Starting phenix.real_space_refine on Thu Jun 19 03:31:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t3d_25655/06_2025/7t3d_25655.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t3d_25655/06_2025/7t3d_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7t3d_25655/06_2025/7t3d_25655.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t3d_25655/06_2025/7t3d_25655.map" model { file = "/net/cci-nas-00/data/ceres_data/7t3d_25655/06_2025/7t3d_25655.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t3d_25655/06_2025/7t3d_25655.cif" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 22122 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2529 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 19, 'TRANS': 304} Chain: "B" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1326 Classifications: {'peptide': 163} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 1, 'TRANS': 161} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 829 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "C" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 900 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "H" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 872 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 3, 'TRANS': 106} Chain: "L" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 820 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: K, J, O, P, U, T, Q, R, E, F, G, I, M, N Time building chain proxies: 10.14, per 1000 atoms: 0.46 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 K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 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: 5.11 Conformation dependent library (CDL) restraints added in 2.9 seconds 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5118 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 66 sheets defined 16.2% alpha, 36.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.83 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: 8.03 Time building geometry restraints manager: 6.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 5426 1.32 - 1.47: 7825 1.47 - 1.61: 9252 1.61 - 1.75: 21 1.75 - 1.89: 111 Bond restraints: 22635 Sorted by residual: bond pdb=" NE1 TRP J 103 " pdb=" CE2 TRP J 103 " ideal model delta sigma weight residual 1.370 1.299 0.071 1.10e-02 8.26e+03 4.16e+01 bond pdb=" NE1 TRP K 103 " pdb=" CE2 TRP K 103 " ideal model delta sigma weight residual 1.370 1.299 0.071 1.10e-02 8.26e+03 4.14e+01 bond pdb=" NE1 TRP C 103 " pdb=" CE2 TRP C 103 " ideal model delta sigma weight residual 1.370 1.299 0.071 1.10e-02 8.26e+03 4.14e+01 bond pdb=" CD2 TRP O 103 " pdb=" CE3 TRP O 103 " ideal model delta sigma weight residual 1.398 1.501 -0.103 1.60e-02 3.91e+03 4.13e+01 bond pdb=" CD2 TRP H 103 " pdb=" CE3 TRP H 103 " ideal model delta sigma weight residual 1.398 1.501 -0.103 1.60e-02 3.91e+03 4.12e+01 ... (remaining 22630 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 26892 2.56 - 5.13: 3266 5.13 - 7.69: 469 7.69 - 10.25: 54 10.25 - 12.81: 12 Bond angle restraints: 30693 Sorted by residual: angle pdb=" N ARG F 255 " pdb=" CA ARG F 255 " pdb=" C ARG F 255 " ideal model delta sigma weight residual 113.43 101.93 11.50 1.26e+00 6.30e-01 8.33e+01 angle pdb=" N ARG A 255 " pdb=" CA ARG A 255 " pdb=" C ARG A 255 " ideal model delta sigma weight residual 113.43 101.93 11.50 1.26e+00 6.30e-01 8.32e+01 angle pdb=" N ARG E 255 " pdb=" CA ARG E 255 " pdb=" C ARG E 255 " ideal model delta sigma weight residual 113.43 101.94 11.49 1.26e+00 6.30e-01 8.31e+01 angle pdb=" N SER J 95 " pdb=" CA SER J 95 " pdb=" C SER J 95 " ideal model delta sigma weight residual 113.16 124.41 -11.25 1.24e+00 6.50e-01 8.23e+01 angle pdb=" N SER K 95 " pdb=" CA SER K 95 " pdb=" C SER K 95 " ideal model delta sigma weight residual 113.16 124.39 -11.23 1.24e+00 6.50e-01 8.20e+01 ... (remaining 30688 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.99: 13184 15.99 - 31.99: 346 31.99 - 47.98: 93 47.98 - 63.97: 81 63.97 - 79.97: 18 Dihedral angle restraints: 13722 sinusoidal: 5682 harmonic: 8040 Sorted by residual: dihedral pdb=" CB CYS K 22 " pdb=" SG CYS K 22 " pdb=" SG CYS K 92 " pdb=" CB CYS K 92 " ideal model delta sinusoidal sigma weight residual 93.00 49.18 43.82 1 1.00e+01 1.00e-02 2.67e+01 dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 92 " pdb=" CB CYS C 92 " ideal model delta sinusoidal sigma weight residual 93.00 49.19 43.81 1 1.00e+01 1.00e-02 2.67e+01 dihedral pdb=" CB CYS J 22 " pdb=" SG CYS J 22 " pdb=" SG CYS J 92 " pdb=" CB CYS J 92 " ideal model delta sinusoidal sigma weight residual 93.00 49.22 43.78 1 1.00e+01 1.00e-02 2.67e+01 ... (remaining 13719 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 2342 0.097 - 0.194: 816 0.194 - 0.291: 136 0.291 - 0.387: 59 0.387 - 0.484: 28 Chirality restraints: 3381 Sorted by residual: chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.33e+02 chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.31e+02 chirality pdb=" C1 NAG T 2 " pdb=" O4 NAG T 1 " pdb=" C2 NAG T 2 " pdb=" O5 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.31e+02 ... (remaining 3378 not shown) Planarity restraints: 3945 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 154 " -0.124 2.00e-02 2.50e+03 1.31e-01 2.15e+02 pdb=" CG ASN B 154 " 0.058 2.00e-02 2.50e+03 pdb=" OD1 ASN B 154 " 0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN B 154 " 0.204 2.00e-02 2.50e+03 pdb=" C1 NAG B 201 " -0.158 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN G 154 " -0.124 2.00e-02 2.50e+03 1.31e-01 2.15e+02 pdb=" CG ASN G 154 " 0.057 2.00e-02 2.50e+03 pdb=" OD1 ASN G 154 " 0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN G 154 " 0.204 2.00e-02 2.50e+03 pdb=" C1 NAG G 201 " -0.158 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN I 154 " 0.124 2.00e-02 2.50e+03 1.31e-01 2.14e+02 pdb=" CG ASN I 154 " -0.057 2.00e-02 2.50e+03 pdb=" OD1 ASN I 154 " -0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN I 154 " -0.204 2.00e-02 2.50e+03 pdb=" C1 NAG I 201 " 0.158 2.00e-02 2.50e+03 ... (remaining 3942 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 591 2.65 - 3.22: 20295 3.22 - 3.78: 35696 3.78 - 4.34: 49314 4.34 - 4.90: 80236 Nonbonded interactions: 186132 Sorted by model distance: nonbonded pdb=" OE1 GLN G 27 " pdb=" CZ2 TRP O 99 " model vdw 2.093 3.340 nonbonded pdb=" OE1 GLN I 27 " pdb=" CZ2 TRP P 99 " model vdw 2.093 3.340 nonbonded pdb=" OE1 GLN B 27 " pdb=" CZ2 TRP H 99 " model vdw 2.093 3.340 nonbonded pdb=" OD2 ASP G 112 " pdb=" NZ LYS G 116 " model vdw 2.401 3.120 nonbonded pdb=" OD2 ASP I 112 " pdb=" NZ LYS I 116 " model vdw 2.401 3.120 ... (remaining 186127 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.15 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'K' selection = chain 'J' } ncs_group { reference = chain 'H' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'S' selection = chain 'U' selection = chain 'T' } ncs_group { reference = chain 'L' selection = chain 'Q' selection = chain 'R' } 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' } 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: 1.950 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: 0.020 