Starting phenix.real_space_refine on Sat Jul 4 16:16:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7t3d_25655/07_2026/7t3d_25655.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t3d_25655/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7t3d_25655/07_2026/7t3d_25655.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7t3d_25655/07_2026/7t3d_25655.cif" model { file = "/net/cci-nas-00/data/ceres_data/7t3d_25655/07_2026/7t3d_25655.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t3d_25655/07_2026/7t3d_25655.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7t3d_25655/07_2026/7t3d_25655.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t3d_25655/07_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-6108/lib/python3.11/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 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 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 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: 3.49, per 1000 atoms: 0.16 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: 1.60 Conformation dependent library (CDL) restraints added in 999.7 milliseconds 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: 0.73 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: 3.52 Time building geometry restraints manager: 2.24 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: 12764 15.99 - 31.99: 325 31.99 - 47.98: 93 47.98 - 63.97: 81 63.97 - 79.97: 18 Dihedral angle restraints: 13281 sinusoidal: 5241 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 13278 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: 0.06 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: 2.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.500 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 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 : 10.124 79.967 8073 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/Z covalent geometry : bond 0.02234 / 1.17 (22635) covalent geometry : angle 1.76460 / 1.18 (30693) SS BOND : bond 0.00729 / 0.47 ( 30) SS BOND : angle 2.60863 / 1.67 ( 60) hydrogen bonds : bond 0.16091 / 10.53 ( 894) hydrogen bonds : angle 7.50698 / 5.18 ( 2529) link_BETA1-4 : bond 0.08044 / 4.52 ( 3) link_BETA1-4 : angle 4.98924 / 2.57 ( 9) link_NAG-ASN : bond 0.08109 / 5.49 ( 18) link_NAG-ASN : angle 2.77266 / 1.74 ( 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 : 0.701 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: 0.1645 time to fit residues: 142.7278 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 : 0.834 ------------------------------------------------------------------------------- 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... 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 = 0.094031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.068202 restraints weight = 54927.887| |-----------------------------------------------------------------------------| 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: 0.8444 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 22686 Z= 0.172 Angle : 0.714 8.674 30816 Z= 0.388 Chirality : 0.045 0.175 3381 Planarity : 0.005 0.075 3927 Dihedral : 5.996 62.398 3042 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.12 % Allowed : 7.50 % Favored : 90.38 % 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: 2.11 (0.25), residues: 378 sheet: 0.50 (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 0.018 0.002 TYR O 91 PHE 0.022 0.002 PHE F 213 TRP 0.019 0.002 TRP C 103 HIS 0.012 0.001 HIS B 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (22635) covalent geometry : angle 0.69782 / 0.38 (30693) SS BOND : bond 0.00613 / 0.36 ( 30) SS BOND : angle 1.60890 / 1.07 ( 60) hydrogen bonds : bond 0.05711 / 3.86 ( 894) hydrogen bonds : angle 5.78843 / 3.99 ( 2529) link_BETA1-4 : bond 0.00147 / 0.08 ( 3) link_BETA1-4 : angle 2.02926 / 1.19 ( 9) link_NAG-ASN : bond 0.00428 / 0.27 ( 18) link_NAG-ASN : angle 3.26770 / 2.00 ( 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 439 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 388 time to evaluate : 0.811 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: 0.8392 (t0) cc_final: 0.8110 (t0) REVERT: B 158 ASP cc_start: 0.8030 (t0) cc_final: 0.6353 (p0) REVERT: D 4 MET cc_start: 0.8365 (mmm) cc_final: 0.7834 (mmm) REVERT: D 5 THR cc_start: 0.8662 (m) cc_final: 0.8298 (p) REVERT: C 72 ASP cc_start: 0.8500 (t0) cc_final: 0.7888 (t0) REVERT: C 75 LYS cc_start: 0.8817 (mtmm) cc_final: 0.8307 (mttt) REVERT: H 64 LYS cc_start: 0.7142 (mtmm) cc_final: 0.6804 (mmmt) REVERT: H 93 VAL cc_start: 0.8255 (t) cc_final: 0.7862 (t) REVERT: H 100 TYR cc_start: 0.7784 (t80) cc_final: 0.7483 (t80) REVERT: L 17 GLU cc_start: 0.6998 (tt0) cc_final: 0.6747 (tt0) REVERT: L 42 GLN cc_start: 0.8587 (mm-40) cc_final: 0.7683 (mp10) REVERT: L 58 ILE cc_start: 0.7197 (OUTLIER) cc_final: 0.6600 (mp) REVERT: L 78 LEU cc_start: 0.5818 (tp) cc_final: 0.4838 (tt) REVERT: E 52 CYS cc_start: 0.6877 (m) cc_final: 0.6423 (m) REVERT: G 37 ASP cc_start: 0.8759 (t70) cc_final: 0.8357 (t70) REVERT: M 5 THR cc_start: 0.8389 (m) cc_final: 0.8051 (p) REVERT: M 42 LYS cc_start: 0.9027 (mmtp) cc_final: 0.8790 (mmmm) REVERT: M 82 ASP cc_start: 0.8407 (m-30) cc_final: 0.8031 (m-30) REVERT: J 3 GLN cc_start: 0.8674 (tt0) cc_final: 0.8443 (tt0) REVERT: J 5 LEU cc_start: 0.8811 (mp) cc_final: 0.8421 (mp) REVERT: O 64 LYS cc_start: 0.7428 (mtmm) cc_final: 0.6922 (mmmt) REVERT: Q 42 GLN cc_start: 0.8615 (mm-40) cc_final: 0.8019 (mp10) REVERT: Q 53 THR cc_start: 0.7482 (m) cc_final: 0.7109 (p) REVERT: Q 54 ARG cc_start: 0.7747 (ptm-80) cc_final: 0.7408 (ptm160) REVERT: Q 78 LEU cc_start: 0.6396 (tp) cc_final: 0.4238 (tt) REVERT: Q 79 GLN cc_start: 0.6876 (mm110) cc_final: 0.6191 (mt0) REVERT: F 105 TYR cc_start: 0.8944 (t80) cc_final: 0.8733 (t80) REVERT: I 17 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8379 (ttt) REVERT: N 5 THR cc_start: 0.8558 (m) cc_final: 0.8061 (p) REVERT: N 42 LYS cc_start: 0.9013 (mmtm) cc_final: 0.8762 (mmmm) REVERT: K 101 GLU cc_start: 0.8047 (pm20) cc_final: 0.7451 (mp0) REVERT: P 34 MET cc_start: 0.8735 (mmm) cc_final: 0.7904 (mmp) REVERT: P 58 TYR cc_start: 0.7100 (m-80) cc_final: 0.6889 (m-80) REVERT: P 100 TYR cc_start: 0.7720 (t80) cc_final: 0.7515 (t80) REVERT: R 4 MET cc_start: 0.7899 (tpp) cc_final: 0.7633 (tpt) REVERT: R 17 GLU cc_start: 0.6978 (tt0) cc_final: 0.6705 (tt0) REVERT: R 42 GLN cc_start: 0.8698 (mm-40) cc_final: 0.8150 (mp10) REVERT: R 53 THR cc_start: 0.7687 (m) cc_final: 0.7379 (t) REVERT: R 54 ARG cc_start: 0.7718 (ptm-80) cc_final: 0.7501 (ptm160) REVERT: R 78 LEU cc_start: 0.6437 (tp) cc_final: 0.5240 (tt) REVERT: R 79 GLN cc_start: 0.7127 (mm-40) cc_final: 0.6806 (mt0) outliers start: 51 outliers final: 34 residues processed: 413 average time/residue: 0.1490 time to fit residues: 94.2687 Evaluate side-chains 361 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 325 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 5.9990 chunk 82 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 chunk 256 optimal weight: 0.9990 chunk 188 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 145 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 ASN ** B 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 3 GLN ** I 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 72 HIS R 37 GLN 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 = 0.090901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.065614 restraints weight = 54237.213| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.78 r_work: 0.2933 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 22686 Z= 0.171 Angle : 0.637 7.857 30816 Z= 0.344 Chirality : 0.043 0.153 3381 Planarity : 0.005 0.066 3927 Dihedral : 5.550 60.160 3042 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.38 % Allowed : 8.42 % Favored : 89.21 % 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: 0.75 (0.15), residues: 2760 helix: 2.44 (0.26), residues: 378 sheet: 0.44 (0.17), residues: 750 loop : 0.13 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 24 TYR 0.016 0.001 TYR H 32 PHE 0.021 0.002 PHE F 213 TRP 0.017 0.002 TRP J 103 HIS 0.007 0.001 HIS I 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 (22635) covalent geometry : angle 0.62835 / 0.34 (30693) SS BOND : bond 0.00306 / 0.21 ( 30) SS BOND : angle 1.14397 / 0.66 ( 60) hydrogen bonds : bond 0.05032 / 3.40 ( 894) hydrogen bonds : angle 5.30310 / 3.66 ( 2529) link_BETA1-4 : bond 0.00334 / 0.18 ( 3) link_BETA1-4 : angle 1.41841 / 0.77 ( 9) link_NAG-ASN : bond 0.00236 / 0.15 ( 18) link_NAG-ASN : angle 2.34964 / 1.41 ( 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 397 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 340 time to evaluate : 0.998 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 158 ASP cc_start: 0.8002 (t0) cc_final: 0.6448 (p0) REVERT: B 163 SER cc_start: 0.8339 (t) cc_final: 0.7939 (m) REVERT: D 4 MET cc_start: 0.8478 (mmm) cc_final: 0.8156 (mmm) REVERT: D 5 THR cc_start: 0.8648 (m) cc_final: 0.8257 (p) REVERT: C 72 ASP cc_start: 0.8431 (t0) cc_final: 0.7880 (t0) REVERT: C 75 LYS cc_start: 0.8895 (mtmm) cc_final: 0.8405 (mttt) REVERT: C 102 PHE cc_start: 0.7623 (OUTLIER) cc_final: 0.6580 (p90) REVERT: H 34 MET cc_start: 0.8401 (mmm) cc_final: 0.7949 (mmm) REVERT: H 93 VAL cc_start: 0.8373 (t) cc_final: 0.7868 (t) REVERT: H 100 TYR cc_start: 0.7831 (t80) cc_final: 0.7397 (t80) REVERT: L 4 MET cc_start: 0.7713 (tpt) cc_final: 0.7476 (tpt) REVERT: L 58 ILE cc_start: 0.7006 (OUTLIER) cc_final: 0.6380 (mp) REVERT: E 113 SER cc_start: 0.9125 (p) cc_final: 0.8923 (t) REVERT: G 163 SER cc_start: 0.8426 (t) cc_final: 0.8059 (m) REVERT: M 4 MET cc_start: 0.8194 (mmm) cc_final: 0.7924 (mmm) REVERT: M 5 THR cc_start: 0.8456 (m) cc_final: 0.8087 (p) REVERT: M 14 PHE cc_start: 0.7304 (p90) cc_final: 0.7025 (p90) REVERT: J 5 LEU cc_start: 0.8820 (mp) cc_final: 0.8563 (mt) REVERT: O 64 LYS cc_start: 0.7204 (mtmm) cc_final: 0.6813 (mmmt) REVERT: Q 24 ARG cc_start: 0.8175 (mmm-85) cc_final: 0.7945 (mmm-85) REVERT: Q 42 GLN cc_start: 0.8545 (mm-40) cc_final: 0.7897 (mp10) REVERT: Q 53 THR cc_start: 0.7706 (m) cc_final: 0.7423 (t) REVERT: Q 54 ARG cc_start: 0.7693 (ptm-80) cc_final: 0.7261 (mtm110) REVERT: Q 71 PHE cc_start: 0.7413 (m-80) cc_final: 0.7074 (m-80) REVERT: Q 85 VAL cc_start: 0.8475 (OUTLIER) cc_final: 0.8216 (p) REVERT: F 56 VAL cc_start: 0.8893 (OUTLIER) cc_final: 0.8354 (m) REVERT: F 105 TYR cc_start: 0.8907 (t80) cc_final: 0.8697 (t80) REVERT: N 5 THR cc_start: 0.8606 (m) cc_final: 0.8132 (p) REVERT: N 42 LYS cc_start: 0.8962 (mmtm) cc_final: 0.8761 (mmmm) REVERT: K 6 GLU cc_start: 0.7437 (mp0) cc_final: 0.7058 (mp0) REVERT: K 13 GLN cc_start: 0.7657 (mm-40) cc_final: 0.7128 (pm20) REVERT: K 101 GLU cc_start: 0.8116 (pm20) cc_final: 0.7657 (mp0) REVERT: K 102 PHE cc_start: 0.7440 (OUTLIER) cc_final: 0.6867 (p90) REVERT: P 93 VAL cc_start: 0.8458 (t) cc_final: 0.8216 (t) REVERT: R 4 MET cc_start: 0.7884 (tpp) cc_final: 0.7468 (tpt) REVERT: R 42 GLN cc_start: 0.8586 (mm-40) cc_final: 0.8063 (mp10) REVERT: R 53 THR cc_start: 0.7686 (m) cc_final: 0.7390 (t) REVERT: R 54 ARG cc_start: 0.7740 (ptm-80) cc_final: 0.7385 (mtm110) outliers start: 57 outliers final: 34 residues processed: 366 average time/residue: 0.1523 time to fit residues: 86.4588 Evaluate side-chains 335 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 296 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 84 TRP 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 H residue 73 ASN 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 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 5 VAL 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 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 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: 