Starting phenix.real_space_refine on Sat Aug 23 18:01:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tp3_41465/08_2025/8tp3_41465.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tp3_41465/08_2025/8tp3_41465.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tp3_41465/08_2025/8tp3_41465.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tp3_41465/08_2025/8tp3_41465.map" model { file = "/net/cci-nas-00/data/ceres_data/8tp3_41465/08_2025/8tp3_41465.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tp3_41465/08_2025/8tp3_41465.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.026 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 59 5.16 5 C 8613 2.51 5 N 2322 2.21 5 O 2697 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 87 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13691 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2530 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 20, 'TRANS': 301} Chain: "B" Number of atoms: 1377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1377 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 1, 'TRANS': 169} Chain: "C" Number of atoms: 2530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2530 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 20, 'TRANS': 301} Chain: "D" Number of atoms: 1328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1328 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 1, 'TRANS': 161} Chain: "G" Number of atoms: 2530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2530 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 20, 'TRANS': 301} Chain: "I" Number of atoms: 1377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1377 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 1, 'TRANS': 169} Chain: "H" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 946 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "L" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 796 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 98} Chain: "E" 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: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" 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: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" 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 Time building chain proxies: 3.22, per 1000 atoms: 0.24 Number of scatterers: 13691 At special positions: 0 Unit cell: (98.9, 96.6, 179.4, 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 59 16.00 O 2697 8.00 N 2322 7.00 C 8613 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, 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=2.05 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS D 137 " distance=2.06 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.06 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.02 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.02 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS G 14 " - pdb=" SG CYS I 137 " distance=2.02 Simple disulfide: pdb=" SG CYS G 52 " - pdb=" SG CYS G 277 " distance=2.04 Simple disulfide: pdb=" SG CYS G 64 " - pdb=" SG CYS G 76 " distance=2.02 Simple disulfide: pdb=" SG CYS G 97 " - pdb=" SG CYS G 139 " distance=2.04 Simple disulfide: pdb=" SG CYS G 281 " - pdb=" SG CYS G 305 " distance=2.02 Simple disulfide: pdb=" SG CYS I 144 " - pdb=" SG CYS I 148 " distance=2.04 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=2.04 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 E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 401 " - " ASN A 21 " " NAG A 402 " - " ASN A 33 " " NAG A 403 " - " ASN A 63 " " NAG A 404 " - " ASN A 129 " " NAG C 401 " - " ASN C 21 " " NAG C 402 " - " ASN C 33 " " NAG C 403 " - " ASN C 63 " " NAG C 404 " - " ASN C 129 " " NAG C 405 " - " ASN C 163 " " NAG E 1 " - " ASN A 95 " " NAG F 1 " - " ASN C 95 " " NAG G 401 " - " ASN G 21 " " NAG G 402 " - " ASN G 33 " " NAG G 403 " - " ASN G 63 " " NAG G 404 " - " ASN G 129 " " NAG J 1 " - " ASN G 95 " Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 642.7 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3128 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 38 sheets defined 25.8% alpha, 29.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 3.896A pdb=" N GLU A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N LEU A 78 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 113 Processing helix chain 'A' and resid 125 through 127 removed outlier: 4.216A pdb=" N TRP A 127 " --> pdb=" O LYS A 125A" (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'B' and resid 37 through 58 Processing helix chain 'B' and resid 74 through 127 Processing helix chain 'B' and resid 145 through 155 Processing helix chain 'B' and resid 158 through 161 Processing helix chain 'B' and resid 162 through 170 Processing helix chain 'C' and resid 53 through 56 Processing helix chain 'C' and resid 65 through 70 Processing helix chain 'C' and resid 73 through 80 removed outlier: 3.929A pdb=" N GLU C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N LEU C 78 " --> pdb=" O