Extract box with map and model: 0.780 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 47.580 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.090 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.133 22686 Z= 1.178 Angle : 1.771 12.814 30816 Z= 1.185 Chirality : 0.109 0.484 3381 Planarity : 0.009 0.058 3927 Dihedral : 9.955 79.967 8514 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 1.86 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (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 TRP 0.066 0.009 TRP F 84 HIS 0.011 0.003 HIS I 142 PHE 0.039 0.008 PHE F 118 TYR 0.047 0.009 TYR O 102 ARG 0.013 0.002 ARG H 71 Details of bonding type rmsd link_NAG-ASN : bond 0.08109 ( 18) link_NAG-ASN : angle 2.77266 ( 54) link_BETA1-4 : bond 0.08044 ( 3) link_BETA1-4 : angle 4.98924 ( 9) hydrogen bonds : bond 0.16091 ( 894) hydrogen bonds : angle 7.50698 ( 2529) SS BOND : bond 0.00729 ( 30) SS BOND : angle 2.60863 ( 60) covalent geometry : bond 0.02234 (22635) covalent geometry : angle 1.76460 (30693) *********************** 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 : 2.937 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: 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: 0.7746 (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: 0.7978 (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: 0.6922 (mm-40) REVERT: H 100 TYR cc_start: 0.7801 (t80) cc_final: 0.7433 (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: 0.6344 (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: 0.6581 (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: 0.5341 time to fit residues: 466.1421 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 : 3.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 230 optimal weight: 0.9990 chunk 206 optimal weight: 0.8980 chunk 114 optimal weight: 0.9980 chunk 70 optimal weight: 8.9990 chunk 139 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 213 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 130 optimal weight: 0.7980 chunk 159 optimal weight: 1.9990 chunk 247 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN A 183 HIS ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 HIS D 92 HIS E 159 ASN E 183 HIS G 26 HIS Q 37 GLN F 159 ASN F 183 HIS ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN R 27 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.093744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.067948 restraints weight = 54729.940| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.88 r_work: 0.2993 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2591 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= 0.179 Angle : 0.732 9.385 30816 Z= 0.401 Chirality : 0.044 0.168 3381 Planarity : 0.005 0.072 3927 Dihedral : 5.987 62.326 3483 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.00 % Allowed : 7.88 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 1.71 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.15), residues: 2760 helix: 2.20 (0.25), residues: 378 sheet: 0.34 (0.17), residues: 783 loop : 0.42 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 103 HIS 0.010 0.001 HIS I 72 PHE 0.024 0.002 PHE F 213 TYR 0.016 0.002 TYR I 94 ARG 0.008 0.001 ARG P 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00236 ( 18) link_NAG-ASN : angle 3.49597 ( 54) link_BETA1-4 : bond 0.00267 ( 3) link_BETA1-4 : angle 1.76476 ( 9) hydrogen bonds : bond 0.06027 ( 894) hydrogen bonds : angle 5.86122 ( 2529) SS BOND : bond 0.00380 ( 30) SS BOND : angle 2.10870 ( 60) covalent geometry : bond 0.00404 (22635) covalent geometry : angle 0.71192 (30693) *********************** 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 433 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 385 time to evaluate : 2.296 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: 0.8396 (t0) cc_final: 0.8124 (t0) REVERT: B 158 ASP cc_start: 0.7981 (t0) cc_final: 0.6297 (p0) REVERT: D 4 MET cc_start: 0.8438 (mmm) cc_final: 0.7787 (mmm) REVERT: D 5 THR cc_start: 0.8552 (m) cc_final: 0.8174 (p) REVERT: D 42 LYS cc_start: 0.8977 (mmtp) cc_final: 0.8748 (mmmm) REVERT: C 72 ASP cc_start: 0.8497 (t0) cc_final: 0.7877 (t0) REVERT: C 75 LYS cc_start: 0.8823 (mtmm) cc_final: 0.8299 (mttt) REVERT: H 64 LYS cc_start: 0.7067 (mtmm) cc_final: 0.6704 (mmmt) REVERT: H 93 VAL cc_start: 0.8335 (t) cc_final: 0.8024 (t) REVERT: H 100 TYR cc_start: 0.7786 (t80) cc_final: 0.7396 (t80) REVERT: L 17 GLU cc_start: 0.6990 (tt0) cc_final: 0.6733 (tt0) REVERT: L 42 GLN cc_start: 0.8606 (mm-40) cc_final: 0.7681 (mp10) REVERT: L 58 ILE cc_start: 0.7023 (OUTLIER) cc_final: 0.6433 (mp) REVERT: L 78 LEU cc_start: 0.5856 (tp) cc_final: 0.5011 (tt) REVERT: M 5 THR cc_start: 0.8406 (m) cc_final: 0.8061 (p) REVERT: M 42 LYS cc_start: 0.9009 (mmtp) cc_final: 0.8756 (mmmm) REVERT: M 82 ASP cc_start: 0.8354 (m-30) cc_final: 0.7969 (m-30) REVERT: J 3 GLN cc_start: 0.8629 (tt0) cc_final: 0.8357 (tt0) REVERT: J 5 LEU cc_start: 0.8837 (mp) cc_final: 0.8434 (mp) REVERT: J 96 ASP cc_start: 0.8554 (t0) cc_final: 0.8334 (t0) REVERT: O 64 LYS cc_start: 0.7337 (mtmm) cc_final: 0.7085 (mttp) REVERT: Q 42 GLN cc_start: 0.8637 (mm-40) cc_final: 0.8009 (mp10) REVERT: Q 53 THR cc_start: 0.7377 (m) cc_final: 0.6992 (p) REVERT: Q 54 ARG cc_start: 0.7767 (ptm-80) cc_final: 0.7428 (ptm160) REVERT: Q 78 LEU cc_start: 0.6403 (tp) cc_final: 0.4342 (tt) REVERT: Q 79 GLN cc_start: 0.6891 (mm110) cc_final: 0.6224 (mt0) REVERT: I 17 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.8399 (ttt) REVERT: N 4 MET cc_start: 0.8489 (mmm) cc_final: 0.7692 (mmm) REVERT: N 5 THR cc_start: 0.8529 (m) cc_final: 0.8022 (p) REVERT: N 42 LYS cc_start: 0.9016 (mmtm) cc_final: 0.8758 (mmmm) REVERT: K 101 GLU cc_start: 0.7988 (pm20) cc_final: 0.7415 (mp0) REVERT: P 34 MET cc_start: 0.8742 (mmm) cc_final: 0.7918 (mmp) REVERT: R 17 GLU cc_start: 0.6972 (tt0) cc_final: 0.6699 (tt0) REVERT: R 42 GLN cc_start: 0.8718 (mm-40) cc_final: 0.8141 (mp10) REVERT: R 53 THR cc_start: 0.7678 (m) cc_final: 0.7368 (t) REVERT: R 54 ARG cc_start: 0.7714 (ptm-80) cc_final: 0.7492 (ptm160) REVERT: R 78 LEU cc_start: 0.6558 (tp) cc_final: 0.5219 (tt) REVERT: R 79 GLN cc_start: 0.7066 (mm110) cc_final: 0.6689 (mt0) outliers start: 48 outliers final: 37 residues processed: 410 average time/residue: 0.3529 time to fit residues: 219.3636 Evaluate side-chains 365 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 326 time to evaluate : 2.