2.9990 chunk 45 optimal weight: 0.9990 chunk 164 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 190 optimal weight: 8.9990 chunk 5 optimal weight: 0.9980 chunk 140 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 240 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 ASN A 231 ASN D 79 GLN M 32 HIS M 79 GLN J 3 GLN I 30 GLN N 32 HIS N 79 GLN K 3 GLN K 56 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.087644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.061975 restraints weight = 55693.985| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.82 r_work: 0.2858 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 22686 Z= 0.256 Angle : 0.678 9.670 30816 Z= 0.360 Chirality : 0.045 0.200 3381 Planarity : 0.005 0.067 3927 Dihedral : 5.516 56.403 3042 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.50 % Allowed : 9.38 % Favored : 88.12 % 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: 0.42 (0.15), residues: 2760 helix: 2.24 (0.25), residues: 378 sheet: 0.32 (0.18), residues: 723 loop : -0.15 (0.14), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 45 TYR 0.025 0.002 TYR P 100C PHE 0.020 0.002 PHE A 213 TRP 0.028 0.002 TRP J 103 HIS 0.007 0.002 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00614 / 0.26 (22635) covalent geometry : angle 0.66683 / 0.36 (30693) SS BOND : bond 0.00771 / 0.54 ( 30) SS BOND : angle 1.95963 / 1.50 ( 60) hydrogen bonds : bond 0.05074 / 3.40 ( 894) hydrogen bonds : angle 5.26101 / 3.64 ( 2529) link_BETA1-4 : bond 0.00408 / 0.24 ( 3) link_BETA1-4 : angle 1.65519 / 0.94 ( 9) link_NAG-ASN : bond 0.00424 / 0.26 ( 18) link_NAG-ASN : angle 2.23517 / 1.35 ( 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 369 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 309 time to evaluate : 0.823 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 56 VAL cc_start: 0.9317 (OUTLIER) cc_final: 0.9067 (m) REVERT: A 159 ASN cc_start: 0.9014 (OUTLIER) cc_final: 0.8805 (t0) REVERT: B 158 ASP cc_start: 0.8162 (t0) cc_final: 0.6649 (p0) REVERT: B 163 SER cc_start: 0.8554 (t) cc_final: 0.8137 (m) REVERT: D 5 THR cc_start: 0.8725 (m) cc_final: 0.8415 (p) REVERT: C 72 ASP cc_start: 0.8653 (t0) cc_final: 0.8108 (t0) REVERT: C 75 LYS cc_start: 0.9084 (mtmm) cc_final: 0.8578 (mttt) REVERT: C 102 PHE cc_start: 0.7995 (OUTLIER) cc_final: 0.6281 (p90) REVERT: H 64 LYS cc_start: 0.8039 (mmmt) cc_final: 0.7711 (mmtm) REVERT: H 93 VAL cc_start: 0.8274 (t) cc_final: 0.8053 (t) REVERT: H 100 TYR cc_start: 0.8139 (t80) cc_final: 0.7874 (t80) REVERT: H 102 TYR cc_start: 0.6902 (m-80) cc_final: 0.6557 (m-10) REVERT: L 4 MET cc_start: 0.7629 (tpt) cc_final: 0.7400 (tpt) REVERT: L 17 GLU cc_start: 0.7129 (tt0) cc_final: 0.6916 (tt0) REVERT: L 58 ILE cc_start: 0.7310 (OUTLIER) cc_final: 0.6818 (mp) REVERT: G 163 SER cc_start: 0.8461 (t) cc_final: 0.8080 (m) REVERT: M 5 THR cc_start: 0.8714 (m) cc_final: 0.8410 (p) REVERT: J 5 LEU cc_start: 0.8954 (mp) cc_final: 0.8707 (mp) REVERT: J 102 PHE cc_start: 0.7780 (OUTLIER) cc_final: 0.7112 (p90) REVERT: O 64 LYS cc_start: 0.7262 (mtmm) cc_final: 0.6907 (mmmt) REVERT: O 72 ASP cc_start: 0.7045 (t0) cc_final: 0.6311 (t70) REVERT: O 102 TYR cc_start: 0.7032 (m-80) cc_final: 0.6811 (m-80) REVERT: Q 42 GLN cc_start: 0.8401 (mm-40) cc_final: 0.7859 (mp10) REVERT: Q 53 THR cc_start: 0.8154 (m) cc_final: 0.7824 (t) REVERT: Q 54 ARG cc_start: 0.7709 (ptm-80) cc_final: 0.7194 (mtm110) REVERT: Q 61 ARG cc_start: 0.8268 (ttp-110) cc_final: 0.8037 (ttp-110) REVERT: Q 79 GLN cc_start: 0.7283 (mm110) cc_final: 0.7001 (mt0) REVERT: Q 85 VAL cc_start: 0.8495 (OUTLIER) cc_final: 0.8213 (p) REVERT: I 163 SER cc_start: 0.8403 (t) cc_final: 0.8107 (m) REVERT: N 4 MET cc_start: 0.8720 (mmm) cc_final: 0.7632 (mmm) REVERT: N 5 THR cc_start: 0.8910 (m) cc_final: 0.8476 (p) REVERT: K 101 GLU cc_start: 0.8366 (pm20) cc_final: 0.7916 (mp0) REVERT: R 42 GLN cc_start: 0.8499 (mm-40) cc_final: 0.8295 (mm-40) REVERT: R 53 THR cc_start: 0.8134 (m) cc_final: 0.7708 (t) REVERT: R 54 ARG cc_start: 0.7906 (ptm-80) cc_final: 0.7440 (mtm110) outliers start: 60 outliers final: 44 residues processed: 342 average time/residue: 0.1597 time to fit residues: 84.2445 Evaluate side-chains 325 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 275 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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 159 ASN 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 5 VAL 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 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 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 83 THR Chi-restraints excluded: chain J residue 101 GLU 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 5 THR 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 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 37 GLN Chi-restraints excluded: chain N residue 72 THR 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: 4.9990 chunk 2 optimal weight: 0.9990 chunk 171 optimal weight: 0.4980 chunk 1 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 242 optimal weight: 0.8980 chunk 233 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 222 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 112 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 231 ASN H 35 ASN J 3 GLN I 26 HIS P 3 GLN R 37 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.090590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.065008 restraints weight = 54642.217| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.82 r_work: 0.2932 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22686 Z= 0.129 Angle : 0.589 9.713 30816 Z= 0.311 Chirality : 0.042 0.151 3381 Planarity : 0.004 0.072 3927 Dihedral : 5.177 53.302 3042 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.38 % Allowed : 10.46 % Favored : 87.17 % 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: 