GLU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 114 Processing helix chain 'C' and resid 125 through 127 removed outlier: 4.221A pdb=" N TRP C 127 " --> pdb=" O LYS C 125A" (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'D' and resid 37 through 58 Processing helix chain 'D' and resid 74 through 127 Processing helix chain 'D' and resid 145 through 155 Processing helix chain 'D' and resid 158 through 161 Processing helix chain 'D' and resid 162 through 170 Processing helix chain 'G' and resid 65 through 72 Processing helix chain 'G' and resid 73 through 80 removed outlier: 3.991A pdb=" N GLU G 77 " --> pdb=" O PRO G 74 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N LEU G 78 " --> pdb=" O GLU G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 114 removed outlier: 4.104A pdb=" N SER G 114 " --> pdb=" O GLU G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 127 removed outlier: 4.697A pdb=" N TRP G 127 " --> pdb=" O LYS G 125A" (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 196 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 161 Processing helix chain 'I' and resid 162 through 170 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 36 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: 6.339A pdb=" N LEU A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 5.630A 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: 6.471A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 6.187A 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: 6.587A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU A 175 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.673A 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: 6.587A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU A 175 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 136 through 141 removed outlier: 4.661A pdb=" N CYS A 139 " --> pdb=" O SER A 146 " (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: 3.991A pdb=" N CYS A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 31 through 36 Processing sheet with id=AB4, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AB5, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AB6, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AB7, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.332A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ILE C 87 " --> pdb=" O ILE C 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 115 through 122 removed outlier: 6.162A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU C 175 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 115 through 122 removed outlier: 6.162A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU C 175 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 144 through 146 removed outlier: 4.719A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AC3, first strand: chain 'C' and resid 286 through 288 removed outlier: 3.908A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 31 through 36 Processing sheet with id=AC5, first strand: chain 'G' and resid 25 through 26 Processing sheet with id=AC6, first strand: chain 'G' and resid 39 through 41 Processing sheet with id=AC7, first strand: chain 'G' and resid 43 through 44 Processing sheet with id=AC8, first strand: chain 'G' and resid 51 through 54 removed outlier: 6.353A pdb=" N LEU G 51 " --> pdb=" O ASP G 275 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N CYS G 277 " --> pdb=" O LEU G 51 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 59 through 62 removed outlier: 6.162A pdb=" N LEU G 59 " --> pdb=" O VAL G 88 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE G 87 " --> pdb=" O ILE G 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'G' and resid 115 through 122 removed outlier: 7.218A pdb=" N SER G 261 " --> pdb=" O SER G 116 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N PHE G 118 " --> pdb=" O ALA G 259 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ALA G 259 " --> pdb=" O PHE G 118 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ARG G 120 " --> pdb=" O ALA G 257 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ALA G 257 " --> pdb=" O ARG G 120 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N TYR G 256 " --> pdb=" O LEU G 179 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LEU G 179 " --> pdb=" O TYR G 256 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU G 175 " --> pdb=" O LEU G 260 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU G 179 " --> pdb=" O PRO G 254 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 115 through 122 removed outlier: 7.218A pdb=" N SER G 261 " --> pdb=" O SER G 116 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N PHE G 118 " --> pdb=" O ALA G 259 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ALA G 259 " --> pdb=" O PHE G 118 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ARG G 120 " --> pdb=" O ALA G 257 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ALA G 257 " --> pdb=" O ARG G 120 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N TYR