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 103 TRP Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain L residue 10 THR 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 F residue 159 ASN 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 79 optimal weight: 8.9990 chunk 267 optimal weight: 10.0000 chunk 250 optimal weight: 3.9990 chunk 201 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 121 optimal weight: 0.7980 chunk 205 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 150 optimal weight: 10.0000 chunk 266 optimal weight: 0.9980 chunk 249 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN J 3 GLN O 3 GLN ** I 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 72 HIS R 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.090955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.065067 restraints weight = 54786.530| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.84 r_work: 0.2933 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 22686 Z= 0.208 Angle : 0.663 8.104 30816 Z= 0.358 Chirality : 0.044 0.152 3381 Planarity : 0.005 0.065 3927 Dihedral : 5.567 60.677 3483 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.50 % Allowed : 9.08 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.15), residues: 2760 helix: 2.35 (0.25), residues: 378 sheet: 0.38 (0.17), residues: 750 loop : 0.10 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP J 103 HIS 0.008 0.001 HIS I 72 PHE 0.022 0.002 PHE F 213 TYR 0.015 0.002 TYR P 32 ARG 0.006 0.001 ARG P 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00289 ( 18) link_NAG-ASN : angle 2.65119 ( 54) link_BETA1-4 : bond 0.00287 ( 3) link_BETA1-4 : angle 1.57913 ( 9) hydrogen bonds : bond 0.05203 ( 894) hydrogen bonds : angle 5.38868 ( 2529) SS BOND : bond 0.00400 ( 30) SS BOND : angle 1.16557 ( 60) covalent geometry : bond 0.00492 (22635) covalent geometry : angle 0.65212 (30693) *********************** 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 392 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 332 time to evaluate : 2.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 MET cc_start: 0.8793 (ttp) cc_final: 0.8356 (ttm) REVERT: B 158 ASP cc_start: 0.8052 (t0) cc_final: 0.6483 (p0) REVERT: B 163 SER cc_start: 0.8330 (t) cc_final: 0.7969 (m) REVERT: D 4 MET cc_start: 0.8592 (mmm) cc_final: 0.8280 (mmm) REVERT: D 5 THR cc_start: 0.8651 (m) cc_final: 0.8306 (p) REVERT: C 72 ASP cc_start: 0.8519 (t0) cc_final: 0.7976 (t0) REVERT: C 75 LYS cc_start: 0.8921 (mtmm) cc_final: 0.8415 (mttt) REVERT: C 102 PHE cc_start: 0.7781 (OUTLIER) cc_final: 0.6743 (p90) REVERT: H 34 MET cc_start: 0.8551 (mmm) cc_final: 0.8284 (mmm) REVERT: H 93 VAL cc_start: 0.8399 (t) cc_final: 0.7996 (t) REVERT: H 100 TYR cc_start: 0.7926 (t80) cc_final: 0.7654 (t80) REVERT: H 102 TYR cc_start: 0.6729 (m-10) cc_final: 0.6497 (m-10) REVERT: L 4 MET cc_start: 0.7710 (tpp) cc_final: 0.7459 (tpt) REVERT: L 58 ILE cc_start: 0.7011 (OUTLIER) cc_final: 0.6399 (mp) REVERT: G 163 SER cc_start: 0.8403 (t) cc_final: 0.8079 (m) REVERT: M 5 THR cc_start: 0.8546 (m) cc_final: 0.8224 (p) REVERT: J 3 GLN cc_start: 0.8723 (tt0) cc_final: 0.8446 (tt0) REVERT: J 5 LEU cc_start: 0.8863 (mp) cc_final: 0.8430 (mp) REVERT: O 64 LYS cc_start: 0.7248 (mtmm) cc_final: 0.6847 (mmmt) REVERT: Q 24 ARG cc_start: 0.8175 (mmm-85) cc_final: 0.7914 (mmm-85) REVERT: Q 42 GLN cc_start: 0.8555 (mm-40) cc_final: 0.7971 (mp10) REVERT: Q 53 THR cc_start: 0.7852 (m) cc_final: 0.7573 (t) REVERT: Q 54 ARG cc_start: 0.7725 (ptm-80) cc_final: 0.7302 (mtm110) REVERT: Q 71 PHE cc_start: 0.7497 (m-80) cc_final: 0.7115 (m-80) REVERT: Q 85 VAL cc_start: 0.8471 (OUTLIER) cc_final: 0.8202 (p) REVERT: F 56 VAL cc_start: 0.9058 (OUTLIER) cc_final: 0.8578 (m) REVERT: N 5 THR cc_start: 0.8793 (m) cc_final: 0.8390 (p) REVERT: K 6 GLU cc_start: 0.7649 (mp0) cc_final: 0.7206 (mp0) REVERT: K 101 GLU cc_start: 0.8013 (pm20) cc_final: 0.7583 (mp0) REVERT: K 102 PHE cc_start: 0.7676 (OUTLIER) cc_final: 0.7179 (p90) REVERT: P 34 MET cc_start: 0.8764 (mmm) cc_final: 0.7646 (mmp) REVERT: R 42 GLN cc_start: 0.8600 (mm-40) cc_final: 0.8054 (mp10) REVERT: R 53 THR cc_start: 0.7844 (m) cc_final: 0.7543 (t) REVERT: R 54 ARG cc_start: 0.7758 (ptm-80) cc_final: 0.7377 (mtm110) outliers start: 60 outliers final: 33 residues processed: 363 average time/residue: 0.3646 time to fit residues: 204.7547 Evaluate side-chains 327 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 289 time to evaluate : 2.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 102 PHE Chi-restraints excluded: chain C residue 103 TRP Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain E residue 84 TRP Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain J residue 50 MET Chi-restraints excluded: chain J residue 103 TRP Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain Q residue 5 THR Chi-restraints excluded: chain Q residue 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 F residue 84 TRP 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 N residue 72 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 24 VAL Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 104 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 228 optimal weight: 6.9990 chunk 234 optimal weight: 0.0170 chunk 66 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 213 optimal weight: 4.9990 chunk 86 optimal weight: 0.0670 chunk 90 optimal weight: 1.9990 chunk 198 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 162 optimal weight: 5.9990 overall best weight: 1.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 GLN M 32 HIS F 159 ASN ** I 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 32 HIS K 3 GLN K 56 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.089657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.063977 restraints weight = 55371.807| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.84 r_work: 0.2903 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 22686 Z= 0.174 Angle : 0.611 9.680 30816 Z= 0.325 Chirality : 0.043 0.146 3381 Planarity : 0.005 0.068 3927 Dihedral : 5.229 56.789 3483 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.00 % Allowed : 10.08 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.15), residues: 2760 helix: 2.50 (0.25), residues: 378 sheet: 0.46 (0.18), residues: 717 loop : -0.04 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP J 103 HIS 0.005 0.001 HIS E 18 PHE 0.017 0.002 PHE F 213 TYR 0.019 0.001 TYR H 32 ARG 0.007 0.001 ARG O 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00257 ( 18) link_NAG-ASN : angle 2.23703 ( 54) link_BETA1-4 : bond 0.00150 ( 3) link_BETA1-4 : angle 1.35960 ( 9) hydrogen bonds : bond 0.04732 ( 894) hydrogen bonds : angle 5.10593 ( 2529) SS BOND : bond 0.00398 ( 30) SS BOND : angle 1.61506 ( 60) covalent geometry : bond 0.00412 (22635) covalent geometry : angle 0.60006 (30693) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 317 time to evaluate : 2.416 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: 0.9153 (OUTLIER) cc_final: 0.8788 (m) REVERT: B 158 ASP cc_start: 0.8077 (t0) cc_final: 0.6580 (p0) REVERT: B 163 SER cc_start: 0.8437 (t) cc_final: 0.8058 (m) REVERT: D 5 THR cc_start: 0.8688 (m) cc_final: 0.8371 (p) REVERT: C 72 ASP cc_start: 0.8545 (t0) cc_final: 0.8030 (t0) REVERT: C 75 LYS cc_start: 0.8957 (mtmm) cc_final: 0.8481 (mttt) REVERT: C 102 PHE cc_start: 0.7740 (OUTLIER) cc_final: 0.6669 (p90) REVERT: H 93 VAL cc_start: 0.8291 (t) cc_final: 0.7984 (t) REVERT: H 100 TYR cc_start: 0.7818 (t80) cc_final: 0.7562 (t80) REVERT: H 102 TYR cc_start: 0.6752 (m-10) cc_final: 0.6547 (m-10) REVERT: L 58 ILE cc_start: 0.7096 (OUTLIER) cc_final: 0.6511 (mp) REVERT: E 105 TYR cc_start: 0.9022 (t80) cc_final: 0.8774 (t80) REVERT: G 163 SER cc_start: 0.8345 (t) cc_final: 0.8003 (m) REVERT: M 5 THR cc_start: 0.8591 (m) cc_final: 0.8282 (p) REVERT: J 5 LEU cc_start: 0.8886 (mp) cc_final: 0.8603 (mt) REVERT: J 101 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7638 (mp0) REVERT: O 64 LYS cc_start: 0.7217 (mtmm) cc_final: 0.6889 (mmmt) REVERT: Q 2 ILE cc_start: 0.8826 (mp) cc_final: 0.8595 (mm) REVERT: Q 42 GLN cc_start: 0.8446 (mm-40) cc_final: 0.7900 (mp10) REVERT: Q 53 THR cc_start: 0.8060 (m) cc_final: 0.7771 (t) REVERT: Q 54 ARG cc_start: 0.7623 (ptm-80) cc_final: 0.7204 (mtm110) REVERT: Q 71 PHE cc_start: 0.7543 (m-80) cc_final: 0.7286 (m-80) REVERT: Q 85 VAL cc_start: 0.8508 (OUTLIER) cc_final: 0.8253 (p) REVERT: F 56 VAL cc_start: 0.9128 (OUTLIER) cc_final: 0.8872 (m) REVERT: N 4 MET cc_start: 0.8536 (mmm) cc_final: 0.7528 (mmm) REVERT: N 5 THR cc_start: 0.8788 (m) cc_final: 0.8367 (p) REVERT: K 13 GLN cc_start: 0.7717 (mm-40) cc_final: 0.7243 (pm20) REVERT: K 101 GLU cc_start: 0.7969 (pm20) cc_final: 0.7655 (mp0) REVERT: K 102 PHE cc_start: 0.7495 (OUTLIER) cc_final: 0.7124 (p90) REVERT: R 4 MET cc_start: 0.7663 (tpt) cc_final: 0.7234 (tpp) REVERT: R 24 ARG cc_start: 0.6562 (mmp80) cc_final: 0.6345 (mmp80) REVERT: R 42 GLN cc_start: 0.8532 (mm-40) cc_final: 0.8077 (mp10) REVERT: R 53 THR cc_start: 0.7994 (m) cc_final: 0.7689 (t) REVERT: R 54 ARG cc_start: 0.7829 (ptm-80) cc_final: 0.7443 (mtm110) outliers start: 48 outliers final: 34 residues processed: 340 average time/residue: 0.3515 time to fit residues: 182.7337 Evaluate side-chains 320 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 279 time to evaluate : 2.377 ------------------------------------------------------------------------------- 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 B residue 40 SER Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 102 PHE Chi-restraints excluded: chain C residue 103 TRP Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain L residue 58 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 G residue 15 THR Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain J residue 50 MET Chi-restraints excluded: chain J residue 101 GLU 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 85 VAL Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain F residue 56 VAL 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 24 VAL Chi-restraints excluded: chain P residue 92 CYS Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 104 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 92 optimal weight: 5.9990 chunk 193 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 189 optimal weight: 0.8980 chunk 178 optimal weight: 20.0000 chunk 98 optimal weight: 3.9990 chunk 82 optimal weight: 40.0000 chunk 269 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 ASN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 79 GLN J 3 GLN O 76 ASN I 26 HIS I 30 GLN N 79 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.087896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.062281 restraints weight = 55531.793| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 2.80 r_work: 0.2867 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 22686 Z= 0.223 Angle : 0.640 10.199 30816 Z= 0.337 Chirality : 0.043 0.152 3381 Planarity : 0.005 0.071 3927 Dihedral : 5.156 50.907 3483 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.58 % Allowed : 10.50 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.15), residues: 2760 helix: 2.44 (0.25), residues: 375 sheet: 0.26 (0.18), residues: 726 loop : -0.22 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 103 HIS 0.007 0.001 HIS E 18 PHE 0.018 0.002 PHE F 213 TYR 0.022 0.002 TYR P 32 ARG 0.009 0.001 ARG L 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00331 ( 18) link_NAG-ASN : angle 2.24814 ( 54) link_BETA1-4 : bond 0.00110 ( 3) link_BETA1-4 : angle 1.41766 ( 9) hydrogen bonds : bond 0.04742 ( 894) hydrogen bonds : angle 5.10913 ( 2529) SS BOND : bond 0.00391 ( 30) SS BOND : angle 1.65717 ( 60) covalent geometry : bond 0.00536 (22635) covalent geometry : angle 0.62999 (30693) *********************** 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 376 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 314 time to evaluate : 2.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 VAL cc_start: 0.9239 (OUTLIER) cc_final: 0.8928 (m) REVERT: B 163 SER cc_start: 0.8511 (t) cc_final: 0.8046 (m) REVERT: D 4 MET cc_start: 0.8599 (mmm) cc_final: 0.8274 (mmm) REVERT: D 5 THR cc_start: 0.8642 (m) cc_final: 0.8315 (p) REVERT: D 81 GLU cc_start: 0.8918 (pm20) cc_final: 0.8689 (pm20) REVERT: C 72 ASP cc_start: 0.8578 (t0) cc_final: 0.8056 (t0) REVERT: C 75 LYS cc_start: 0.9069 (mtmm) cc_final: 0.8584 (mttt) REVERT: C 102 PHE cc_start: 0.7881 (OUTLIER) cc_final: 0.6570 (p90) REVERT: H 64 LYS cc_start: 0.7973 (mmmt) cc_final: 0.7549 (mmtm) REVERT: H 72 ASP cc_start: 0.6757 (t0) cc_final: 0.5921 (t0) REVERT: H 75 LYS cc_start: 0.8955 (pttm) cc_final: 0.8592 (pttm) REVERT: L 4 MET cc_start: 0.7168 (mmm) cc_final: 0.6356 (tpt) REVERT: L 42 GLN cc_start: 0.8502 (mm-40) cc_final: 0.7983 (mm-40) REVERT: L 58 ILE cc_start: 0.7166 (OUTLIER) cc_final: 0.6629 (mp) REVERT: L 72 THR cc_start: 0.7919 (m) cc_final: 0.7617 (p) REVERT: G 163 SER cc_start: 0.8461 (t) cc_final: 0.8051 (m) REVERT: M 5 THR cc_start: 0.8646 (m) cc_final: 0.8290 (p) REVERT: M 14 PHE cc_start: 0.7462 (p90) cc_final: 0.7168 (p90) REVERT: J 5 LEU cc_start: 0.8895 (mp) cc_final: 0.8628 (mp) REVERT: O 64 LYS cc_start: 0.7309 (OUTLIER) cc_final: 0.7049 (mmmt) REVERT: O 72 ASP cc_start: 0.6997 (t0) cc_final: 0.6335 (t70) REVERT: Q 1 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7270 (mt-10) REVERT: Q 2 ILE cc_start: 0.8888 (mp) cc_final: 0.8601 (mm) REVERT: Q 42 GLN cc_start: 0.8395 (mm-40) cc_final: 0.7883 (mp10) REVERT: Q 53 THR cc_start: 0.8064 (m) cc_final: 0.7710 (t) REVERT: Q 54 ARG cc_start: 0.7750 (ptm-80) cc_final: 0.7334 (mtm110) REVERT: Q 61 ARG cc_start: 0.8225 (ttp-110) cc_final: 0.7999 (mtp-110) REVERT: Q 70 GLU cc_start: 0.8041 (tp30) cc_final: 0.7618 (tp30) REVERT: Q 71 PHE cc_start: 0.7505 (m-80) cc_final: 0.7157 (m-80) REVERT: Q 79 GLN cc_start: 0.7184 (mm-40) cc_final: 0.6713 (mt0) REVERT: Q 85 VAL cc_start: 0.8557 (OUTLIER) cc_final: 0.8291 (p) REVERT: N 4 MET cc_start: 0.8602 (mmm) cc_final: 0.8209 (mmm) REVERT: N 5 THR cc_start: 0.8886 (m) cc_final: 0.8448 (p) REVERT: K 82 LEU cc_start: 0.8484 (mm) cc_final: 0.8204 (mm) REVERT: K 101 GLU cc_start: 0.8450 (pm20) cc_final: 0.8016 (mp0) REVERT: R 4 MET cc_start: 0.7954 (tpt) cc_final: 0.7627 (tpp) REVERT: R 42 GLN cc_start: 0.8449 (mm-40) cc_final: 0.8227 (mm-40) REVERT: R 53 THR cc_start: 0.8057 (m) cc_final: 0.7550 (t) REVERT: R 54 ARG cc_start: 0.7997 (ptm-80) cc_final: 0.7470 (ttm-80) outliers start: 62 outliers final: 48 residues processed: 353 average time/residue: 0.3387 time to fit residues: 183.9973 Evaluate side-chains 339 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 286 time to evaluate : 2.349 ------------------------------------------------------------------------------- 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 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 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 L residue 5 THR Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain E residue 