0.51 (0.15), residues: 2760 helix: 2.31 (0.25), residues: 396 sheet: 0.44 (0.18), residues: 705 loop : -0.15 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG P 94 TYR 0.019 0.001 TYR P 32 PHE 0.014 0.001 PHE F 213 TRP 0.016 0.001 TRP C 103 HIS 0.005 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (22635) covalent geometry : angle 0.58098 / 0.31 (30693) SS BOND : bond 0.00238 / 0.16 ( 30) SS BOND : angle 1.58024 / 1.16 ( 60) hydrogen bonds : bond 0.04385 / 2.96 ( 894) hydrogen bonds : angle 4.88000 / 3.35 ( 2529) link_BETA1-4 : bond 0.00318 / 0.18 ( 3) link_BETA1-4 : angle 1.31048 / 0.85 ( 9) link_NAG-ASN : bond 0.00198 / 0.12 ( 18) link_NAG-ASN : angle 1.81155 / 1.08 ( 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 379 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 322 time to evaluate : 0.789 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 163 SER cc_start: 0.8387 (t) cc_final: 0.8040 (m) REVERT: D 4 MET cc_start: 0.8634 (mmm) cc_final: 0.8271 (mmm) REVERT: D 5 THR cc_start: 0.8736 (m) cc_final: 0.8460 (p) REVERT: C 72 ASP cc_start: 0.8562 (t0) cc_final: 0.8058 (t0) REVERT: C 75 LYS cc_start: 0.8991 (mtmm) cc_final: 0.8513 (mttt) REVERT: C 102 PHE cc_start: 0.7783 (OUTLIER) cc_final: 0.6622 (p90) REVERT: H 34 MET cc_start: 0.8670 (mmm) cc_final: 0.8180 (mmm) REVERT: H 93 VAL cc_start: 0.8351 (t) cc_final: 0.8030 (t) REVERT: L 54 ARG cc_start: 0.8429 (ptm-80) cc_final: 0.8066 (mtp-110) REVERT: G 163 SER cc_start: 0.8291 (t) cc_final: 0.7978 (m) REVERT: M 5 THR cc_start: 0.8705 (m) cc_final: 0.8471 (p) REVERT: J 5 LEU cc_start: 0.8938 (mp) cc_final: 0.8656 (mp) REVERT: O 64 LYS cc_start: 0.7263 (OUTLIER) cc_final: 0.7041 (mmmt) REVERT: O 72 ASP cc_start: 0.6923 (t0) cc_final: 0.6258 (t70) REVERT: O 102 TYR cc_start: 0.6952 (m-80) cc_final: 0.6737 (m-80) REVERT: Q 42 GLN cc_start: 0.8463 (mm-40) cc_final: 0.8035 (mp10) REVERT: Q 53 THR cc_start: 0.8182 (m) cc_final: 0.7904 (t) REVERT: Q 54 ARG cc_start: 0.7609 (ptm-80) cc_final: 0.7383 (mtm110) REVERT: Q 61 ARG cc_start: 0.8322 (ttp-110) cc_final: 0.8045 (ttp-110) REVERT: Q 71 PHE cc_start: 0.7587 (m-80) cc_final: 0.7175 (m-80) REVERT: Q 79 GLN cc_start: 0.7279 (mm110) cc_final: 0.7028 (mt0) REVERT: Q 85 VAL cc_start: 0.8465 (OUTLIER) cc_final: 0.8209 (p) REVERT: I 163 SER cc_start: 0.8170 (t) cc_final: 0.7915 (m) REVERT: N 5 THR cc_start: 0.8843 (m) cc_final: 0.8446 (p) REVERT: K 101 GLU cc_start: 0.7978 (pm20) cc_final: 0.7670 (mp0) REVERT: P 34 MET cc_start: 0.8864 (mmm) cc_final: 0.8543 (mmt) REVERT: R 42 GLN cc_start: 0.8437 (mm-40) cc_final: 0.8080 (mp10) REVERT: R 53 THR cc_start: 0.8158 (m) cc_final: 0.7752 (t) REVERT: R 54 ARG cc_start: 0.7848 (ptm-80) cc_final: 0.7511 (mtm110) REVERT: R 79 GLN cc_start: 0.8149 (mt0) cc_final: 0.7921 (mt0) outliers start: 57 outliers final: 38 residues processed: 353 average time/residue: 0.1633 time to fit residues: 88.4781 Evaluate side-chains 330 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 289 time to evaluate : 0.843 ------------------------------------------------------------------------------- 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 35 ASN Chi-restraints excluded: chain H residue 73 ASN 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 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 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 5 VAL Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 64 LYS 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 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: 9.9990 chunk 83 optimal weight: 7.9990 chunk 208 optimal weight: 0.0770 chunk 64 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 181 optimal weight: 0.8980 chunk 214 optimal weight: 0.8980 chunk 179 optimal weight: 9.9990 chunk 187 optimal weight: 0.8980 chunk 167 optimal weight: 8.9990 chunk 117 optimal weight: 4.9990 overall best weight: 1.5540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.089804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.064249 restraints weight = 55057.445| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.82 r_work: 0.2916 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 22686 Z= 0.166 Angle : 0.600 9.918 30816 Z= 0.314 Chirality : 0.042 0.147 3381 Planarity : 0.005 0.070 3927 Dihedral : 5.050 50.133 3042 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.46 % Allowed : 10.88 % Favored : 86.67 % 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: 0.51 (0.15), residues: 2760 helix: 2.60 (0.25), residues: 378 sheet: 0.45 (0.19), residues: 696 loop : -0.21 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 94 TYR 0.015 0.001 TYR P 32 PHE 0.020 0.002 PHE C 67 TRP 0.020 0.001 TRP C 103 HIS 0.005 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (22635) covalent geometry : angle 0.59215 / 0.31 (30693) SS BOND : bond 0.00315 / 0.22 ( 30) SS BOND : angle 1.60551 / 1.13 ( 60) hydrogen bonds : bond 0.04335 / 2.92 ( 894) hydrogen bonds : angle 4.89087 / 3.36 ( 2529) link_BETA1-4 : bond 0.00228 / 0.13 ( 3) link_BETA1-4 : angle 1.23183 / 0.71 ( 9) link_NAG-ASN : bond 0.00229 / 0.14 ( 18) link_NAG-ASN : angle 1.77667 / 1.07 ( 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 365 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 306 time to evaluate : 0.541 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: B 158 ASP cc_start: 0.8054 (t0) cc_final: 0.6172 (p0) REVERT: B 163 SER cc_start: 0.8431 (t) cc_final: 0.8031 (m) REVERT: D 4 MET cc_start: 0.8577 (mmm) cc_final: 0.8259 (mmm) REVERT: D 5 THR cc_start: 0.8744 (m) cc_final: 0.8462 (p) REVERT: C 72 ASP cc_start: 0.8670 (t0) cc_final: 0.8159 (t0) REVERT: C 75 LYS cc_start: 0.9069 (mtmm) cc_final: 0.8569 (mttt) REVERT: C 102 PHE cc_start: 0.7875 (OUTLIER) cc_final: 0.6663 (p90) REVERT: H 35 ASN cc_start: 0.8994 (p0) cc_final: 0.8789 (p0) REVERT: H 72 ASP cc_start: 0.6781 (t0) cc_final: 