigma weight residual 1.398 1.501 -0.103 1.60e-02 3.91e+03 4.12e+01 ... (remaining 22630 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 26892 2.56 - 5.13: 3266 5.13 - 7.69: 469 7.69 - 10.25: 54 10.25 - 12.81: 12 Bond angle restraints: 30693 Sorted by residual: angle pdb=" N ARG F 255 " pdb=" CA ARG F 255 " pdb=" C ARG F 255 " ideal model delta sigma weight residual 113.43 101.93 11.50 1.26e+00 6.30e-01 8.33e+01 angle pdb=" N ARG A 255 " pdb=" CA ARG A 255 " pdb=" C ARG A 255 " ideal model delta sigma weight residual 113.43 101.93 11.50 1.26e+00 6.30e-01 8.32e+01 angle pdb=" N ARG E 255 " pdb=" CA ARG E 255 " pdb=" C ARG E 255 " ideal model delta sigma weight residual 113.43 101.94 11.49 1.26e+00 6.30e-01 8.31e+01 angle pdb=" N SER J 95 " pdb=" CA SER J 95 " pdb=" C SER J 95 " ideal model delta sigma weight residual 113.16 124.41 -11.25 1.24e+00 6.50e-01 8.23e+01 angle pdb=" N SER K 95 " pdb=" CA SER K 95 " pdb=" C SER K 95 " ideal model delta sigma weight residual 113.16 124.39 -11.23 1.24e+00 6.50e-01 8.20e+01 ... (remaining 30688 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.99: 13184 15.99 - 31.99: 346 31.99 - 47.98: 93 47.98 - 63.97: 81 63.97 - 79.97: 18 Dihedral angle restraints: 13722 sinusoidal: 5682 harmonic: 8040 Sorted by residual: dihedral pdb=" CB CYS K 22 " pdb=" SG CYS K 22 " pdb=" SG CYS K 92 " pdb=" CB CYS K 92 " ideal model delta sinusoidal sigma weight residual 93.00 49.18 43.82 1 1.00e+01 1.00e-02 2.67e+01 dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 92 " pdb=" CB CYS C 92 " ideal model delta sinusoidal sigma weight residual 93.00 49.19 43.81 1 1.00e+01 1.00e-02 2.67e+01 dihedral pdb=" CB CYS J 22 " pdb=" SG CYS J 22 " pdb=" SG CYS J 92 " pdb=" CB CYS J 92 " ideal model delta sinusoidal sigma weight residual 93.00 49.22 43.78 1 1.00e+01 1.00e-02 2.67e+01 ... (remaining 13719 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 2342 0.097 - 0.194: 816 0.194 - 0.291: 136 0.291 - 0.387: 59 0.387 - 0.484: 28 Chirality restraints: 3381 Sorted by residual: chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.33e+02 chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.31e+02 chirality pdb=" C1 NAG T 2 " pdb=" O4 NAG T 1 " pdb=" C2 NAG T 2 " pdb=" O5 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.31e+02 ... (remaining 3378 not shown) Planarity restraints: 3945 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 154 " -0.124 2.00e-02 2.50e+03 1.31e-01 2.15e+02 pdb=" CG ASN B 154 " 0.058 2.00e-02 2.50e+03 pdb=" OD1 ASN B 154 " 0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN B 154 " 0.204 2.00e-02 2.50e+03 pdb=" C1 NAG B 201 " -0.158 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN G 154 " -0.124 2.00e-02 2.50e+03 1.31e-01 2.15e+02 pdb=" CG ASN G 154 " 0.057 2.00e-02 2.50e+03 pdb=" OD1 ASN G 154 " 0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN G 154 " 0.204 2.00e-02 2.50e+03 pdb=" C1 NAG G 201 " -0.158 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN I 154 " 0.124 2.00e-02 2.50e+03 1.31e-01 2.14e+02 pdb=" CG ASN I 154 " -0.057 2.00e-02 2.50e+03 pdb=" OD1 ASN I 154 " -0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN I 154 " -0.204 2.00e-02 2.50e+03 pdb=" C1 NAG I 201 " 0.158 2.00e-02 2.50e+03 ... (remaining 3942 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 591 2.65 - 3.22: 20295 3.22 - 3.78: 35696 3.78 - 4.34: 49314 4.34 - 4.90: 80236 Nonbonded interactions: 186132 Sorted by model distance: nonbonded pdb=" OE1 GLN G 27 " pdb=" CZ2 TRP O 99 " model vdw 2.093 3.340 nonbonded pdb=" OE1 GLN I 27 " pdb=" CZ2 TRP P 99 " model vdw 2.093 3.340 nonbonded pdb=" OE1 GLN B 27 " pdb=" CZ2 TRP H 99 " model vdw 2.093 3.340 nonbonded pdb=" OD2 ASP G 112 " pdb=" NZ LYS G 116 " model vdw 2.401 3.120 nonbonded pdb=" OD2 ASP I 112 " pdb=" NZ LYS I 116 " model vdw 2.401 3.120 ... (remaining 186127 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'C' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'L' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'S' selection = chain 'T' selection = chain 'U' } 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: 2.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 19.610 Find NCS groups from input model: 0.170 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: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 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 0.133 22686 Z= 1.178 Angle : 1.771 12.814 30816 Z= 1.185 Chirality : 0.109 0.484 3381 Planarity : 0.009 0.058 3927 Dihedral : 9.955 79.967 8514 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.15), residues: 2760 helix: 0.81 (0.23), residues: 375 sheet: 0.57 (0.18), residues: 726 loop : 0.82 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG H 71 TYR 0.047 0.009 TYR O 102 PHE 0.039 0.008 PHE F 118 TRP 0.066 0.009 TRP F 84 HIS 0.011 0.003 HIS I 142 Details of bonding type rmsd covalent geometry : bond 0.02234 (22635) covalent geometry : angle 1.76460 (30693) SS BOND : bond 0.00729 ( 30) SS BOND : angle 2.60863 ( 60) hydrogen bonds : bond 0.16091 ( 894) hydrogen bonds : angle 7.50698 ( 2529) link_BETA1-4 : bond 0.08044 ( 3) link_BETA1-4 : angle 4.98924 ( 9) link_NAG-ASN : bond 0.08109 ( 18) link_NAG-ASN : angle 2.77266 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 581 time to evaluate : 0.925 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 VAL cc_start: 0.8820 (t) cc_final: 0.8538 (m) REVERT: D 4 MET cc_start: 0.8441 (mmm) cc_final: 0.8183 (mmm) REVERT: D 82 ASP cc_start: 0.8011 (m-30) cc_final: 0.7745 (m-30) REVERT: C 72 ASP cc_start: 0.8197 (t0) cc_final: 0.7979 (t0) REVERT: C 75 LYS cc_start: 0.8854 (mtmm) cc_final: 0.8465 (mttt) REVERT: C 83 THR cc_start: 0.8680 (t) cc_final: 0.7979 (p) REVERT: C 96 ASP cc_start: 0.8203 (t0) cc_final: 0.7931 (t0) REVERT: H 3 GLN cc_start: 0.7226 (mt0) cc_final: 0.6923 (mm-40) REVERT: H 100 TYR cc_start: 0.7801 (t80) cc_final: 0.7432 (t80) REVERT: L 17 GLU cc_start: 0.7099 (tt0) cc_final: 0.6803 (tt0) REVERT: L 82 ASP cc_start: 0.6864 (m-30) cc_final: 0.6309 (m-30) REVERT: E 148 TYR cc_start: 0.9109 (m-80) cc_final: 0.8837 (m-80) REVERT: J 83 THR cc_start: 0.8577 (t) cc_final: 0.8003 (p) REVERT: O 3 GLN cc_start: 0.7099 (mt0) cc_final: 0.6747 (mm-40) REVERT: O 100 TYR cc_start: 0.7969 (t80) cc_final: 0.7636 (t80) REVERT: Q 42 GLN cc_start: 0.8825 (mm-40) cc_final: 0.7941 (mp10) REVERT: Q 82 ASP cc_start: 0.6981 (m-30) cc_final: 0.6580 (m-30) REVERT: F 56 VAL cc_start: 0.8700 (t) cc_final: 0.8426 (m) REVERT: N 82 ASP cc_start: 0.8006 (m-30) cc_final: 0.7615 (m-30) REVERT: K 28 THR cc_start: 0.8642 (m) cc_final: 0.8270 (p) REVERT: K 83 THR cc_start: 0.8724 (t) cc_final: 0.8144 (p) REVERT: K 96 ASP cc_start: 0.8261 (t0) cc_final: 0.8050 (t0) REVERT: P 34 MET cc_start: 