84 TRP Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 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 102 PHE Chi-restraints excluded: chain J residue 103 TRP Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 64 LYS Chi-restraints excluded: chain Q residue 5 THR Chi-restraints excluded: chain Q residue 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 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 5 THR Chi-restraints excluded: chain R residue 75 ILE 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 217 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 187 optimal weight: 2.9990 chunk 222 optimal weight: 1.9990 chunk 121 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 chunk 56 optimal weight: 8.9990 chunk 17 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN J 3 GLN F 159 ASN K 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.090157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.064615 restraints weight = 54981.920| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.82 r_work: 0.2924 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 22686 Z= 0.134 Angle : 0.580 10.487 30816 Z= 0.305 Chirality : 0.041 0.148 3381 Planarity : 0.005 0.075 3927 Dihedral : 4.902 46.481 3483 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.25 % Allowed : 11.25 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.15), residues: 2760 helix: 2.67 (0.25), residues: 375 sheet: 0.41 (0.19), residues: 702 loop : -0.28 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 103 HIS 0.005 0.001 HIS E 18 PHE 0.014 0.001 PHE F 213 TYR 0.020 0.001 TYR P 32 ARG 0.011 0.000 ARG P 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00215 ( 18) link_NAG-ASN : angle 1.94136 ( 54) link_BETA1-4 : bond 0.00253 ( 3) link_BETA1-4 : angle 1.23393 ( 9) hydrogen bonds : bond 0.04288 ( 894) hydrogen bonds : angle 4.88015 ( 2529) SS BOND : bond 0.00275 ( 30) SS BOND : angle 1.56587 ( 60) covalent geometry : bond 0.00315 (22635) covalent geometry : angle 0.57107 (30693) *********************** 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 369 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 315 time to evaluate : 2.307 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: 0.8504 (OUTLIER) cc_final: 0.8287 (t0) REVERT: B 19 ASP cc_start: 0.7656 (p0) cc_final: 0.7388 (p0) REVERT: B 158 ASP cc_start: 0.7988 (t0) cc_final: 0.6137 (p0) REVERT: B 163 SER cc_start: 0.8358 (t) cc_final: 0.7992 (m) REVERT: D 5 THR cc_start: 0.8735 (m) cc_final: 0.8472 (p) REVERT: D 81 GLU cc_start: 0.8969 (pm20) cc_final: 0.8704 (pm20) REVERT: C 72 ASP cc_start: 0.8585 (t0) cc_final: 0.8112 (t0) REVERT: C 75 LYS cc_start: 0.9038 (mtmm) cc_final: 0.8558 (mttt) REVERT: C 102 PHE cc_start: 0.7709 (OUTLIER) cc_final: 0.6661 (p90) REVERT: H 72 ASP cc_start: 0.6739 (t0) cc_final: 0.5731 (t0) REVERT: H 75 LYS cc_start: 0.8887 (pttm) cc_final: 0.8515 (pttm) REVERT: L 4 MET cc_start: 0.7448 (mmm) cc_final: 0.6836 (tpt) REVERT: L 54 ARG cc_start: 0.8395 (ptm-80) cc_final: 0.8029 (mtp-110) REVERT: G 62 GLN cc_start: 0.8427 (mp10) cc_final: 0.8083 (mp10) REVERT: G 163 SER cc_start: 0.8296 (t) cc_final: 0.7992 (m) REVERT: M 5 THR cc_start: 0.8706 (m) cc_final: 0.8390 (p) REVERT: M 14 PHE cc_start: 0.7397 (p90) cc_final: 0.7075 (p90) REVERT: J 5 LEU cc_start: 0.8919 (mp) cc_final: 0.8645 (mt) REVERT: O 64 LYS cc_start: 0.7243 (OUTLIER) cc_final: 0.7036 (mmmt) REVERT: O 72 ASP cc_start: 0.7002 (t0) cc_final: 0.6486 (t70) REVERT: Q 2 ILE cc_start: 0.8934 (mp) cc_final: 0.8668 (mm) REVERT: Q 24 ARG cc_start: 0.7285 (mmm-85) cc_final: 0.6962 (mmm-85) REVERT: Q 42 GLN cc_start: 0.8391 (mm-40) cc_final: 0.8048 (mp10) REVERT: Q 53 THR cc_start: 0.8191 (m) cc_final: 0.7862 (t) REVERT: Q 61 ARG cc_start: 0.8253 (ttp-110) cc_final: 0.8030 (ttp-110) REVERT: Q 71 PHE cc_start: 0.7608 (m-80) cc_final: 0.7227 (m-80) REVERT: Q 85 VAL cc_start: 0.8461 (OUTLIER) cc_final: 0.8184 (p) REVERT: I 163 SER cc_start: 0.8190 (t) cc_final: 0.7935 (m) REVERT: N 4 MET cc_start: 0.8511 (mmm) cc_final: 0.8264 (mmm) REVERT: N 5 THR cc_start: 0.8859 (m) cc_final: 0.8467 (p) REVERT: K 101 GLU cc_start: 0.7956 (pm20) cc_final: 0.7667 (mp0) REVERT: P 72 ASP cc_start: 0.6776 (t0) cc_final: 0.6162 (t70) REVERT: R 4 MET cc_start: 0.7803 (tpt) cc_final: 0.7496 (tpt) REVERT: R 53 THR cc_start: 0.8192 (m) cc_final: 0.7749 (t) REVERT: R 54 ARG cc_start: 0.7837 (ptm-80) cc_final: 0.7597 (ttm110) outliers start: 54 outliers final: 37 residues processed: 350 average time/residue: 0.3537 time to fit residues: 189.1873 Evaluate side-chains 331 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 290 time to evaluate : 2.429 ------------------------------------------------------------------------------- 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 L residue 5 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain E residue 84 TRP Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain 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 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 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 250 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 264 optimal weight: 5.9990 chunk 243 optimal weight: 7.9990 chunk 221 optimal weight: 1.9990 chunk 195 optimal weight: 7.9990 chunk 258 optimal weight: 0.0870 chunk 63 optimal weight: 6.9990 chunk 246 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN J 3 GLN Q 92 ASN F 159 ASN K 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.087710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.062196 restraints weight = 55454.237| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.80 r_work: 0.2869 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 22686 Z= 0.253 Angle : 0.653 9.499 30816 Z= 0.341 Chirality : 0.044 0.146 3381 Planarity : 0.005 0.075 3927 Dihedral : 5.069 43.977 3483 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.50 % Allowed : 11.67 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.15), residues: 2760 helix: 2.31 (0.26), residues: 372 sheet: 0.30 (0.19), residues: 699 loop : -0.39 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 103 HIS 0.006 0.001 HIS E 18 PHE 0.019 0.002 PHE F 213 TYR 0.017 0.002 TYR P 32 ARG 0.006 0.001 ARG P 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00396 ( 18) link_NAG-ASN : angle 2.16199 ( 54) link_BETA1-4 : bond 0.00149 ( 3) link_BETA1-4 : angle 1.47289 ( 9) hydrogen bonds : bond 0.04688 ( 894) hydrogen bonds : angle 5.03911 ( 2529) SS BOND : bond 0.00443 ( 30) SS BOND : angle 1.53799 ( 60) covalent geometry : bond 0.00611 (22635) covalent geometry : angle 0.64357 (30693) *********************** 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 364 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 304 time to evaluate : 2.