0.5819 (t0) REVERT: H 75 LYS cc_start: 0.8895 (pttm) cc_final: 0.8571 (pttm) REVERT: L 4 MET cc_start: 0.7275 (tpt) cc_final: 0.7067 (tpt) REVERT: L 54 ARG cc_start: 0.8419 (ptm-80) cc_final: 0.8070 (mtp-110) REVERT: G 163 SER cc_start: 0.8305 (t) cc_final: 0.7946 (m) REVERT: M 5 THR cc_start: 0.8771 (m) cc_final: 0.8525 (p) REVERT: J 5 LEU cc_start: 0.8962 (mp) cc_final: 0.8622 (mp) REVERT: O 72 ASP cc_start: 0.7059 (t0) cc_final: 0.6509 (t70) REVERT: O 102 TYR cc_start: 0.6916 (m-80) cc_final: 0.6678 (m-80) REVERT: Q 42 GLN cc_start: 0.8434 (mm-40) cc_final: 0.7936 (mp10) REVERT: Q 53 THR cc_start: 0.8218 (m) cc_final: 0.7900 (t) REVERT: Q 54 ARG cc_start: 0.7666 (ptm-80) cc_final: 0.7393 (mtm110) REVERT: Q 61 ARG cc_start: 0.8317 (ttp-110) cc_final: 0.8042 (ttp-110) REVERT: Q 71 PHE cc_start: 0.7630 (m-80) cc_final: 0.7322 (m-80) REVERT: Q 78 LEU cc_start: 0.5687 (OUTLIER) cc_final: 0.5060 (tp) REVERT: Q 85 VAL cc_start: 0.8519 (OUTLIER) cc_final: 0.8244 (p) REVERT: I 163 SER cc_start: 0.8256 (t) cc_final: 0.7972 (m) REVERT: N 5 THR cc_start: 0.8885 (m) cc_final: 0.8474 (p) REVERT: K 101 GLU cc_start: 0.8274 (pm20) cc_final: 0.7869 (mp0) REVERT: P 82 ASN cc_start: 0.8419 (m-40) cc_final: 0.8204 (m-40) REVERT: R 4 MET cc_start: 0.7995 (tpp) cc_final: 0.7420 (tpp) REVERT: R 42 GLN cc_start: 0.8401 (mm-40) cc_final: 0.8193 (mm-40) REVERT: R 53 THR cc_start: 0.8217 (m) cc_final: 0.7758 (t) REVERT: R 54 ARG cc_start: 0.7910 (ptm-80) cc_final: 0.7537 (ttm-80) outliers start: 59 outliers final: 42 residues processed: 342 average time/residue: 0.1601 time to fit residues: 84.3732 Evaluate side-chains 337 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 292 time to evaluate : 0.687 ------------------------------------------------------------------------------- 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 22 CYS Chi-restraints excluded: chain H residue 24 VAL 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 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 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 78 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 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 20 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 203 optimal weight: 0.3980 chunk 249 optimal weight: 6.9990 chunk 139 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 237 optimal weight: 0.9990 chunk 122 optimal weight: 6.9990 chunk 185 optimal weight: 8.9990 chunk 258 optimal weight: 6.9990 chunk 131 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 79 GLN K 3 GLN P 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.090324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.064765 restraints weight = 54681.113| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.81 r_work: 0.2928 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.4197 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= 0.140 Angle : 0.580 9.936 30816 Z= 0.302 Chirality : 0.042 0.206 3381 Planarity : 0.004 0.075 3927 Dihedral : 4.851 45.496 3042 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.46 % Allowed : 11.29 % Favored : 86.25 % 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: 0.48 (0.16), residues: 2760 helix: 2.78 (0.26), residues: 375 sheet: 0.45 (0.19), residues: 696 loop : -0.28 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 94 TYR 0.017 0.001 TYR P 32 PHE 0.018 0.001 PHE L 71 TRP 0.018 0.001 TRP C 103 HIS 0.005 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (22635) covalent geometry : angle 0.57290 / 0.30 (30693) SS BOND : bond 0.00273 / 0.18 ( 30) SS BOND : angle 1.48122 / 1.06 ( 60) hydrogen bonds : bond 0.04125 / 2.78 ( 894) hydrogen bonds : angle 4.75020 / 3.26 ( 2529) link_BETA1-4 : bond 0.00187 / 0.10 ( 3) link_BETA1-4 : angle 1.08253 / 0.63 ( 9) link_NAG-ASN : bond 0.00175 / 0.11 ( 18) link_NAG-ASN : angle 1.61205 / 0.97 ( 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 382 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 323 time to evaluate : 0.692 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: A 101 ASP cc_start: 0.8498 (OUTLIER) cc_final: 0.8293 (t0) REVERT: B 158 ASP cc_start: 0.8033 (t0) cc_final: 0.6216 (p0) REVERT: B 163 SER cc_start: 0.8323 (t) cc_final: 0.7944 (m) REVERT: D 5 THR cc_start: 0.8741 (m) cc_final: 0.8473 (p) REVERT: C 5 LEU cc_start: 0.9030 (tt) cc_final: 0.8478 (mt) REVERT: C 72 ASP cc_start: 0.8562 (t0) cc_final: 0.8088 (t0) REVERT: C 75 LYS cc_start: 0.9075 (mtmm) cc_final: 0.8575 (mttt) REVERT: C 102 PHE cc_start: 0.7700 (OUTLIER) cc_final: 0.6628 (p90) REVERT: H 72 ASP cc_start: 0.6749 (t0) cc_final: 0.5887 (t0) REVERT: H 75 LYS cc_start: 0.8837 (pttm) cc_final: 0.8471 (pttm) REVERT: L 54 ARG cc_start: 0.8456 (ptm-80) cc_final: 0.8189 (mtm110) REVERT: G 62 GLN cc_start: 0.8363 (mp10) cc_final: 0.7971 (mp10) REVERT: G 158 ASP cc_start: 0.7976 (t0) cc_final: 0.6086 (p0) REVERT: G 163 SER cc_start: 0.8237 (t) cc_final: 0.7904 (m) REVERT: M 5 THR cc_start: 0.8769 (m) cc_final: 0.8521 (p) REVERT: J 5 LEU cc_start: 0.8958 (mp) cc_final: 0.8612 (mp) REVERT: J 101 GLU cc_start: 0.7898 (pm20) cc_final: 0.7667 (mp0) REVERT: O 64 LYS cc_start: 0.7606 (mmmt) cc_final: 0.7290 (mmtm) REVERT: O 72 ASP cc_start: 0.7019 (t0) cc_final: 0.6436 (t70) REVERT: O 75 LYS cc_start: 0.8589 (pttm) cc_final: 0.8350 (ptpp) REVERT: O 102 TYR cc_start: 0.6965 (m-80) cc_final: 0.6763 (m-80) REVERT: Q 24 ARG cc_start: 0.7666 (mmm-85) cc_final: 0.7420 (mmm-85) REVERT: Q 42 GLN cc_start: 0.8346 (mm-40) cc_final: 0.7871 (mp10) REVERT: Q 53 THR cc_start: 0.8217 (m) cc_final: 0.7794 (p) REVERT: Q 54 ARG cc_start: 0.7706 (ptm-80) cc_final: 0.7357 (ttm110) REVERT: Q 71 PHE cc_start: 0.7612 (m-80) cc_final: 0.7268 (m-80) REVERT: Q 85 VAL cc_start: 0.8502 (OUTLIER) cc_final: 0.8275 (p) REVERT: I 163 SER cc_start: 0.8199 (t) cc_final: 0.7946 (m) REVERT: N 4 MET cc_start: 0.8582 (mmm) cc_final: 0.8155 (mtp) REVERT: N 5 THR cc_start: 0.8839 (m) cc_final: 0.8443 (p) REVERT: K 101 GLU cc_start: 0.7891 (pm20) cc_final: 0.7548 (mp0) REVERT: P 58 TYR cc_start: 0.7732 (m-80) cc_final: 0.7469 (m-80) REVERT: R 33 LEU cc_start: 0.7170 (tt) cc_final: 0.6905 (tt) REVERT: R 53 THR cc_start: 0.8266 (m) cc_final: 0.7844 (t) REVERT: R 105 GLU cc_start: 0.6118 (pm20) cc_final: 0.5902 (tp30) outliers start: 59 outliers final: 42 residues processed: 358 average time/residue: 0.1505 time to fit residues: 83.0772 Evaluate side-chains 344 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 299 time to evaluate : 0.893 ------------------------------------------------------------------------------- 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 72 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 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 69 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 222 optimal weight: 4.9990 chunk 173 optimal weight: 0.5980 chunk 108 optimal weight: 3.9990 chunk 242 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 223 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 135 optimal weight: 10.0000 chunk 265 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 3 GLN K 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 = 0.3543 r_free = 0.3543 target = 0.089243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.063664 restraints weight = 54515.263| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.80 r_work: 0.2912 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.4304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 22686 Z= 0.187 Angle : 0.609 8.997 30816 Z= 0.317 Chirality : 0.042 0.162 3381 Planarity : 0.005 0.072 3927 Dihedral : 4.868 42.505 3042 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.21 % Allowed : 11.71 % Favored : 86.08 % 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: 0.34 (0.16), residues: 2760 helix: 2.68 (0.26), residues: 375 sheet: 0.28 (0.18), residues: 717 loop : -0.34 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 83 TYR 0.015 0.001 TYR P 32 PHE 0.019 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/Z covalent geometry : bond 0.00449 / 0.19 (22635) covalent geometry : angle 0.60151 / 0.31 (30693) SS BOND : bond 0.00344 / 0.24 ( 30) SS BOND : angle 1.51411 / 1.07 ( 60) hydrogen bonds : bond 0.04300 / 2.88 ( 894) hydrogen bonds : angle 4.84410 / 3.34 ( 2529) link_BETA1-4 : bond 0.00185 / 0.10 ( 3) link_BETA1-4 : angle 1.18454 / 0.68 ( 9) link_NAG-ASN : bond 0.00262 / 0.16 ( 18) link_NAG-ASN : angle 1.70728 / 1.04 ( 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 364 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 311 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: A 101 ASP cc_start: 0.8759 (OUTLIER) cc_final: 0.8555 (t0) REVERT: B 163 SER cc_start: 0.8447 (t) cc_final: 0.8039 (m) REVERT: D 5 THR cc_start: 0.8720 (m) cc_final: 0.8349 (p) REVERT: C 72 ASP cc_start: 0.8635 (t0) cc_final: 0.8142 (t0) REVERT: C 75 LYS cc_start: 0.9142 (mtmm) cc_final: 0.8628 (mttt) REVERT: C 102 PHE cc_start: 0.7850 (OUTLIER) cc_final: 0.6630 (p90) REVERT: H 72 ASP cc_start: 0.6900 (t0) cc_final: 0.6202 (t0) REVERT: H 75 LYS cc_start: 0.8848 (pttm) cc_final: 0.8489 (pttm) REVERT: L 42 GLN cc_start: 0.8261 (mm-40) cc_final: 0.7558 (mp10) REVERT: L 54 ARG cc_start: 0.8563 (ptm-80) cc_final: 0.8197 (mtm110) REVERT: G 62 GLN cc_start: 0.8533 (mp10) cc_final: 0.8125 (mp10) REVERT: G 163 SER cc_start: 0.8300 (t) cc_final: 0.7925 (m) REVERT: M 5 THR cc_start: 0.8799 (m) cc_final: 0.8562 (p) REVERT: J 5 LEU cc_start: 0.8994 (mp) cc_final: 0.8635 (mp) REVERT: J 101 GLU cc_start: 0.8019 (pm20) cc_final: 0.7684 (mp0) REVERT: O 72 ASP cc_start: 0.7143 (t0) cc_final: 0.6518 (t70) REVERT: O 75 LYS cc_start: 0.8600 (pttm) cc_final: 0.8342 (ptpp) REVERT: Q 24 ARG cc_start: 0.7774 (mmm-85) cc_final: 0.7468 (mmm-85) REVERT: Q 42 GLN cc_start: 0.8279 (mm-40) cc_final: 0.7940 (mp10) REVERT: Q 53 THR cc_start: 0.8367 (m) cc_final: 0.8018 (t) REVERT: Q 54 ARG cc_start: 0.7834 (ptm-80) cc_final: 0.7480 (ttm110) REVERT: Q 71 PHE cc_start: 0.7641 (m-80) cc_final: 0.7215 (m-80) REVERT: Q 85 VAL cc_start: 0.8569 (OUTLIER) cc_final: 0.8345 (p) REVERT: I 163 SER cc_start: 0.8275 (t) cc_final: 0.8001 (m) REVERT: N 4 MET cc_start: 0.8667 (mmm) cc_final: 0.8311 (mtp) REVERT: N 5 THR cc_start: 0.8894 (m) cc_final: 0.8523 (p) REVERT: K 101 GLU cc_start: 0.8224 (pm20) cc_final: 0.7723 (mp0) REVERT: P 58 TYR cc_start: 0.8067 (m-80) cc_final: 0.7774 (m-80) REVERT: P 72 ASP cc_start: 0.7409 (t0) cc_final: 0.7018 (t0) REVERT: R 4 MET cc_start: 0.7028 (mmm) cc_final: 0.6517 (tpt) REVERT: R 33 LEU cc_start: 0.7423 (tt) cc_final: 0.7207 (tt) REVERT: R 53 THR cc_start: 0.8448 (m) cc_final: 0.7954 (t) REVERT: R 54 ARG cc_start: 0.7943 (ptm-80) cc_final: 0.7682 (ttm-80) outliers start: 53 outliers final: 45 residues processed: 343 average time/residue: 0.1489 time to fit residues: 79.4239 Evaluate side-chains 338 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 290 time to evaluate : 0.850 ------------------------------------------------------------------------------- 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 72 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 69 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 61 THR Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 20 THR 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 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 F residue 190 ASP Chi-restraints excluded: chain I residue 61 THR 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 171 optimal weight: 0.0970 chunk 270 optimal weight: 10.0000 chunk 159 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 169 optimal weight: 0.7980 chunk 99 optimal weight: 5.9990 chunk 113 optimal weight: 0.1980 chunk 80 optimal weight: 0.9990 chunk 259 optimal weight: 5.9990 chunk 206 