0.8680 (mmm) cc_final: 0.8458 (mmm) REVERT: R 17 GLU cc_start: 0.7038 (tt0) cc_final: 0.6759 (tt0) REVERT: R 42 GLN cc_start: 0.8568 (mm-40) cc_final: 0.7841 (mp10) outliers start: 0 outliers final: 0 residues processed: 581 average time/residue: 0.1844 time to fit residues: 158.4705 Evaluate side-chains 320 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 320 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN A 183 HIS ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 HIS D 32 HIS D 92 HIS E 159 ASN E 183 HIS G 26 HIS J 3 GLN Q 37 GLN F 183 HIS ** I 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN R 27 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.094024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.068186 restraints weight = 54913.694| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.89 r_work: 0.2999 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 22686 Z= 0.168 Angle : 0.712 9.043 30816 Z= 0.386 Chirality : 0.045 0.173 3381 Planarity : 0.005 0.071 3927 Dihedral : 6.012 62.442 3483 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.12 % Allowed : 7.54 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 1.71 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.15), residues: 2760 helix: 2.14 (0.25), residues: 378 sheet: 0.49 (0.17), residues: 753 loop : 0.28 (0.15), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P 94 TYR 0.017 0.002 TYR I 94 PHE 0.020 0.002 PHE F 213 TRP 0.020 0.002 TRP C 103 HIS 0.012 0.001 HIS B 72 Details of bonding type rmsd covalent geometry : bond 0.00381 (22635) covalent geometry : angle 0.69543 (30693) SS BOND : bond 0.00770 ( 30) SS BOND : angle 1.52457 ( 60) hydrogen bonds : bond 0.05709 ( 894) hydrogen bonds : angle 5.78681 ( 2529) link_BETA1-4 : bond 0.00315 ( 3) link_BETA1-4 : angle 2.02335 ( 9) link_NAG-ASN : bond 0.00301 ( 18) link_NAG-ASN : angle 3.30780 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 391 time to evaluate : 0.911 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: symmetry clash REVERT: A 20 ASN cc_start: 0.8380 (t0) cc_final: 0.8107 (t0) REVERT: B 158 ASP cc_start: 0.8022 (t0) cc_final: 0.6353 (p0) REVERT: D 4 MET cc_start: 0.8377 (mmm) cc_final: 0.7846 (mmm) REVERT: D 5 THR cc_start: 0.8661 (m) cc_final: 0.8300 (p) REVERT: C 72 ASP cc_start: 0.8503 (t0) cc_final: 0.7897 (t0) REVERT: C 75 LYS cc_start: 0.8818 (mtmm) cc_final: 0.8313 (mttt) REVERT: H 64 LYS cc_start: 0.7182 (mtmm) cc_final: 0.6845 (mmmt) REVERT: H 93 VAL cc_start: 0.8257 (t) cc_final: 0.7742 (t) REVERT: H 100 TYR cc_start: 0.7792 (t80) cc_final: 0.7556 (t80) REVERT: L 17 GLU cc_start: 0.6995 (tt0) cc_final: 0.6740 (tt0) REVERT: L 42 GLN cc_start: 0.8588 (mm-40) cc_final: 0.7685 (mp10) REVERT: L 58 ILE cc_start: 0.7191 (OUTLIER) cc_final: 0.6574 (mp) REVERT: L 78 LEU cc_start: 0.5823 (tp) cc_final: 0.4826 (tt) REVERT: L 85 VAL cc_start: 0.8451 (t) cc_final: 0.8115 (p) REVERT: E 52 CYS cc_start: 0.6756 (m) cc_final: 0.6265 (m) REVERT: M 5 THR cc_start: 0.8391 (m) cc_final: 0.8057 (p) REVERT: M 42 LYS cc_start: 0.9033 (mmtp) cc_final: 0.8795 (mmmm) REVERT: M 82 ASP cc_start: 0.8426 (m-30) cc_final: 0.8042 (m-30) REVERT: J 5 LEU cc_start: 0.8815 (mp) cc_final: 0.8446 (mp) REVERT: O 64 LYS cc_start: 0.7426 (mtmm) cc_final: 0.6920 (mmmt) REVERT: Q 42 GLN cc_start: 0.8615 (mm-40) cc_final: 0.8040 (mp10) REVERT: Q 53 THR cc_start: 0.7493 (m) cc_final: 0.7119 (p) REVERT: Q 54 ARG cc_start: 0.7740 (ptm-80) cc_final: 0.7406 (ptm160) REVERT: Q 58 ILE cc_start: 0.7256 (OUTLIER) cc_final: 0.7049 (mp) REVERT: Q 78 LEU cc_start: 0.6424 (tp) cc_final: 0.4416 (tt) REVERT: Q 79 GLN cc_start: 0.6881 (mm110) cc_final: 0.6201 (mt0) REVERT: F 105 TYR cc_start: 0.8944 (t80) cc_final: 0.8728 (t80) REVERT: I 17 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8367 (ttt) REVERT: N 5 THR cc_start: 0.8556 (m) cc_final: 0.8063 (p) REVERT: N 42 LYS cc_start: 0.9015 (mmtm) cc_final: 0.8765 (mmmm) REVERT: K 101 GLU cc_start: 0.8053 (pm20) cc_final: 0.7455 (mp0) REVERT: P 34 MET cc_start: 0.8701 (mmm) cc_final: 0.7883 (mmp) REVERT: P 58 TYR cc_start: 0.7120 (m-80) cc_final: 0.6906 (m-80) REVERT: P 100 TYR cc_start: 0.7732 (t80) cc_final: 0.7511 (t80) REVERT: R 4 MET cc_start: 0.7933 (tpp) cc_final: 0.7649 (tpt) REVERT: R 17 GLU cc_start: 0.6972 (tt0) cc_final: 0.6693 (tt0) REVERT: R 42 GLN cc_start: 0.8712 (mm-40) cc_final: 0.8153 (mp10) REVERT: R 53 THR cc_start: 0.7702 (m) cc_final: 0.7396 (t) REVERT: R 54 ARG cc_start: 0.7717 (ptm-80) cc_final: 0.7507 (ptm160) REVERT: R 78 LEU cc_start: 0.6442 (tp) cc_final: 0.5233 (tt) REVERT: R 79 GLN cc_start: 0.7127 (mm-40) cc_final: 0.6869 (mt0) outliers start: 51 outliers final: 35 residues processed: 416 average time/residue: 0.1736 time to fit residues: 109.9053 Evaluate side-chains 361 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 323 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 103 TRP Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain E residue 159 ASN Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 116 LYS Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain J residue 50 MET Chi-restraints excluded: chain J residue 103 TRP Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 105 GLU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain I residue 17 MET Chi-restraints excluded: chain I residue 72 HIS Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain K residue 50 MET Chi-restraints excluded: chain K residue 103 TRP Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 105 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 17 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 82 optimal weight: 0.9990 chunk 136 optimal weight: 0.5980 chunk 256 optimal weight: 4.9990 chunk 188 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 145 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN O 3 GLN ** I 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 72 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.090563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.064826 restraints weight = 54846.093| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.86 r_work: 0.2917 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 22686 Z= 0.194 Angle : 0.654 8.054 30816 Z= 0.352 Chirality : 0.043 0.146 3381 Planarity : 0.005 0.065 3927 Dihedral : 5.509 60.446 3483 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.33 % Allowed : 9.08 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 1.71 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.15), residues: 2760 helix: 2.39 (0.25), residues: 378 sheet: 0.36 (0.17), residues: 768 loop : 0.11 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 45 TYR 0.015 0.001 TYR H 32 PHE 0.021 0.002 PHE F 213 TRP 0.019 0.002 TRP