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 VAL cc_start: 0.9326 (OUTLIER) cc_final: 0.9071 (m) REVERT: A 101 ASP cc_start: 0.8798 (OUTLIER) cc_final: 0.8588 (t0) REVERT: B 19 ASP cc_start: 0.8089 (p0) cc_final: 0.7786 (p0) REVERT: B 163 SER cc_start: 0.8480 (t) cc_final: 0.8047 (m) REVERT: D 5 THR cc_start: 0.8731 (m) cc_final: 0.8354 (p) REVERT: D 81 GLU cc_start: 0.9067 (pm20) cc_final: 0.8774 (pm20) REVERT: C 72 ASP cc_start: 0.8702 (t0) cc_final: 0.8192 (t0) REVERT: C 75 LYS cc_start: 0.9175 (mtmm) cc_final: 0.8670 (mttt) REVERT: C 102 PHE cc_start: 0.7966 (OUTLIER) cc_final: 0.6554 (p90) REVERT: H 34 MET cc_start: 0.8816 (mmm) cc_final: 0.8158 (mmm) REVERT: H 64 LYS cc_start: 0.8033 (mmmt) cc_final: 0.7455 (mmtm) REVERT: H 72 ASP cc_start: 0.6951 (t0) cc_final: 0.6276 (t0) REVERT: H 75 LYS cc_start: 0.8873 (pttm) cc_final: 0.8530 (pttm) REVERT: L 4 MET cc_start: 0.7523 (mmm) cc_final: 0.6879 (tpt) REVERT: L 42 GLN cc_start: 0.8349 (mm-40) cc_final: 0.7727 (mm-40) REVERT: L 54 ARG cc_start: 0.8407 (ptm-80) cc_final: 0.7846 (mtp-110) REVERT: L 79 GLN cc_start: 0.8290 (mt0) cc_final: 0.7979 (mt0) REVERT: G 62 GLN cc_start: 0.8649 (mp10) cc_final: 0.8290 (mp10) REVERT: G 158 ASP cc_start: 0.8095 (t0) cc_final: 0.6267 (p0) REVERT: G 163 SER cc_start: 0.8347 (t) cc_final: 0.7959 (m) REVERT: M 5 THR cc_start: 0.8793 (m) cc_final: 0.8465 (p) REVERT: J 5 LEU cc_start: 0.8959 (mp) cc_final: 0.8699 (mp) REVERT: O 72 ASP cc_start: 0.7200 (t0) cc_final: 0.6600 (t70) REVERT: O 75 LYS cc_start: 0.8703 (pttm) cc_final: 0.8486 (pttm) REVERT: Q 1 GLU cc_start: 0.7220 (mt-10) cc_final: 0.6913 (mt-10) REVERT: Q 24 ARG cc_start: 0.7615 (mmm-85) cc_final: 0.7122 (mmm-85) REVERT: Q 42 GLN cc_start: 0.8331 (mm-40) cc_final: 0.8002 (mp10) REVERT: Q 53 THR cc_start: 0.8301 (m) cc_final: 0.7897 (t) REVERT: Q 54 ARG cc_start: 0.7805 (ptm-80) cc_final: 0.7426 (ttm110) REVERT: Q 61 ARG cc_start: 0.8258 (ttp-110) cc_final: 0.7987 (mtp-110) REVERT: Q 71 PHE cc_start: 0.7650 (m-80) cc_final: 0.7286 (m-80) REVERT: Q 85 VAL cc_start: 0.8584 (OUTLIER) cc_final: 0.8356 (p) REVERT: Q 105 GLU cc_start: 0.6176 (OUTLIER) cc_final: 0.5946 (pm20) REVERT: N 4 MET cc_start: 0.8685 (mmm) cc_final: 0.8387 (mmm) REVERT: N 5 THR cc_start: 0.8916 (m) cc_final: 0.8530 (p) REVERT: K 101 GLU cc_start: 0.8309 (pm20) cc_final: 0.7878 (mp0) REVERT: P 34 MET cc_start: 0.9045 (mmm) cc_final: 0.8663 (mmm) REVERT: P 58 TYR cc_start: 0.8016 (m-80) cc_final: 0.7723 (m-80) REVERT: P 72 ASP cc_start: 0.7188 (t0) cc_final: 0.6744 (t0) REVERT: R 2 ILE cc_start: 0.8785 (mp) cc_final: 0.8570 (mt) REVERT: R 4 MET cc_start: 0.7935 (tpt) cc_final: 0.7610 (tpt) REVERT: R 42 GLN cc_start: 0.7928 (mm-40) cc_final: 0.7702 (mp-120) REVERT: R 54 ARG cc_start: 0.7864 (ptm-80) cc_final: 0.7435 (ttm-80) outliers start: 60 outliers final: 46 residues processed: 345 average time/residue: 0.3482 time to fit residues: 185.8970 Evaluate side-chains 333 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 282 time to evaluate : 2.355 ------------------------------------------------------------------------------- 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 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 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 68 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain E residue 84 TRP Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain 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 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 Q residue 105 GLU Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 84 TRP Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 50 MET Chi-restraints excluded: chain K residue 103 TRP Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain P residue 92 CYS Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 89 optimal weight: 5.9990 chunk 224 optimal weight: 0.9980 chunk 144 optimal weight: 0.8980 chunk 233 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 191 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 229 optimal weight: 10.0000 chunk 252 optimal weight: 9.9990 chunk 151 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 27 GLN J 3 GLN K 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.090126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.064557 restraints weight = 54916.076| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.82 r_work: 0.2923 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.4305 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 : 0.592 9.933 30816 Z= 0.309 Chirality : 0.042 0.216 3381 Planarity : 0.004 0.076 3927 Dihedral : 4.769 39.458 3483 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.83 % Allowed : 12.75 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.16), residues: 2760 helix: 2.64 (0.26), residues: 372 sheet: 0.25 (0.19), residues: 717 loop : -0.37 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 103 HIS 0.004 0.001 HIS E 18 PHE 0.019 0.001 PHE R 71 TYR 0.019 0.001 TYR H 32 ARG 0.006 0.000 ARG P 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00223 ( 18) link_NAG-ASN : angle 1.77965 ( 54) link_BETA1-4 : bond 0.00254 ( 3) link_BETA1-4 : angle 1.12816 ( 9) hydrogen bonds : bond 0.04111 ( 894) hydrogen bonds : angle 4.79747 ( 2529) SS BOND : bond 0.00527 ( 30) SS BOND : angle 1.48408 ( 60) covalent geometry : bond 0.00301 (22635) covalent geometry : angle 0.58445 (30693) *********************** 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 368 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 324 time to evaluate : 2.674 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: A 101 ASP cc_start: 0.8818 (OUTLIER) cc_final: 0.8567 (t0) REVERT: B 19 ASP cc_start: 0.8073 (p0) cc_final: 0.7752 (p0) REVERT: B 158 ASP cc_start: 0.8109 (t0) cc_final: 0.6331 (p0) REVERT: B 163 SER cc_start: 0.8415 (t) cc_final: 0.7995 (m) REVERT: D 81 GLU cc_start: 0.9084 (pm20) cc_final: 0.8763 (pm20) REVERT: C 72 ASP cc_start: 0.8579 (t0) cc_final: 0.8060 (t0) REVERT: C 75 LYS cc_start: 0.9113 (mtmm) cc_final: 0.8605 (mttt) REVERT: C 101 GLU cc_start: 0.8239 (pm20) cc_final: 0.7938 (mp0) REVERT: C 102 PHE cc_start: 0.7810 (OUTLIER) cc_final: 0.6804 (p90) REVERT: H 34 MET cc_start: 0.8760 (mmm) cc_final: 0.8091 (mmm) REVERT: H 64 LYS cc_start: 0.7956 (mmmt) cc_final: 0.7461 (mmtm) REVERT: H 72 ASP cc_start: 0.6937 (t0) cc_final: 0.6407 (t70) REVERT: L 4 MET cc_start: 0.7480 (mmm) cc_final: 0.6814 (tpt) REVERT: L 54 ARG cc_start: 0.8482 (ptm-80) cc_final: 0.8138 (mtm110) REVERT: L 72 THR cc_start: 0.8001 (m) cc_final: 0.7635 (p) REVERT: L 85 VAL cc_start: 0.8556 (OUTLIER) cc_final: 0.8294 (p) REVERT: L 105 GLU cc_start: 0.3764 (tp30) cc_final: 0.3010 (pm20) REVERT: G 62 GLN cc_start: 0.8616 (mp10) cc_final: 0.8259 (mp10) REVERT: G 158 ASP cc_start: 0.8171 (t0) cc_final: 0.6285 (p0) REVERT: G 163 SER cc_start: 0.8302 (t) cc_final: 0.7914 (m) REVERT: M 5 THR cc_start: 0.8786 (m) cc_final: 0.8463 (p) REVERT: J 5 LEU cc_start: 0.8919 (mp) cc_final: 0.8650 (mt) REVERT: J 101 GLU cc_start: 0.8010 (pm20) cc_final: 0.7701 (mp0) REVERT: O 64 LYS cc_start: 0.7748 (mmmt) cc_final: 0.7350 (mmtm) REVERT: O 72 ASP cc_start: 0.7171 (t0) cc_final: 0.6550 (t70) REVERT: O 75 LYS cc_start: 0.8586 (pttm) cc_final: 0.8333 (ptpp) REVERT: Q 1 GLU cc_start: 0.7214 (mt-10) cc_final: 0.6816 (mt-10) REVERT: Q 24 ARG cc_start: 0.7708 (mmm-85) cc_final: 0.7275 (mmm-85) REVERT: Q 42 GLN cc_start: 0.8291 (mm-40) cc_final: 0.8015 (mp10) REVERT: Q 49 TYR cc_start: 0.8311 (p90) cc_final: 0.8030 (p90) REVERT: Q 53 THR cc_start: 0.8284 (m) cc_final: 0.7797 (t) REVERT: Q 54 ARG cc_start: 0.7766 (ptm-80) cc_final: 0.7432 (ttm110) REVERT: Q 71 PHE cc_start: 0.7638 (m-80) cc_final: 0.7255 (m-80) REVERT: Q 85 VAL cc_start: 0.8531 (OUTLIER) cc_final: 0.8306 (p) REVERT: Q 105 GLU cc_start: 0.6193 (OUTLIER) cc_final: 0.5973 (pm20) REVERT: I 163 SER cc_start: 0.8247 (t) cc_final: 0.7968 (m) REVERT: N 4 MET cc_start: 0.8537 (mmm) cc_final: 0.8328 (mmm) REVERT: N 5 THR cc_start: 0.8870 (m) cc_final: 0.8477 (p) REVERT: P 58 TYR cc_start: 0.7911 (m-80) cc_final: 0.7615 (m-80) REVERT: P 72 ASP cc_start: 0.7068 (t0) cc_final: 0.6448 (t70) REVERT: P 75 LYS cc_start: 0.8516 (pttm) cc_final: 0.8293 (pttm) REVERT: R 4 MET cc_start: 0.7865 (tpt) cc_final: 0.7495 (tpt) REVERT: R 105 GLU cc_start: 0.3867 (tp30) cc_final: 0.2982 (pm20) outliers start: 44 outliers final: 30 residues processed: 347 average time/residue: 0.4170 time to fit residues: 225.9448 Evaluate side-chains 332 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 297 time to evaluate : 3.080 ------------------------------------------------------------------------------- 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 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 68 THR 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 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 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 F residue 84 TRP Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 50 MET Chi-restraints excluded: chain K residue 103 TRP Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain P residue 92 CYS Chi-restraints excluded: chain R residue 104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 146 optimal weight: 1.9990 chunk 186 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 37 optimal weight: 0.9980 chunk 153 optimal weight: 0.7980 chunk 133 optimal weight: 0.9990 chunk 220 optimal weight: 2.9990 chunk 219 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 157 optimal weight: 8.9990 chunk 135 optimal weight: 6.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 92 ASN J 3 GLN K 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.089406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.063813 restraints weight = 54901.147| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.80 r_work: 0.2914 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.4422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 22686 Z= 0.166 Angle : 0.614 9.439 30816 Z= 0.320 Chirality : 0.042 0.169 3381 Planarity : 0.005 0.076 3927 Dihedral : 4.750 36.928 3483 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.83 % Allowed : 12.75 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.16), residues: 2760 helix: 2.60 (0.26), residues: 372 sheet: 0.21 (0.19), residues: 717 loop : -0.41 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 103 HIS 0.005 0.001 HIS E 18 PHE 0.021 0.002 PHE J 67 TYR 0.017 0.001 TYR H 32 ARG 0.008 0.000 ARG H 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00255 ( 18) link_NAG-ASN : angle 1.81943 ( 54) link_BETA1-4 : bond 0.00214 ( 3) link_BETA1-4 : angle 1.22796 ( 9) hydrogen bonds : bond 0.04222 ( 894) hydrogen bonds : angle 4.82077 ( 2529) SS BOND : bond 0.00327 ( 30) SS BOND : angle 1.83090 ( 60) covalent geometry : bond 0.00399 (22635) covalent geometry : angle 0.60513 (30693) *********************** 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 351 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 307 time to evaluate : 2.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 ASP cc_start: 0.8065 (p0) cc_final: 0.7725 (p0) REVERT: B 158 ASP cc_start: 0.8131 (t0) cc_final: 0.6350 (p0) REVERT: B 163 SER cc_start: 0.8425 (t) cc_final: 0.8021 (m) REVERT: D 81 GLU cc_start: 0.9101 (pm20) cc_final: 0.8750 (pm20) REVERT: D 105 GLU cc_start: 0.5310 (OUTLIER) cc_final: 0.5011 (tm-30) REVERT: C 3 GLN cc_start: 0.8945 (tt0) cc_final: 0.8655 (tt0) REVERT: C 5 LEU cc_start: 0.8976 (tt) cc_final: 0.8444 (mp) REVERT: C 72 ASP cc_start: 0.8623 (t0) cc_final: 0.8106 (t0) REVERT: C 75 LYS cc_start: 0.9145 (mtmm) cc_final: 0.8641 (mttt) REVERT: C 101 GLU cc_start: 0.8256 (pm20) cc_final: 0.7889 (mp0) REVERT: C 102 PHE cc_start: 0.7769 (OUTLIER) cc_final: 0.6697 (p90) REVERT: H 34 MET cc_start: 0.8860 (mmm) cc_final: 0.8525 (mmm) REVERT: H 72 ASP cc_start: 0.7251 (t0) cc_final: 0.6735 (t70) REVERT: L 4 MET cc_start: 0.7511 (mmm) cc_final: 0.6834 (tpt) REVERT: L 42 GLN cc_start: 0.8235 (mm-40) cc_final: 0.7624 (mp-120) REVERT: L 54 ARG cc_start: 0.8480 (ptm-80) cc_final: 0.8085 (ptp-110) REVERT: L 103 LYS cc_start: 0.8754 (tppt) cc_final: 0.8307 (tppt) REVERT: L 105 GLU cc_start: 0.3907 (tp30) cc_final: 0.2863 (pm20) REVERT: G 62 GLN cc_start: 0.8674 (mp10) cc_final: 0.8336 (mp10) REVERT: G 163 SER cc_start: 0.8313 (t) cc_final: 0.7938 (m) REVERT: M 5 THR cc_start: 0.8774 (m) cc_final: 0.8451 (p) REVERT: J 5 LEU cc_start: 0.8939 (mp) cc_final: 0.8636 (mt) REVERT: J 101 GLU cc_start: 0.8075 (pm20) cc_final: 0.7717 (mp0) REVERT: O 72 ASP cc_start: 0.7201 (t0) cc_final: 0.6560 (t70) REVERT: O 75 LYS cc_start: 0.8587 (pttm) cc_final: 0.8343 (ptpp) REVERT: Q 1 GLU cc_start: 0.7183 (mt-10) cc_final: 0.6866 (mt-10) REVERT: Q 4 MET cc_start: 0.7162 (mmm) cc_final: 0.6904 (mmm) REVERT: Q 24 ARG cc_start: 0.7725 (mmm-85) cc_final: 0.7313 (mmm-85) REVERT: Q 42 GLN cc_start: 0.8268 (mm-40) cc_final: 0.7999 (mp10) REVERT: Q 53 THR cc_start: 0.8373 (m) cc_final: 0.7961 (t) REVERT: Q 54 ARG cc_start: 0.7809 (ptm-80) cc_final: 0.7436 (ttm110) REVERT: Q 71 PHE cc_start: 0.7686 (m-80) cc_final: 0.7292 (m-80) REVERT: Q 85 VAL cc_start: 0.8553 (OUTLIER) cc_final: 0.8330 (p) REVERT: Q 105 GLU cc_start: 0.6213 (OUTLIER) cc_final: 0.5990 (pm20) REVERT: I 163 SER cc_start: 0.8338 (t) cc_final: 0.8069 (m) REVERT: N 4 MET cc_start: 0.8600 (mmm) cc_final: 0.8286 (mmm) REVERT: N 5 THR cc_start: 0.8891 (m) cc_final: 0.8499 (p) REVERT: K 101 GLU cc_start: 0.8287 (pm20) cc_final: 0.7888 (mp0) REVERT: P 58 TYR cc_start: 0.8021 (m-80) cc_final: 0.7657 (m-80) REVERT: P 72 ASP cc_start: 0.7124 (t0) cc_final: 0.6456 (t70) REVERT: P 75 LYS cc_start: 0.8477 (pttm) cc_final: 0.8241 (pttm) REVERT: R 4 MET cc_start: 0.7734 (tpt) cc_final: 0.7222 (tpt) REVERT: R 54 ARG cc_start: 0.7950 (ptm-80) cc_final: 0.7697 (ttm-80) REVERT: R 105 GLU cc_start: 0.3925 (tp30) cc_final: 0.2964 (pm20) outliers start: 44 outliers final: 36 residues processed: 330 average time/residue: 0.3405 time to fit residues: 172.4896 Evaluate side-chains 333 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 293 time to evaluate : 2.611 ------------------------------------------------------------------------------- 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 61 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain D residue 105 GLU 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 68 THR 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 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 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 F residue 84 TRP 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 104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 4 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 246 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 chunk 143 optimal weight: 4.9990 chunk 251 optimal weight: 0.9990 chunk 193 optimal weight: 1.9990 chunk 230 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 255 optimal weight: 9.