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 53 ASN Q 79 GLN P 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.091443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.065926 restraints weight = 54533.766| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.82 r_work: 0.2957 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22686 Z= 0.115 Angle : 0.582 10.521 30816 Z= 0.303 Chirality : 0.041 0.155 3381 Planarity : 0.004 0.075 3927 Dihedral : 4.619 37.471 3042 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.79 % Allowed : 12.33 % Favored : 85.88 % 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: 0.36 (0.16), residues: 2760 helix: 2.90 (0.26), residues: 375 sheet: 0.24 (0.19), residues: 687 loop : -0.35 (0.15), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 83 TYR 0.018 0.001 TYR H 32 PHE 0.013 0.001 PHE L 71 TRP 0.014 0.001 TRP C 103 HIS 0.004 0.001 HIS B 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (22635) covalent geometry : angle 0.57637 / 0.30 (30693) SS BOND : bond 0.00257 / 0.16 ( 30) SS BOND : angle 1.43889 / 1.03 ( 60) hydrogen bonds : bond 0.03830 / 2.59 ( 894) hydrogen bonds : angle 4.62733 / 3.18 ( 2529) link_BETA1-4 : bond 0.00236 / 0.13 ( 3) link_BETA1-4 : angle 0.89702 / 0.55 ( 9) link_NAG-ASN : bond 0.00166 / 0.11 ( 18) link_NAG-ASN : angle 1.44890 / 0.88 ( 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 368 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 325 time to evaluate : 0.806 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: A 101 ASP cc_start: 0.8541 (OUTLIER) cc_final: 0.8314 (t0) REVERT: B 158 ASP cc_start: 0.8061 (t0) cc_final: 0.6313 (p0) REVERT: B 163 SER cc_start: 0.8353 (t) cc_final: 0.7970 (m) REVERT: C 72 ASP cc_start: 0.8513 (t0) cc_final: 0.8179 (t0) REVERT: C 75 LYS cc_start: 0.9073 (mtmm) cc_final: 0.8680 (mttt) REVERT: C 102 PHE cc_start: 0.7576 (OUTLIER) cc_final: 0.6761 (p90) REVERT: H 72 ASP cc_start: 0.6839 (t0) cc_final: 0.6442 (t70) REVERT: L 54 ARG cc_start: 0.8477 (ptm-80) cc_final: 0.8245 (ttm110) REVERT: L 61 ARG cc_start: 0.8031 (ttp-110) cc_final: 0.7183 (ttp-110) REVERT: L 79 GLN cc_start: 0.7424 (mm110) cc_final: 0.6861 (mp10) REVERT: L 105 GLU cc_start: 0.3403 (tp30) cc_final: 0.2637 (pm20) REVERT: G 62 GLN cc_start: 0.8411 (mp10) cc_final: 0.8018 (mp10) REVERT: G 158 ASP cc_start: 0.8106 (t0) cc_final: 0.6249 (p0) REVERT: G 163 SER cc_start: 0.8249 (t) cc_final: 0.7897 (m) REVERT: M 5 THR cc_start: 0.8779 (m) cc_final: 0.8519 (p) REVERT: J 5 LEU cc_start: 0.8931 (mp) cc_final: 0.8583 (mp) REVERT: J 101 GLU cc_start: 0.7788 (pm20) cc_final: 0.7531 (mp0) REVERT: O 64 LYS cc_start: 0.7577 (mmmt) cc_final: 0.6991 (mmtm) REVERT: O 72 ASP cc_start: 0.7102 (t0) cc_final: 0.6488 (t70) REVERT: O 75 LYS cc_start: 0.8561 (pttm) cc_final: 0.8320 (ptpp) REVERT: Q 1 GLU cc_start: 0.6453 (mt-10) cc_final: 0.6247 (mt-10) REVERT: Q 24 ARG cc_start: 0.7817 (mmm-85) cc_final: 0.7543 (mmm-85) REVERT: Q 42 GLN cc_start: 0.8220 (mm-40) cc_final: 0.7924 (mp10) REVERT: Q 53 THR cc_start: 0.8306 (m) cc_final: 0.7951 (t) REVERT: Q 67 SER cc_start: 0.7738 (t) cc_final: 0.7372 (p) REVERT: Q 71 PHE cc_start: 0.7626 (m-80) cc_final: 0.7196 (m-80) REVERT: Q 85 VAL cc_start: 0.8500 (OUTLIER) cc_final: 0.8282 (p) REVERT: I 158 ASP cc_start: 0.7987 (t0) cc_final: 0.6189 (p0) REVERT: I 163 SER cc_start: 0.8230 (t) cc_final: 0.7991 (m) REVERT: N 5 THR cc_start: 0.8827 (m) cc_final: 0.8439 (p) REVERT: K 82 MET cc_start: 0.8257 (mmt) cc_final: 0.7196 (mmt) REVERT: K 101 GLU cc_start: 0.7854 (pm20) cc_final: 0.7385 (mp0) REVERT: K 102 PHE cc_start: 0.7378 (OUTLIER) cc_final: 0.7017 (p90) REVERT: P 58 TYR cc_start: 0.7797 (m-80) cc_final: 0.7454 (m-80) REVERT: P 72 ASP cc_start: 0.7257 (t0) cc_final: 0.6772 (t70) REVERT: R 4 MET cc_start: 0.7311 (mmm) cc_final: 0.6979 (tpt) REVERT: R 33 LEU cc_start: 0.7298 (tt) cc_final: 0.7098 (tt) REVERT: R 53 THR cc_start: 0.8438 (m) cc_final: 0.8014 (t) REVERT: R 105 GLU cc_start: 0.3796 (tp30) cc_final: 0.2888 (pm20) outliers start: 43 outliers final: 33 residues processed: 349 average time/residue: 0.1456 time to fit residues: 79.0302 Evaluate side-chains 338 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 301 time to evaluate : 0.863 ------------------------------------------------------------------------------- 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 85 THR 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 24 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain G residue 15 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 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 F residue 190 ASP Chi-restraints excluded: chain N residue 20 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 102 PHE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 114 optimal weight: 1.9990 chunk 143 optimal weight: 5.9990 chunk 186 optimal weight: 5.9990 chunk 241 optimal weight: 0.0070 chunk 198 optimal weight: 5.9990 chunk 57 optimal weight: 0.4980 chunk 68 optimal weight: 0.6980 chunk 226 optimal weight: 3.9990 chunk 133 optimal weight: 0.9990 chunk 244 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 overall best weight: 0.8402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 3 GLN P 82AASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.091162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.065607 restraints weight = 54810.763| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.82 r_work: 0.2946 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 22686 Z= 0.125 Angle : 0.588 10.566 30816 Z= 0.305 Chirality : 0.042 0.173 3381 Planarity : 0.004 0.071 3927 Dihedral : 4.575 34.070 3042 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.71 % Allowed : 12.42 % Favored : 85.88 % 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: 0.40 (0.16), residues: 2760 helix: 2.91 (0.26), residues: 375 sheet: 0.35 (0.19), residues: 711 loop : -0.37 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 83 TYR 0.016 0.001 TYR E 105 PHE 0.023 0.001 PHE L 71 TRP 0.016 0.001 TRP C 103 HIS 0.005 0.001 HIS I 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.12 (22635) covalent geometry : angle 0.57994 / 0.30 (30693) SS BOND : bond 0.00267 / 0.18 ( 30) SS BOND : angle 1.78724 / 1.26 ( 60) hydrogen bonds : bond 0.03849 / 2.59 ( 894) hydrogen bonds : angle 4.60658 / 3.17 ( 2529) link_BETA1-4 : bond 0.00232 / 0.14 ( 3) link_BETA1-4 : angle 0.95737 / 0.59 ( 9) link_NAG-ASN : bond 0.00142 / 0.09 ( 18) link_NAG-ASN : angle 1.45097 / 0.88 ( 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 354 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 313 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 VAL cc_start: 0.9216 (OUTLIER) cc_final: 0.8942 (m) REVERT: A 101 ASP cc_start: 0.8543 (OUTLIER) cc_final: 0.8321 (t0) REVERT: B 158 ASP cc_start: 0.8070 (t0) cc_final: 0.6300 (p0) REVERT: B 163 SER cc_start: 0.8350 (t) cc_final: 0.7958 (m) REVERT: C 72 ASP cc_start: 0.8510 (t0) cc_final: 0.7575 (t0) REVERT: C 75 LYS cc_start: 0.9079 (mtmm) cc_final: 0.8777 (mtmm) REVERT: C 102 PHE cc_start: 0.7550 (OUTLIER) cc_final: 0.6694 (p90) REVERT: H 72 ASP cc_start: 0.6840 (t0) cc_final: 0.6431 (t70) REVERT: L 54 ARG cc_start: 0.8445 (ptm-80) cc_final: 0.8204 (ttm110) REVERT: G 62 GLN cc_start: 0.8439 (mp10) cc_final: 0.8050 (mp10) REVERT: G 158 ASP cc_start: 0.8140 (t0) cc_final: 0.6291 (p0) REVERT: G 163 SER cc_start: 0.8241 (t) cc_final: 0.7880 (m) REVERT: M 5 THR cc_start: 0.8798 (m) cc_final: 0.8522 (p) REVERT: M 103 LYS cc_start: 0.8695 (tptp) cc_final: 0.8405 (ttpp) REVERT: J 5 LEU cc_start: 0.8927 (mp) cc_final: 0.8573 (mp) REVERT: J 101 GLU cc_start: 0.7802 (pm20) cc_final: 0.7516 (mp0) REVERT: O 64 LYS cc_start: 0.7559 (mmmt) cc_final: 0.6902 (mmtm) REVERT: O 72 ASP cc_start: 0.7104 (t0) cc_final: 0.6469 (t70) REVERT: O 75 LYS cc_start: 0.8549 (pttm) cc_final: 0.8314 (ptpp) REVERT: O 100 TYR cc_start: 0.7860 (t80) cc_final: 0.7550 (t80) REVERT: Q 4 MET cc_start: 0.7051 (mmm) cc_final: 0.6778 (mmm) REVERT: Q 24 ARG cc_start: 0.7753 (mmm-85) cc_final: 0.7430 (mmm-85) REVERT: Q 42 GLN cc_start: 0.8202 (mm-40) cc_final: 0.7915 (mp10) REVERT: Q 53 THR cc_start: 0.8383 (m) cc_final: 0.7967 (t) REVERT: Q 67 SER cc_start: 0.7866 (t) cc_final: 0.7570 (p) REVERT: Q 71 PHE cc_start: 0.7671 (m-80) cc_final: 0.7313 (m-80) REVERT: Q 85 VAL cc_start: 0.8516 (OUTLIER) cc_final: 0.8301 (p) REVERT: F 290 THR cc_start: 0.8430 (t) cc_final: 0.8142 (m) REVERT: I 158 ASP cc_start: 0.7974 (t0) cc_final: 0.6140 (p0) REVERT: I 163 SER cc_start: 0.8236 (t) cc_final: 0.7987 (m) REVERT: N 5 THR cc_start: 0.8789 (m) cc_final: 0.8379 (p) REVERT: K 82 MET cc_start: 0.8860 (mmt) cc_final: 0.8592 (mmt) REVERT: K 101 GLU cc_start: 0.7889 (pm20) cc_final: 0.7388 (mp0) REVERT: K 102 PHE cc_start: 0.7406 (OUTLIER) cc_final: 0.7060 (p90) REVERT: P 58 TYR cc_start: 0.7826 (m-80) cc_final: 0.7488 (m-80) REVERT: P 64 LYS cc_start: 0.7623 (mmmt) cc_final: 0.6934 (mmtm) REVERT: P 72 ASP cc_start: 0.7403 (t0) cc_final: 0.6919 (t70) REVERT: R 4 MET cc_start: 0.7252 (mmm) cc_final: 0.7017 (tpt) REVERT: R 53 THR cc_start: 0.8478 (m) cc_final: 0.8038 (t) REVERT: R 105 GLU cc_start: 0.3652 (tp30) cc_final: 0.2723 (pm20) outliers start: 41 outliers final: 32 residues processed: 335 average time/residue: 0.1397 time to fit residues: 72.8760 Evaluate side-chains 334 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 297 time to evaluate : 0.552 ------------------------------------------------------------------------------- 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 85 THR 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 24 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain G residue 15 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 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 F residue 190 ASP Chi-restraints excluded: chain N residue 20 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 102 PHE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 188 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 268 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 75 optimal weight: 8.9990 chunk 191 optimal weight: 0.7980 chunk 164 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 chunk 159 optimal weight: 3.9990 chunk 172 optimal weight: 0.6980 chunk 132 optimal weight: 4.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 141 HIS K 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 = 0.3560 r_free = 0.3560 target = 0.090246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.064683 restraints weight = 54685.573| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.80 r_work: 0.2927 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 22686 Z= 0.155 Angle : 0.604 10.397 30816 Z= 0.312 Chirality : 0.042 0.184 3381 Planarity : 0.004 0.073 3927 Dihedral : 4.599 31.405 3042 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.79 % Allowed : 12.71 % Favored : 85.50 % 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: 0.32 (0.16), residues: 2760 helix: 2.88 (0.26), residues: 375 sheet: 0.28 (0.20), residues: 648 loop : -0.41 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 61 TYR 0.019 0.001 TYR A 105 PHE 0.020 0.002 PHE L 71 TRP 0.019 0.001 TRP C 103 HIS 0.005 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (22635) covalent geometry : angle 0.59652 / 0.31 (30693) SS BOND : bond 0.00297 / 0.20 ( 30) SS BOND : angle 1.77081 / 1.24 ( 60) hydrogen bonds : bond 0.03991 / 2.68 ( 894) hydrogen bonds : angle 4.63858 / 3.20 ( 2529) link_BETA1-4 : bond 0.00240 / 0.14 ( 3) link_BETA1-4 : angle 1.00603 / 0.61 ( 9) link_NAG-ASN : bond 0.00181 / 0.11 ( 18) link_NAG-ASN : angle 1.52141 / 0.93 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4667.72 seconds wall clock time: 81 minutes 12.01 seconds (4872.01 seconds total)