J 103 HIS 0.007 0.001 HIS I 72 Details of bonding type rmsd covalent geometry : bond 0.00459 (22635) covalent geometry : angle 0.64382 (30693) SS BOND : bond 0.00344 ( 30) SS BOND : angle 1.10273 ( 60) hydrogen bonds : bond 0.05134 ( 894) hydrogen bonds : angle 5.35713 ( 2529) link_BETA1-4 : bond 0.00514 ( 3) link_BETA1-4 : angle 1.49991 ( 9) link_NAG-ASN : bond 0.00260 ( 18) link_NAG-ASN : angle 2.60014 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 332 time to evaluate : 0.791 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: symmetry clash REVERT: B 158 ASP cc_start: 0.8024 (t0) cc_final: 0.6475 (p0) REVERT: B 163 SER cc_start: 0.8357 (t) cc_final: 0.7956 (m) REVERT: D 4 MET cc_start: 0.8506 (mmm) cc_final: 0.8154 (mmm) REVERT: D 5 THR cc_start: 0.8585 (m) cc_final: 0.8188 (p) REVERT: C 72 ASP cc_start: 0.8408 (t0) cc_final: 0.7840 (t0) REVERT: C 75 LYS cc_start: 0.8901 (mtmm) cc_final: 0.8405 (mttt) REVERT: C 102 PHE cc_start: 0.7629 (OUTLIER) cc_final: 0.6605 (p90) REVERT: H 34 MET cc_start: 0.8346 (mmm) cc_final: 0.7935 (mmm) REVERT: H 93 VAL cc_start: 0.8344 (t) cc_final: 0.7888 (t) REVERT: H 100 TYR cc_start: 0.7858 (t80) cc_final: 0.7430 (t80) REVERT: L 4 MET cc_start: 0.7625 (tpt) cc_final: 0.7340 (tpt) REVERT: L 58 ILE cc_start: 0.7136 (OUTLIER) cc_final: 0.6541 (mp) REVERT: G 163 SER cc_start: 0.8442 (t) cc_final: 0.8073 (m) REVERT: M 4 MET cc_start: 0.8190 (mmm) cc_final: 0.7878 (mmm) REVERT: M 5 THR cc_start: 0.8470 (m) cc_final: 0.8098 (p) REVERT: M 14 PHE cc_start: 0.7341 (p90) cc_final: 0.7046 (p90) REVERT: J 5 LEU cc_start: 0.8759 (mp) cc_final: 0.8448 (mp) REVERT: J 102 PHE cc_start: 0.7380 (OUTLIER) cc_final: 0.7082 (p90) REVERT: O 64 LYS cc_start: 0.7210 (mtmm) cc_final: 0.6813 (mmmt) REVERT: Q 24 ARG cc_start: 0.8181 (mmm-85) cc_final: 0.7899 (mmm-85) REVERT: Q 42 GLN cc_start: 0.8505 (mm-40) cc_final: 0.7898 (mp10) REVERT: Q 53 THR cc_start: 0.7629 (m) cc_final: 0.7297 (t) REVERT: Q 54 ARG cc_start: 0.7893 (ptm-80) cc_final: 0.7680 (ptm160) REVERT: Q 58 ILE cc_start: 0.7326 (OUTLIER) cc_final: 0.7111 (mp) REVERT: Q 85 VAL cc_start: 0.8507 (OUTLIER) cc_final: 0.8249 (p) REVERT: F 56 VAL cc_start: 0.8855 (OUTLIER) cc_final: 0.8330 (m) REVERT: F 105 TYR cc_start: 0.8951 (t80) cc_final: 0.8743 (t80) REVERT: N 5 THR cc_start: 0.8601 (m) cc_final: 0.8121 (p) REVERT: N 42 LYS cc_start: 0.8959 (mmtm) cc_final: 0.8752 (mmmm) REVERT: K 6 GLU cc_start: 0.7549 (mp0) cc_final: 0.7130 (mp0) REVERT: K 13 GLN cc_start: 0.7615 (mm-40) cc_final: 0.7131 (pm20) REVERT: K 101 GLU cc_start: 0.8148 (pm20) cc_final: 0.7668 (mp0) REVERT: K 102 PHE cc_start: 0.7493 (OUTLIER) cc_final: 0.6897 (p90) REVERT: P 93 VAL cc_start: 0.8452 (t) cc_final: 0.8242 (t) REVERT: R 2 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8522 (mp) REVERT: R 4 MET cc_start: 0.7867 (tpp) cc_final: 0.7396 (tpt) REVERT: R 17 GLU cc_start: 0.7312 (tt0) cc_final: 0.7099 (tt0) REVERT: R 42 GLN cc_start: 0.8593 (mm-40) cc_final: 0.8036 (mp10) REVERT: R 53 THR cc_start: 0.7710 (m) cc_final: 0.7415 (t) REVERT: R 54 ARG cc_start: 0.7753 (ptm-80) cc_final: 0.7379 (mtm110) REVERT: R 79 GLN cc_start: 0.7445 (mm-40) cc_final: 0.7162 (mt0) outliers start: 56 outliers final: 35 residues processed: 359 average time/residue: 0.1577 time to fit residues: 87.1974 Evaluate side-chains 334 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 291 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 102 PHE Chi-restraints excluded: chain C residue 103 TRP Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain E residue 84 TRP Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 116 LYS Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain J residue 50 MET Chi-restraints excluded: chain J residue 102 PHE Chi-restraints excluded: chain J residue 103 TRP Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 105 GLU Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 61 THR Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain K residue 50 MET Chi-restraints excluded: chain K residue 102 PHE Chi-restraints excluded: chain K residue 103 TRP Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain R residue 2 ILE Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 105 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 156 optimal weight: 4.9990 chunk 238 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 164 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 190 optimal weight: 7.9990 chunk 5 optimal weight: 0.1980 chunk 140 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 240 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 GLN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 32 HIS M 79 GLN J 3 GLN O 3 GLN ** I 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 32 HIS N 79 GLN K 56 ASN P 3 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.088698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.062752 restraints weight = 55169.866| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.88 r_work: 0.2867 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 22686 Z= 0.227 Angle : 0.649 10.745 30816 Z= 0.346 Chirality : 0.043 0.160 3381 Planarity : 0.005 0.066 3927 Dihedral : 5.344 57.387 3483 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.67 % Allowed : 9.67 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 1.71 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.15), residues: 2760 helix: 2.38 (0.25), residues: 378 sheet: 0.30 (0.17), residues: 753 loop : -0.09 (0.15), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 45 TYR 0.021 0.002 TYR P 100C PHE 0.019 0.002 PHE A 213 TRP 0.023 0.002 TRP C 103 HIS 0.007 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00544 (22635) covalent geometry : angle 0.63522 (30693) SS BOND : bond 0.00393 ( 30) SS BOND : angle 2.12536 ( 60) hydrogen bonds : bond 0.04951 ( 894) hydrogen bonds : angle 5.19247 ( 2529) link_BETA1-4 : bond 0.00213 ( 3) link_BETA1-4 : angle 1.48663 ( 9) link_NAG-ASN : bond 0.00332 ( 18) link_NAG-ASN : angle 2.39435 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 301 time to evaluate : 0.748 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 56 VAL cc_start: 0.9140 (OUTLIER) cc_final: 0.8802 (m) REVERT: B 158 ASP cc_start: 0.8133 (t0) cc_final: 0.6629 (p0) REVERT: B 163 SER cc_start: 0.8495 (t) cc_final: 0.8082 (m) REVERT: D 4 MET cc_start: 0.8698 (mmm) cc_final: 0.8435 (mmm) REVERT: D 5 THR cc_start: 0.8682 (m) cc_final: 0.8351 (p) REVERT: C 72 ASP cc_start: 0.8537 (t0) cc_final: 0.8006 (t0) REVERT: C 75 LYS cc_start: 0.8973 (mtmm) cc_final: 0.8489 (mttt) REVERT: C 82 MET cc_start: 0.8260 (mtp) cc_final: 0.8057 (mtp) REVERT: C 102 PHE cc_start: 0.7790 (OUTLIER) cc_final: 0.6369 (p90) REVERT: H 100 TYR cc_start: 0.7952 (t80) cc_final: 0.7615 (t80) REVERT: H 102 TYR cc_start: 0.6735 (m-80) cc_final: 0.6417 (m-10) REVERT: L 58 ILE cc_start: 0.7165 (OUTLIER) cc_final: 0.6606 (mp) REVERT: G 163 SER cc_start: 0.8408 (t) cc_final: 0.8035 (m) REVERT: M 5 THR cc_start: 0.8621 (m) cc_final: 0.8301 (p) REVERT: J 5 LEU cc_start: 0.8883 (mp) cc_final: 0.8576 (mp) REVERT: O 64 LYS cc_start: 0.7219 (mtmm) cc_final: 0.6864 (mmmt) REVERT: O 102 TYR cc_start: 0.6818 (m-80) cc_final: 0.6595 (m-80) REVERT: Q 42 GLN cc_start: 0.8458 (mm-40) cc_final: 0.7886 (mp10) REVERT: Q 53 THR cc_start: 0.7966 (m) cc_final: 0.7603 (t) REVERT: Q 54 ARG cc_start: 0.8046 (ptm-80) cc_final: 0.7808 (mtp-110) REVERT: Q 58 ILE cc_start: 0.7344 (OUTLIER) cc_final: 0.7048 (mp) REVERT: Q 85 VAL cc_start: 0.8544 (OUTLIER) cc_final: 0.8289 (p) REVERT: F 56 VAL cc_start: 0.9128 (OUTLIER) cc_final: 0.8884 (m) REVERT: N 5 THR cc_start: 0.8825 (m) cc_final: 0.8379 (p) REVERT: K 6 GLU cc_start: 0.7868 (mp0) cc_final: 0.7389 (mp0) REVERT: K 101 GLU cc_start: 0.8059 (pm20) cc_final: 0.7675 (mp0) REVERT: R 17 GLU cc_start: 0.7235 (tt0) cc_final: 0.7024 (tt0) REVERT: R 53 THR cc_start: 0.7976 (m) cc_final: 0.7646 (t) REVERT: R 54 ARG cc_start: 0.7917 (ptm-80) cc_final: 0.7465 (mtm110) outliers start: 64 outliers final: 41 residues processed: 334 average time/residue: 0.1615 time to fit residues: 83.4178 Evaluate side-chains 322 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 275 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 102 PHE Chi-restraints excluded: chain C residue 103 TRP Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain E residue 84 TRP Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain J residue 50 MET Chi-restraints excluded: chain J residue 103 TRP Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain Q residue 5 THR Chi-restraints excluded: chain Q residue 46 LEU Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 84 TRP Chi-restraints excluded: chain I residue 61 THR Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 50 MET Chi-restraints excluded: chain K residue 103 TRP Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain P residue 92 CYS Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 104 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 228 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 171 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 242 optimal weight: 0.9980 chunk 233 optimal weight: 0.7980 chunk 144 optimal weight: 4.9990 chunk 222 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 112 optimal weight: 8.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 3 GLN I 26 HIS I 30 GLN P 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.090421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.064820 restraints weight = 54627.754| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.82 r_work: 0.2930 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 22686 Z= 0.152 Angle : 0.593 9.076 30816 Z= 0.313 Chirality : 0.042 0.149 3381 Planarity : 0.005 0.069 3927 Dihedral : 5.033 53.874 3483 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.46 % Allowed : 10.08 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.15), residues: 2760 helix: 2.53 (0.25), residues: 378 sheet: 0.41 (0.18), residues: 705 loop : -0.09 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 45 TYR 0.018 0.001 TYR P 32 PHE 0.016 0.002 PHE F 213 TRP 0.018 0.001 TRP C 103 HIS 0.005 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00361 (22635) covalent geometry : angle 0.58307 (30693) SS BOND : bond 0.00336 ( 30) SS BOND : angle 1.59797 ( 60) hydrogen bonds : bond 0.04440 ( 894) hydrogen bonds : angle 4.91877 ( 2529) link_BETA1-4 : bond 0.00281 ( 3) link_BETA1-4 : angle 1.23300 ( 9) link_NAG-ASN : bond 0.00223 ( 18) link_NAG-ASN : angle 2.05606 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 331 time to evaluate : 0.878 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: symmetry clash REVERT: B 158 ASP cc_start: 0.7999 (t0) cc_final: 0.6498 (p0) REVERT: B 163 SER cc_start: 0.8393 (t) cc_final: 0.8047 (m) REVERT: D 5 THR cc_start: 0.8736 (m) cc_final: 0.8434 (p) REVERT: C 72 ASP cc_start: 0.8530 (t0) cc_final: 0.8010 (t0) REVERT: C 75 LYS cc_start: 0.8983 (mtmm) cc_final: 0.8504 (mttt) REVERT: C 102 PHE cc_start: 0.7755 (OUTLIER) cc_final: 0.6593 (p90) REVERT: H 34 MET cc_start: 0.8665 (mmm) cc_final: 0.8040 (mmm) REVERT: H 64 LYS cc_start: 0.7910 (mmmt) cc_final: 0.7531 (mmtm) REVERT: H 100 TYR cc_start: 0.7895 (t80) cc_final: 0.7667 (t80) REVERT: L 58 ILE cc_start: 0.7085 (OUTLIER) cc_final: 0.6504 (mp) REVERT: G 163 SER cc_start: 0.8303 (t) cc_final: 0.7993 (m) REVERT: M 5 THR cc_start: 0.8657 (m) cc_final: 0.8382 (p) REVERT: J 5 LEU cc_start: 0.8931 (mp) cc_final: 0.8550 (mt) REVERT: J 101 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7624 (mp0) REVERT: O 64 LYS cc_start: 0.7268 (OUTLIER) cc_final: 0.7048 (mmmt) REVERT: O 72 ASP cc_start: 0.6938 (t0) cc_final: 0.6284 (t70) REVERT: Q 1 GLU cc_start: 0.7353 (mt-10) cc_final: 0.7115 (mt-10) REVERT: Q 42 GLN cc_start: 0.8431 (mm-40) cc_final: 0.7954 (mp10) REVERT: Q 53 THR cc_start: 0.8085 (m) cc_final: 0.7720 (t) REVERT: Q 54 ARG cc_start: 0.7917 (ptm-80) cc_final: 0.7601 (mtp-110) REVERT: Q 67 SER cc_start: 0.8185 (t) cc_final: 0.7974 (t) REVERT: Q 70 GLU cc_start: 0.8040 (tp30) cc_final: 0.7597 (tp30) REVERT: Q 85 VAL cc_start: 0.8546 (OUTLIER) cc_final: 0.8303 (p) REVERT: F 56 VAL cc_start: 0.9186 (OUTLIER) cc_final: 0.8950 (m) REVERT: I 163 SER cc_start: 0.8173 (t) cc_final: 0.7917 (m) REVERT: N 4 MET cc_start: 0.8550 (mmm) cc_final: 0.8250 (mmm) REVERT: N 5 THR cc_start: 0.8845 (m) cc_final: 0.8438 (p) REVERT: K 101 GLU cc_start: 0.7985 (pm20) cc_final: 0.7675 (mp0) REVERT: R 4 MET cc_start: 0.8080 (tpp) cc_final: 0.7489 (tpt) REVERT: R 17 GLU cc_start: 0.7229 (tt0) cc_final: 0.6995 (tt0) REVERT: R 42 GLN cc_start: 0.8063 (mm-40) cc_final: 0.7766 (mp10) REVERT: R 53 THR cc_start: 0.8156 (m) cc_final: 0.7763 (t) REVERT: R 54 ARG cc_start: 0.7868 (ptm-80) cc_final: 0.7508 (mtm110) outliers start: 59 outliers final: 37 residues processed: 365 average time/residue: 0.1661 time to fit residues: 93.2700 Evaluate side-chains 335 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 292 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 102 PHE Chi-restraints excluded: chain C residue 103 TRP Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 84 TRP Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain J residue 50 MET Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 101 GLU Chi-restraints excluded: chain J residue 103 TRP Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 64 LYS Chi-restraints excluded: chain Q residue 5 THR Chi-restraints excluded: chain Q residue 46 LEU Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 84 TRP Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 50 MET Chi-restraints excluded: chain K residue 103 TRP Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain P residue 92 CYS Chi-restraints excluded: chain R residue 104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 149 optimal weight: 8.9990 chunk 83 optimal weight: 5.9990 chunk 208 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 181 optimal weight: 0.4980 chunk 214 optimal weight: 0.5980 chunk 179 optimal weight: 10.0000 chunk 187 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 3 GLN O 3 GLN Q 79 GLN K 3 GLN P 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.089844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.064255 restraints weight = 55091.225| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.82 r_work: 0.2916 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 22686 Z= 0.170 Angle : 0.600 9.691 30816 Z= 0.315 Chirality : 0.042 0.142 3381 Planarity : 0.005 0.067 3927 Dihedral : 4.933 50.149 3483 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.58 % Allowed : 10.54 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.15), residues: 2760 helix: 2.62 (0.25), residues: 375 sheet: 0.46 (0.18), residues: 696 loop : -0.18 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG P 83 TYR 0.018 0.001 TYR P 32 PHE 0.017 0.002 PHE K 67 TRP 0.020 0.001 TRP C 103 HIS 0.005 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00408 (22635) covalent geometry : angle 0.59115 (30693) SS BOND : bond 0.00323 ( 30) SS BOND : angle 1.60003 ( 60) hydrogen bonds : bond 0.04388 ( 894) hydrogen bonds : angle 4.92999 ( 2529) link_BETA1-4 : bond 0.00193 ( 3) link_BETA1-4 : angle 1.25867 ( 9) link_NAG-ASN : bond 0.00251 ( 18) link_NAG-ASN : angle 1.99868 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 312 time to evaluate : 0.620 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: symmetry clash revert: symmetry clash REVERT: B 19 ASP cc_start: 0.7614 (p0) cc_final: 0.7378 (p0) REVERT: B 163 SER cc_start: 0.8380 (t) cc_final: 0.8021 (m) REVERT: D 4 MET cc_start: 0.8620 (mmm) cc_final: 0.8320 (mmm) REVERT: D 5 THR cc_start: 0.8732 (m) cc_final: 0.8444 (p) REVERT: C 72 ASP cc_start: 0.8575 (t0) cc_final: 0.8086 (t0) REVERT: C 75 LYS cc_start: 0.9048 (mtmm) cc_final: 0.8560 (mttt) REVERT: C 102 PHE cc_start: 0.7786 (OUTLIER) cc_final: 0.6593 (p90) REVERT: H 34 MET cc_start: 0.8716 (mmm) cc_final: 0.8472 (mmm) REVERT: H 72 ASP cc_start: 0.6781 (t0) cc_final: 0.5991 (t0) REVERT: H 75 LYS cc_start: 0.8917 (pttm) cc_final: 0.8655 (pttm) REVERT: L 54 ARG cc_start: 0.8408 (ptm-80) cc_final: 0.8021 (mtp-110) REVERT: G 163 SER cc_start: 0.8240 (t) cc_final: 0.7922 (m) REVERT: M 4 MET cc_start: 0.8818 (mmm) cc_final: 0.8312 (ttm) REVERT: M 5 THR cc_start: 0.8699 (m) cc_final: 0.8390 (p) REVERT: J 5 LEU cc_start: 0.8924 (mp) cc_final: 0.8628 (mt) REVERT: J 101 GLU cc_start: 0.7912 (pm20) cc_final: 0.7612 (mp0) REVERT: O 72 ASP cc_start: 0.6956 (t0) cc_final: 0.6540 (t0) REVERT: Q 24 ARG cc_start: 0.7397 (mmm-85) cc_final: 0.7157 (mmm-85) REVERT: Q 42 GLN cc_start: 0.8442 (mm-40) cc_final: 0.8044 (mp10) REVERT: Q 53 THR cc_start: 0.8154 (m) cc_final: 0.7810 (t) REVERT: Q 54 ARG cc_start: 0.7852 (ptm-80) cc_final: 0.7340 (mtm110) REVERT: Q 67 SER cc_start: 0.8052 (t) cc_final: 0.7826 (t) REVERT: Q 85 VAL cc_start: 0.8459 (OUTLIER) cc_final: 0.8193 (p) REVERT: F 56 VAL cc_start: 0.9224 (OUTLIER) cc_final: 0.9013 (m) REVERT: I 163 SER cc_start: 0.8198 (t) cc_final: 0.7944 (m) REVERT: N 5 THR cc_start: 0.8871 (m) cc_final: 0.8478 (p) REVERT: K 101 GLU cc_start: 0.7962 (pm20) cc_final: 0.7672 (mp0) REVERT: R 4 MET cc_start: 0.8043 (tpp) cc_final: 0.7472 (tpt) REVERT: R 17 GLU cc_start: 0.7301 (tt0) cc_final: 0.7093 (tt0) REVERT: R 42 GLN cc_start: 0.7952 (mm-40) cc_final: 0.7648 (mp10) REVERT: R 53 THR cc_start: 0.8172 (m) cc_final: 0.7787 (t) outliers start: 62 outliers final: 49 residues processed: 346 average time/residue: 0.1632 time to fit residues: 87.4457 Evaluate side-chains 343 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 291 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 102 PHE Chi-restraints excluded: chain C residue 103 TRP Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain E residue 84 TRP Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 90 HIS Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 50 MET Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 102 PHE Chi-restraints excluded: chain J residue 103 TRP Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain Q residue 46 LEU Chi-restraints excluded: chain Q residue 75 ILE Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 84 TRP Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 50 MET Chi-restraints excluded: chain K residue 103 TRP Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain P residue 75 LYS Chi-restraints excluded: chain P residue 92 CYS Chi-restraints excluded: chain R residue 104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 203 optimal weight: 2.9990 chunk 249 optimal weight: 7.9990 chunk 139 optimal weight: 0.5980 chunk 37 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 237 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 185 optimal weight: 8.9990 chunk 258 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN J 3 GLN O 3 GLN Q 92 ASN K 3 GLN P 3 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.088027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.062478 restraints weight = 55034.229| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.80 r_work: 0.2876 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 22686 Z= 0.249 Angle : 0.652 10.441 30816 Z= 0.342 Chirality : 0.044 0.153 3381 Planarity : 0.005 0.067 3927 Dihedral : 5.070 47.389 3483 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.79 % Allowed : 11.50 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.15), residues: 2760 helix: 2.39 (0.26), residues: 372 sheet: 0.29 (0.18), residues: 699 loop : -0.37 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 83 TYR 0.019 0.002 TYR H 32 PHE 0.018 0.002 PHE F 213 TRP 0.027 0.002 TRP C 103 HIS 0.006 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00594 (22635) covalent geometry : angle 0.64330 (30693) SS BOND : bond 0.00425 ( 30) SS BOND : angle 1.58939 ( 60) hydrogen bonds : bond 0.04641 ( 894) hydrogen bonds : angle 5.01346 ( 2529) link_BETA1-4 : bond 0.00246 ( 3) link_BETA1-4 : angle 1.42941 ( 9) link_NAG-ASN : bond 0.00384 ( 18) link_NAG-ASN : angle 2.14243 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 313 time to evaluate : 0.904 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 56 