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 141 HIS J 3 GLN K 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.089659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.064043 restraints weight = 55065.661| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.81 r_work: 0.2913 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 22686 Z= 0.153 Angle : 0.607 9.142 30816 Z= 0.315 Chirality : 0.042 0.162 3381 Planarity : 0.005 0.076 3927 Dihedral : 4.686 33.776 3483 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.92 % Allowed : 12.83 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.16), residues: 2760 helix: 2.65 (0.26), residues: 372 sheet: 0.25 (0.19), residues: 714 loop : -0.39 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 103 HIS 0.004 0.001 HIS E 18 PHE 0.017 0.001 PHE L 71 TYR 0.017 0.001 TYR G 110 ARG 0.008 0.000 ARG H 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00221 ( 18) link_NAG-ASN : angle 1.74088 ( 54) link_BETA1-4 : bond 0.00291 ( 3) link_BETA1-4 : angle 1.18297 ( 9) hydrogen bonds : bond 0.04143 ( 894) hydrogen bonds : angle 4.77060 ( 2529) SS BOND : bond 0.00274 ( 30) SS BOND : angle 1.71470 ( 60) covalent geometry : bond 0.00370 (22635) covalent geometry : angle 0.59888 (30693) ********************** 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 342 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 296 time to evaluate : 2.391 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: B 19 ASP cc_start: 0.8108 (p0) cc_final: 0.7758 (p0) REVERT: B 158 ASP cc_start: 0.8162 (t0) cc_final: 0.6373 (p0) REVERT: B 163 SER cc_start: 0.8439 (t) cc_final: 0.8011 (m) REVERT: D 105 GLU cc_start: 0.5409 (OUTLIER) cc_final: 0.5102 (tm-30) REVERT: C 3 GLN cc_start: 0.8936 (tt0) cc_final: 0.8628 (tt0) REVERT: C 5 LEU cc_start: 0.8975 (tt) cc_final: 0.8407 (mp) REVERT: C 72 ASP cc_start: 0.8584 (t0) cc_final: 0.8061 (t0) REVERT: C 75 LYS cc_start: 0.9144 (mtmm) cc_final: 0.8633 (mttt) REVERT: C 101 GLU cc_start: 0.8275 (pm20) cc_final: 0.7911 (mp0) REVERT: C 102 PHE cc_start: 0.7748 (OUTLIER) cc_final: 0.6765 (p90) REVERT: H 34 MET cc_start: 0.8811 (mmm) cc_final: 0.8499 (mmm) REVERT: H 72 ASP cc_start: 0.7235 (t0) cc_final: 0.6745 (t70) REVERT: L 4 MET cc_start: 0.7477 (mmm) cc_final: 0.6809 (tpt) REVERT: L 42 GLN cc_start: 0.8225 (mm-40) cc_final: 0.7600 (mp10) REVERT: L 54 ARG cc_start: 0.8539 (ptm-80) cc_final: 0.8292 (ttm110) REVERT: L 103 LYS cc_start: 0.8688 (tppt) cc_final: 0.8226 (tppt) REVERT: L 105 GLU cc_start: 0.3526 (tp30) cc_final: 0.2592 (pm20) REVERT: G 62 GLN cc_start: 0.8688 (mp10) cc_final: 0.8345 (mp10) REVERT: G 158 ASP cc_start: 0.8206 (t0) cc_final: 0.6317 (p0) REVERT: G 163 SER cc_start: 0.8331 (t) cc_final: 0.7936 (m) REVERT: M 5 THR cc_start: 0.8776 (m) cc_final: 0.8441 (p) REVERT: M 103 LYS cc_start: 0.8668 (tptp) cc_final: 0.8424 (ttpp) REVERT: J 5 LEU cc_start: 0.8941 (mp) cc_final: 0.8673 (mt) REVERT: J 101 GLU cc_start: 0.8070 (pm20) cc_final: 0.7696 (mp0) REVERT: O 64 LYS cc_start: 0.7733 (mmmt) cc_final: 0.7088 (mmtm) REVERT: O 72 ASP cc_start: 0.7217 (t0) cc_final: 0.6573 (t70) REVERT: O 75 LYS cc_start: 0.8604 (pttm) cc_final: 0.8360 (ptpp) REVERT: Q 1 GLU cc_start: 0.7127 (mt-10) cc_final: 0.6628 (mt-10) REVERT: Q 4 MET cc_start: 0.7048 (mmm) cc_final: 0.6659 (mmm) REVERT: Q 24 ARG cc_start: 0.7692 (mmm-85) cc_final: 0.7203 (mmm-85) REVERT: Q 42 GLN cc_start: 0.8253 (mm-40) cc_final: 0.7972 (mp-120) REVERT: Q 53 THR cc_start: 0.8366 (m) cc_final: 0.7963 (p) REVERT: Q 54 ARG cc_start: 0.7910 (ptm-80) cc_final: 0.7649 (ttm110) REVERT: Q 67 SER cc_start: 0.7899 (t) cc_final: 0.7588 (p) REVERT: Q 71 PHE cc_start: 0.7663 (m-80) cc_final: 0.7252 (m-80) REVERT: Q 85 VAL cc_start: 0.8584 (OUTLIER) cc_final: 0.8361 (p) REVERT: Q 105 GLU cc_start: 0.6260 (OUTLIER) cc_final: 0.5998 (pm20) REVERT: I 163 SER cc_start: 0.8344 (t) cc_final: 0.8065 (m) REVERT: N 4 MET cc_start: 0.8528 (mmm) cc_final: 0.8235 (mmm) REVERT: N 5 THR cc_start: 0.8891 (m) cc_final: 0.8496 (p) REVERT: K 6 GLU cc_start: 0.7906 (mp0) cc_final: 0.7677 (mt-10) REVERT: P 58 TYR cc_start: 0.8014 (m-80) cc_final: 0.7671 (m-80) REVERT: P 72 ASP cc_start: 0.7108 (t0) cc_final: 0.6412 (t70) REVERT: P 75 LYS cc_start: 0.8472 (pttm) cc_final: 0.8248 (pttm) REVERT: R 4 MET cc_start: 0.7719 (tpt) cc_final: 0.7200 (tpt) REVERT: R 105 GLU cc_start: 0.3948 (tp30) cc_final: 0.3000 (pm20) outliers start: 46 outliers final: 38 residues processed: 320 average time/residue: 0.3666 time to fit residues: 181.8338 Evaluate side-chains 327 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 285 time to evaluate : 2.640 ------------------------------------------------------------------------------- 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 61 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain D residue 105 GLU 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 68 THR 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 15 VAL Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 83 ILE 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 Q residue 105 GLU Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 84 TRP 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 5 THR 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 95 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 chunk 245 optimal weight: 1.9990 chunk 6 optimal weight: 0.4980 chunk 164 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 195 optimal weight: 0.0770 chunk 120 optimal weight: 2.9990 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 HIS J 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.090685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.065097 restraints weight = 54640.693| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.81 r_work: 0.2944 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.4597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22686 Z= 0.122 Angle : 0.585 8.786 30816 Z= 0.304 Chirality : 0.042 0.154 3381 Planarity : 0.004 0.074 3927 Dihedral : 4.517 31.836 3483 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.83 % Allowed : 13.00 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.16), residues: 2760 helix: 2.79 (0.26), residues: 372 sheet: 0.37 (0.19), residues: 693 loop : -0.39 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 103 HIS 0.004 0.001 HIS E 18 PHE 0.016 0.001 PHE L 71 TYR 0.019 0.001 TYR B 162 ARG 0.009 0.000 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00195 ( 18) link_NAG-ASN : angle 1.59079 ( 54) link_BETA1-4 : bond 0.00272 ( 3) link_BETA1-4 : angle 1.05911 ( 9) hydrogen bonds : bond 0.03898 ( 894) hydrogen bonds : angle 4.65867 ( 2529) SS BOND : bond 0.00252 ( 30) SS BOND : angle 1.61702 ( 60) covalent geometry : bond 0.00289 (22635) covalent geometry : angle 0.57768 (30693) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12016.77 seconds wall clock time: 210 minutes 6.85 seconds (12606.85 seconds total)