VAL cc_start: 0.9317 (OUTLIER) cc_final: 0.9062 (m) REVERT: A 101 ASP cc_start: 0.8780 (OUTLIER) cc_final: 0.8570 (t0) REVERT: B 19 ASP cc_start: 0.7855 (p0) cc_final: 0.7569 (p0) REVERT: B 158 ASP cc_start: 0.8145 (t0) cc_final: 0.6315 (p0) REVERT: B 163 SER cc_start: 0.8480 (t) cc_final: 0.8043 (m) REVERT: D 4 MET cc_start: 0.8656 (mmm) cc_final: 0.8295 (mmm) REVERT: D 5 THR cc_start: 0.8769 (m) cc_final: 0.8489 (p) REVERT: C 72 ASP cc_start: 0.8693 (t0) cc_final: 0.8181 (t0) REVERT: C 75 LYS cc_start: 0.9161 (mtmm) cc_final: 0.8648 (mttt) REVERT: C 102 PHE cc_start: 0.7938 (OUTLIER) cc_final: 0.6337 (p90) REVERT: H 72 ASP cc_start: 0.6898 (t0) cc_final: 0.6350 (t0) REVERT: H 75 LYS cc_start: 0.8915 (pttm) cc_final: 0.8664 (pttm) REVERT: L 42 GLN cc_start: 0.8347 (mm-40) cc_final: 0.7718 (mm-40) REVERT: L 54 ARG cc_start: 0.8409 (ptm-80) cc_final: 0.7858 (mtp-110) REVERT: E 105 TYR cc_start: 0.9229 (t80) cc_final: 0.8993 (t80) REVERT: G 37 ASP cc_start: 0.8751 (t0) cc_final: 0.8522 (t70) REVERT: G 158 ASP cc_start: 0.8079 (t0) cc_final: 0.6187 (p0) REVERT: G 163 SER cc_start: 0.8353 (t) cc_final: 0.7955 (m) REVERT: M 4 MET cc_start: 0.8970 (mmm) cc_final: 0.8491 (ttm) REVERT: M 5 THR cc_start: 0.8783 (m) cc_final: 0.8434 (p) REVERT: J 5 LEU cc_start: 0.8954 (mp) cc_final: 0.8661 (mp) REVERT: O 64 LYS cc_start: 0.7733 (mmmt) cc_final: 0.7148 (mmtm) REVERT: O 72 ASP cc_start: 0.7160 (t0) cc_final: 0.6601 (t70) REVERT: Q 24 ARG cc_start: 0.7810 (mmm-85) cc_final: 0.7320 (mmm-85) REVERT: Q 42 GLN cc_start: 0.8348 (mm-40) cc_final: 0.8021 (mp10) REVERT: Q 53 THR cc_start: 0.8280 (m) cc_final: 0.7899 (t) REVERT: Q 54 ARG cc_start: 0.7785 (ptm-80) cc_final: 0.7401 (mtm110) REVERT: Q 85 VAL cc_start: 0.8573 (OUTLIER) cc_final: 0.8345 (p) REVERT: N 5 THR cc_start: 0.8916 (m) cc_final: 0.8512 (p) REVERT: P 58 TYR cc_start: 0.8101 (m-80) cc_final: 0.7789 (m-80) REVERT: R 33 LEU cc_start: 0.7381 (tt) cc_final: 0.7178 (tt) REVERT: R 42 GLN cc_start: 0.7951 (mm-40) cc_final: 0.7619 (mp10) REVERT: R 53 THR cc_start: 0.8327 (m) cc_final: 0.7882 (t) REVERT: R 105 GLU cc_start: 0.3664 (tp30) cc_final: 0.2946 (pm20) outliers start: 67 outliers final: 50 residues processed: 359 average time/residue: 0.1681 time to fit residues: 92.3943 Evaluate side-chains 348 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 294 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 102 PHE Chi-restraints excluded: chain C residue 103 TRP Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain E residue 84 TRP Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 90 HIS Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 50 MET Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 102 PHE Chi-restraints excluded: chain J residue 103 TRP Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain Q residue 46 LEU Chi-restraints excluded: chain Q residue 75 ILE Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain F residue 84 TRP Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 90 HIS Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 50 MET Chi-restraints excluded: chain K residue 103 TRP Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain P residue 92 CYS Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 222 optimal weight: 3.9990 chunk 173 optimal weight: 7.9990 chunk 108 optimal weight: 0.6980 chunk 242 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 223 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 135 optimal weight: 10.0000 chunk 265 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 3 GLN O 3 GLN P 3 GLN P 82AASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.088673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.063082 restraints weight = 54593.709| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.80 r_work: 0.2891 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 22686 Z= 0.188 Angle : 0.631 10.437 30816 Z= 0.328 Chirality : 0.043 0.220 3381 Planarity : 0.005 0.068 3927 Dihedral : 4.985 45.111 3483 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.46 % Allowed : 11.75 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.15), residues: 2760 helix: 2.47 (0.26), residues: 372 sheet: 0.29 (0.19), residues: 699 loop : -0.39 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 61 TYR 0.018 0.001 TYR P 32 PHE 0.018 0.002 PHE L 71 TRP 0.023 0.001 TRP C 103 HIS 0.005 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00452 (22635) covalent geometry : angle 0.62272 (30693) SS BOND : bond 0.00344 ( 30) SS BOND : angle 1.51576 ( 60) hydrogen bonds : bond 0.04435 ( 894) hydrogen bonds : angle 4.93777 ( 2529) link_BETA1-4 : bond 0.00182 ( 3) link_BETA1-4 : angle 1.33530 ( 9) link_NAG-ASN : bond 0.00280 ( 18) link_NAG-ASN : angle 2.00773 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 314 time to evaluate : 0.896 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 56 VAL cc_start: 0.9298 (OUTLIER) cc_final: 0.9045 (m) REVERT: A 101 ASP cc_start: 0.8779 (OUTLIER) cc_final: 0.8554 (t0) REVERT: B 19 ASP cc_start: 0.7873 (p0) cc_final: 0.7563 (p0) REVERT: B 158 ASP cc_start: 0.8130 (t0) cc_final: 0.6299 (p0) REVERT: B 163 SER cc_start: 0.8451 (t) cc_final: 0.8016 (m) REVERT: D 4 MET cc_start: 0.8604 (mmm) cc_final: 0.8375 (mmm) REVERT: D 5 THR cc_start: 0.8767 (m) cc_final: 0.8493 (p) REVERT: C 72 ASP cc_start: 0.8664 (t0) cc_final: 0.8138 (t0) REVERT: C 75 LYS cc_start: 0.9137 (mtmm) cc_final: 0.8628 (mttt) REVERT: C 102 PHE cc_start: 0.7935 (OUTLIER) cc_final: 0.6542 (p90) REVERT: H 64 LYS cc_start: 0.7938 (mmmt) cc_final: 0.7223 (mmtm) REVERT: H 72 ASP cc_start: 0.6963 (t0) cc_final: 0.6346 (t0) REVERT: H 75 LYS cc_start: 0.8833 (pttm) cc_final: 0.8594 (pttm) REVERT: L 42 GLN cc_start: 0.8297 (mm-40) cc_final: 0.7641 (mp-120) REVERT: L 54 ARG cc_start: 0.8520 (ptm-80) cc_final: 0.8101 (mtm110) REVERT: E 105 TYR cc_start: 0.9219 (t80) cc_final: 0.8963 (t80) REVERT: G 37 ASP cc_start: 0.8733 (t0) cc_final: 0.8518 (t70) REVERT: G 158 ASP cc_start: 0.8149 (t0) cc_final: 0.6262 (p0) REVERT: G 163 SER cc_start: 0.8338 (t) cc_final: 0.7934 (m) REVERT: M 4 MET cc_start: 0.8917 (mmm) cc_final: 0.8513 (ttm) REVERT: M 5 THR cc_start: 0.8779 (m) cc_final: 0.8449 (p) REVERT: J 5 LEU cc_start: 0.8961 (mp) cc_final: 0.8684 (mp) REVERT: O 72 ASP cc_start: 0.7155 (t0) cc_final: 0.6561 (t70) REVERT: O 75 LYS cc_start: 0.8636 (pttm) cc_final: 0.8375 (ptpp) REVERT: Q 1 GLU cc_start: 0.7290 (mt-10) cc_final: 0.7063 (mt-10) REVERT: Q 24 ARG cc_start: 0.7861 (mmm-85) cc_final: 0.7634 (mmm-85) REVERT: Q 42 GLN cc_start: 0.8331 (mm-40) cc_final: 0.8018 (mp10) REVERT: Q 53 THR cc_start: 0.8338 (m) cc_final: 0.7931 (t) REVERT: Q 54 ARG cc_start: 0.7767 (ptm-80) cc_final: 0.7465 (mtm110) REVERT: Q 61 ARG cc_start: 0.8268 (ttp-110) cc_final: 0.7780 (mtp180) REVERT: Q 85 VAL cc_start: 0.8557 (OUTLIER) cc_final: 0.8329 (p) REVERT: I 163 SER cc_start: 0.8291 (t) cc_final: 0.8003 (m) REVERT: N 4 MET cc_start: 0.8851 (mtp) cc_final: 0.8582 (mtp) REVERT: N 5 THR cc_start: 0.8845 (m) cc_final: 0.8428 (p) REVERT: P 58 TYR cc_start: 0.7985 (m-80) cc_final: 0.7656 (m-80) REVERT: P 72 ASP cc_start: 0.7148 (t0) cc_final: 0.6749 (t70) REVERT: R 4 MET cc_start: 0.8152 (tpp) cc_final: 0.7329 (tpt) REVERT: R 33 LEU cc_start: 0.7450 (tt) cc_final: 0.7200 (tt) REVERT: R 42 GLN cc_start: 0.7896 (mm-40) cc_final: 0.7629 (mp10) REVERT: R 53 THR cc_start: 0.8376 (m) cc_final: 0.7843 (t) REVERT: R 54 ARG cc_start: 0.7974 (ptm-80) cc_final: 0.7583 (ttm-80) REVERT: R 103 LYS cc_start: 0.8696 (tppt) cc_final: 0.8461 (tppt) REVERT: R 105 GLU cc_start: 0.3932 (tp30) cc_final: 0.3162 (pm20) outliers start: 59 outliers final: 47 residues processed: 350 average time/residue: 0.1617 time to fit residues: 87.5197 Evaluate side-chains 350 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 299 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 70 ASP Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 102 PHE Chi-restraints excluded: chain C residue 103 TRP Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain E residue 84 TRP Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 90 HIS Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 50 MET Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 103 TRP Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain Q residue 46 LEU Chi-restraints excluded: chain Q residue 75 ILE Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain F residue 84 TRP Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 50 MET Chi-restraints excluded: chain K residue 103 TRP Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain P residue 92 CYS Chi-restraints excluded: chain R residue 104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 171 optimal weight: 7.9990 chunk 270 optimal weight: 10.0000 chunk 159 optimal weight: 0.2980 chunk 67 optimal weight: 3.9990 chunk 169 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 259 optimal weight: 10.0000 chunk 206 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 3 GLN O 3 GLN O 76 ASN K 3 GLN P 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.087986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.062394 restraints weight = 55111.978| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.75 r_work: 0.2875 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 22686 Z= 0.240 Angle : 0.659 10.623 30816 Z= 0.343 Chirality : 0.043 0.164 3381 Planarity : 0.005 0.067 3927 Dihedral : 5.082 42.884 3483 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.50 % Allowed : 12.21 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.15), residues: 2760 helix: 2.31 (0.26), residues: 372 sheet: 0.11 (0.18), residues: 720 loop : -0.47 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 61 TYR 0.019 0.002 TYR P 32 PHE 0.022 0.002 PHE K 67 TRP 0.027 0.002 TRP C 103 HIS 0.005 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00575 (22635) covalent geometry : angle 0.65065 (30693) SS BOND : bond 0.00395 ( 30) SS BOND : angle 1.53280 ( 60) hydrogen bonds : bond 0.04604 ( 894) hydrogen bonds : angle 5.01498 ( 2529) link_BETA1-4 : bond 0.00185 ( 3) link_BETA1-4 : angle 1.44772 ( 9) link_NAG-ASN : bond 0.00353 ( 18) link_NAG-ASN : angle 2.08175 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 300 time to evaluate : 0.812 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: symmetry clash revert: symmetry clash REVERT: A 56 VAL cc_start: 0.9347 (OUTLIER) cc_final: 0.9081 (m) REVERT: A 101 ASP cc_start: 0.8784 (OUTLIER) cc_final: 0.8559 (t0) REVERT: B 19 ASP cc_start: 0.8042 (p0) cc_final: 0.7696 (p0) REVERT: B 163 SER cc_start: 0.8470 (t) cc_final: 0.8021 (m) REVERT: D 4 MET cc_start: 0.8610 (mmm) cc_final: 0.8370 (mmm) REVERT: D 5 THR cc_start: 0.8788 (m) cc_final: 0.8499 (p) REVERT: C 72 ASP cc_start: 0.8654 (t0) cc_final: 0.8132 (t0) REVERT: C 75 LYS cc_start: 0.9174 (mtmm) cc_final: 0.8650 (mttt) REVERT: C 102 PHE cc_start: 0.7897 (OUTLIER) cc_final: 0.6425 (p90) REVERT: H 72 ASP cc_start: 0.6993 (t0) cc_final: 0.6415 (t70) REVERT: L 42 GLN cc_start: 0.8229 (mm-40) cc_final: 0.7605 (mp-120) REVERT: E 105 TYR cc_start: 0.9236 (t80) cc_final: 0.8979 (t80) REVERT: G 37 ASP cc_start: 0.8907 (t0) cc_final: 0.8691 (t70) REVERT: G 163 SER cc_start: 0.8384 (t) cc_final: 0.7951 (m) REVERT: M 4 MET cc_start: 0.8908 (mmm) cc_final: 0.8499 (ttm) REVERT: M 5 THR cc_start: 0.8852 (m) cc_final: 0.8523 (p) REVERT: J 5 LEU cc_start: 0.8964 (mp) cc_final: 0.8667 (mp) REVERT: O 72 ASP cc_start: 0.7191 (t0) cc_final: 0.6579 (t70) REVERT: O 75 LYS cc_start: 0.8656 (pttm) cc_final: 0.8391 (ptpp) REVERT: Q 1 GLU cc_start: 0.7369 (mt-10) cc_final: 0.7132 (mt-10) REVERT: Q 24 ARG cc_start: 0.7898 (mmm-85) cc_final: 0.7676 (mmm-85) REVERT: Q 42 GLN cc_start: 0.8277 (mm-40) cc_final: 0.8031 (mm-40) REVERT: Q 53 THR cc_start: 0.8337 (m) cc_final: 0.7928 (t) REVERT: Q 54 ARG cc_start: 0.7857 (ptm-80) cc_final: 0.7505 (mtm110) REVERT: Q 85 VAL cc_start: 0.8613 (OUTLIER) cc_final: 0.8387 (p) REVERT: I 158 ASP cc_start: 0.8129 (t0) cc_final: 0.6454 (p0) REVERT: N 5 THR cc_start: 0.8864 (m) cc_final: 0.8482 (p) REVERT: P 72 ASP cc_start: 0.7407 (t0) cc_final: 0.6881 (t70) REVERT: R 4 MET cc_start: 0.8114 (tpp) cc_final: 0.7270 (tpt) REVERT: R 33 LEU cc_start: 0.7606 (tt) cc_final: 0.7364 (tt) REVERT: R 42 GLN cc_start: 0.7874 (mm-40) cc_final: 0.7604 (mp10) REVERT: R 53 THR cc_start: 0.8348 (m) cc_final: 0.7863 (t) REVERT: R 54 ARG cc_start: 0.8029 (ptm-80) cc_final: 0.7652 (ttm-80) REVERT: R 103 LYS cc_start: 0.8721 (tppt) cc_final: 0.8451 (tppt) REVERT: R 105 GLU cc_start: 0.3845 (tp30) cc_final: 0.3029 (pm20) outliers start: 60 outliers final: 48 residues processed: 340 average time/residue: 0.1594 time to fit residues: 84.1246 Evaluate side-chains 340 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 288 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 70 ASP Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 102 PHE Chi-restraints excluded: chain C residue 103 TRP Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain E residue 84 TRP Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 70 ASP Chi-restraints excluded: chain M residue 90 HIS Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 50 MET Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 103 TRP Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain Q residue 46 LEU Chi-restraints excluded: chain Q residue 75 ILE Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain F residue 84 TRP Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 90 HIS Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 50 MET Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain P residue 92 CYS Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 114 optimal weight: 0.9990 chunk 143 optimal weight: 3.9990 chunk 186 optimal weight: 4.9990 chunk 241 optimal weight: 0.7980 chunk 198 optimal weight: 3.9990 chunk 57 optimal weight: 0.0000 chunk 68 optimal weight: 0.9980 chunk 226 optimal weight: 3.9990 chunk 133 optimal weight: 0.7980 chunk 244 optimal weight: 0.9980 chunk 136 optimal weight: 5.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 27 GLN J 3 GLN O 3 GLN O 82AASN P 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.090029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.064510 restraints weight = 54655.057| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.80 r_work: 0.2922 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22686 Z= 0.124 Angle : 0.612 10.265 30816 Z= 0.318 Chirality : 0.042 0.158 3381 Planarity : 0.004 0.068 3927 Dihedral : 4.814 39.293 3483 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.92 % Allowed : 12.50 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.16), residues: 2760 helix: 2.65 (0.26), residues: 372 sheet: 0.22 (0.19), residues: 714 loop : -0.40 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 83 TYR 0.018 0.001 TYR H 32 PHE 0.023 0.001 PHE K 67 TRP 0.017 0.001 TRP C 103 HIS 0.004 0.001 HIS B 72 Details of bonding type rmsd covalent geometry : bond 0.00289 (22635) covalent geometry : angle 0.60501 (30693) SS BOND : bond 0.00257 ( 30) SS BOND : angle 1.47232 ( 60) hydrogen bonds : bond 0.04071 ( 894) hydrogen bonds : angle 4.77996 ( 2529) link_BETA1-4 : bond 0.00305 ( 3) link_BETA1-4 : angle 1.12807 ( 9) link_NAG-ASN : bond 0.00210 ( 18) link_NAG-ASN : angle 1.73400 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 312 time to evaluate : 0.865 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 ASP cc_start: 0.8807 (OUTLIER) cc_final: 0.8569 (t0) REVERT: B 19 ASP cc_start: 0.7993 (p0) cc_final: 0.7656 (p0) REVERT: B 158 ASP cc_start: 0.8178 (t0) cc_final: 0.6391 (p0) REVERT: B 163 SER cc_start: 0.8412 (t) cc_final: 0.7997 (m) REVERT: D 5 THR cc_start: 0.8766 (m) cc_final: 0.8489 (p) REVERT: C 72 ASP cc_start: 0.8546 (t0) cc_final: 0.7589 (t0) REVERT: C 75 LYS cc_start: 0.9121 (mtmm) cc_final: 0.8810 (mtmm) REVERT: C 102 PHE cc_start: 0.7750 (OUTLIER) cc_final: 0.6759 (p90) REVERT: H 34 MET cc_start: 0.8740 (mmm) cc_final: 0.8400 (mmp) REVERT: H 72 ASP cc_start: 0.7311 (t0) cc_final: 0.6794 (t70) REVERT: L 42 GLN cc_start: 0.8170 (mm-40) cc_final: 0.7552 (mp10) REVERT: L 54 ARG cc_start: 0.8501 (ptm-80) cc_final: 0.8182 (ttm110) REVERT: G 37 ASP cc_start: 0.8871 (t0) cc_final: 0.8657 (t70) REVERT: G 158 ASP cc_start: 0.8180 (t0) cc_final: 0.6291 (p0) REVERT: G 163 SER cc_start: 0.8303 (t) cc_final: 0.7914 (m) REVERT: M 5 THR cc_start: 0.8794 (m) cc_final: 0.8505 (p) REVERT: J 5 LEU cc_start: 0.8940 (mp) cc_final: 0.8689 (mt) REVERT: J 101 GLU cc_start: 0.8085 (pm20) cc_final: 0.7844 (mp0) REVERT: O 64 LYS cc_start: 0.7734 (mmmt) cc_final: 0.7072 (mmtm) REVERT: O 72 ASP cc_start: 0.7217 (t0) cc_final: 0.6601 (t70) REVERT: O 75 LYS cc_start: 0.8601 (pttm) cc_final: 0.8345 (ptpp) REVERT: Q 42 GLN cc_start: 0.8280 (mm-40) cc_final: 0.8005 (mp10) REVERT: Q 53 THR cc_start: 0.8368 (m) cc_final: 0.7926 (p) REVERT: Q 54 ARG cc_start: 0.7831 (ptm-80) cc_final: 0.7501 (ttm110) REVERT: Q 85 VAL cc_start: 0.8488 (OUTLIER) cc_final: 0.8255 (p) REVERT: F 105 TYR cc_start: 0.9224 (t80) cc_final: 0.8982 (t80) REVERT: I 158 ASP cc_start: 0.8120 (t0) cc_final: 0.6348 (p0) REVERT: I 163 SER cc_start: 0.8267 (t) cc_final: 0.7978 (m) REVERT: N 5 THR cc_start: 0.8746 (m) cc_final: 0.8394 (p) REVERT: P 72 ASP cc_start: 0.7338 (t0) cc_final: 0.6817 (t70) REVERT: R 4 MET cc_start: 0.7962 (tpp) cc_final: 0.7169 (tpt) REVERT: R 33 LEU cc_start: 0.7616 (tt) cc_final: 0.7348 (tt) REVERT: R 53 THR cc_start: 0.8417 (m) cc_final: 0.7988 (t) REVERT: R 103 LYS cc_start: 0.8839 (tppt) cc_final: 0.8595 (tppt) REVERT: R 105 GLU cc_start: 0.3982 (tp30) cc_final: 0.3208 (pm20) outliers start: 46 outliers final: 35 residues processed: 339 average time/residue: 0.1573 time to fit residues: 82.8398 Evaluate side-chains 336 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 298 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 102 PHE Chi-restraints excluded: chain C residue 103 TRP Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 70 ASP Chi-restraints excluded: chain M residue 90 HIS Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 103 TRP Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 84 TRP Chi-restraints excluded: chain N residue 90 HIS Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 50 MET Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain P residue 92 CYS Chi-restraints excluded: chain R residue 104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 188 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 268 optimal weight: 0.3980 chunk 43 optimal weight: 5.9990 chunk 75 optimal weight: 8.9990 chunk 191 optimal weight: 0.6980 chunk 164 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 159 optimal weight: 3.9990 chunk 172 optimal weight: 0.6980 chunk 132 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 3 GLN O 3 GLN P 3 GLN P 82AASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.089851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.064304 restraints weight = 54601.135| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.80 r_work: 0.2918 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.4543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 22686 Z= 0.144 Angle : 0.613 10.144 30816 Z= 0.318 Chirality : 0.042 0.168 3381 Planarity : 0.004 0.067 3927 Dihedral : 4.744 36.842 3483 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.88 % Allowed : 12.50 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.16), residues: 2760 helix: 2.66 (0.26), residues: 372 sheet: 0.18 (0.19), residues: 714 loop : -0.41 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 83 TYR 0.029 0.001 TYR P 100C PHE 0.023 0.001 PHE K 67 TRP 0.019 0.001 TRP K 103 HIS 0.004 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00345 (22635) covalent geometry : angle 0.60443 (30693) SS BOND : bond 0.00334 ( 30) SS BOND : angle 1.84877 ( 60) hydrogen bonds : bond 0.04080 ( 894) hydrogen bonds : angle 4.76853 ( 2529) link_BETA1-4 : bond 0.00272 ( 3) link_BETA1-4 : angle 1.17604 ( 9) link_NAG-ASN : bond 0.00217 ( 18) link_NAG-ASN : angle 1.71254 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5123.75 seconds wall clock time: 88 minutes 53.15 seconds (5333.15 seconds total)