G 256 " --> pdb=" O LEU G 179 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LEU G 179 " --> pdb=" O TYR G 256 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU G 175 " --> pdb=" O LEU G 260 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 136 through 141 removed outlier: 7.266A pdb=" N SER G 138 " --> pdb=" O LYS G 144 " (cutoff:3.500A) removed outlier: 10.016A pdb=" N LYS G 144 " --> pdb=" O SER G 138 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 164 through 169 Processing sheet with id=AD5, first strand: chain 'G' and resid 286 through 288 removed outlier: 3.842A pdb=" N CYS G 281 " --> pdb=" O ILE G 288 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD7, first strand: chain 'H' and resid 56 through 59 removed outlier: 5.493A pdb=" N TYR H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ARG H 38 " --> pdb=" O TYR H 47 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N TYR H 33 " --> pdb=" O ASP H 95 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 56 through 59 removed outlier: 5.493A pdb=" N TYR H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ARG H 38 " --> pdb=" O TYR H 47 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N TYR H 33 " --> pdb=" O ASP H 95 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AE1, first strand: chain 'L' and resid 10 through 12 removed outlier: 5.948A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 10 through 12 removed outlier: 5.948A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) 613 hydrogen bonds defined for protein. 1650 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: 2.24 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 3995 1.33 - 1.47: 4264 1.47 - 1.61: 5680 1.61 - 1.75: 8 1.75 - 1.89: 73 Bond restraints: 14020 Sorted by residual: bond pdb=" CB HIS H 52 " pdb=" CG HIS H 52 " ideal model delta sigma weight residual 1.497 1.400 0.097 1.40e-02 5.10e+03 4.79e+01 bond pdb=" CB HIS G 47 " pdb=" CG HIS G 47 " ideal model delta sigma weight residual 1.497 1.407 0.090 1.40e-02 5.10e+03 4.13e+01 bond pdb=" N CYS D 137 " pdb=" CA CYS D 137 " ideal model delta sigma weight residual 1.458 1.522 -0.065 1.19e-02 7.06e+03 2.95e+01 bond pdb=" CB HIS A 18 " pdb=" CG HIS A 18 " ideal model delta sigma weight residual 1.497 1.423 0.074 1.40e-02 5.10e+03 2.76e+01 bond pdb=" CG PHE D 9 " pdb=" CD1 PHE D 9 " ideal model delta sigma weight residual 1.384 1.493 -0.109 2.10e-02 2.27e+03 2.67e+01 ... (remaining 14015 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 16958 2.66 - 5.32: 1843 5.32 - 7.98: 210 7.98 - 10.64: 16 10.64 - 13.30: 5 Bond angle restraints: 19032 Sorted by residual: angle pdb=" C HIS A 184 " pdb=" N PRO A 185 " pdb=" CA PRO A 185 " ideal model delta sigma weight residual 119.66 126.54 -6.88 7.30e-01 1.88e+00 8.88e+01 angle pdb=" C HIS G 184 " pdb=" N PRO G 185 " pdb=" CA PRO G 185 " ideal model delta sigma weight residual 119.66 126.33 -6.67 7.30e-01 1.88e+00 8.35e+01 angle pdb=" C ILE A 323 " pdb=" N PRO A 324 " pdb=" CA PRO A 324 " ideal model delta sigma weight residual 120.31 127.58 -7.27 9.80e-01 1.04e+00 5.50e+01 angle pdb=" N LYS A 32 " pdb=" CA LYS A 32 " pdb=" C LYS A 32 " ideal model delta sigma weight residual 111.82 120.16 -8.34 1.16e+00 7.43e-01 5.17e+01 angle pdb=" C CYS C 305 " pdb=" N PRO C 306 " pdb=" CA PRO C 306 " ideal model delta sigma weight residual 119.78 127.11 -7.33 1.03e+00 9.43e-01 5.07e+01 ... (remaining 19027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.02: 8348 21.02 - 42.05: 168 42.05 - 63.07: 51 63.07 - 84.09: 16 84.09 - 105.12: 7 Dihedral angle restraints: 8590 sinusoidal: 3687 harmonic: 4903 Sorted by residual: dihedral pdb=" CB CYS C 14 " pdb=" SG CYS C 14 " pdb=" SG CYS D 137 " pdb=" CB CYS D 137 " ideal model delta sinusoidal sigma weight residual -86.00 -9.50 -76.50 1 1.00e+01 1.00e-02 7.36e+01 dihedral pdb=" CB CYS D 144 " pdb=" SG CYS D 144 " pdb=" SG CYS D 148 " pdb=" CB CYS D 148 " ideal model delta sinusoidal sigma weight residual 93.00 148.33 -55.33 1 1.00e+01 1.00e-02 4.14e+01 dihedral pdb=" CB CYS C 64 " pdb=" SG CYS C 64 " pdb=" SG CYS C 76 " pdb=" CB CYS C 76 " ideal model delta sinusoidal sigma weight residual -86.00 -45.01 -40.99 1 1.00e+01 1.00e-02 2.35e+01 ... (remaining 8587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 1526 0.104 - 0.208: 454 0.208 - 0.312: 71 0.312 - 0.416: 30 0.416 - 0.520: 14 Chirality restraints: 2095 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 9.29e+01 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.67e+01 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.24e+01 ... (remaining 2092 not shown) Planarity restraints: 2467 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 401 " -0.122 2.00e-02 2.50e+03 1.00e-01 1.25e+02 pdb=" C7 NAG A 401 " 0.033 2.00e-02 2.50e+03 pdb=" C8 NAG A 401 " -0.091 2.00e-02 2.50e+03 pdb=" N2 NAG A 401 " 0.159 2.00e-02 2.50e+03 pdb=" O7 NAG A 401 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 401 " 0.096 2.00e-02 2.50e+03 8.10e-02 8.21e+01 pdb=" C7 NAG G 401 " -0.021 2.00e-02 2.50e+03 pdb=" C8 NAG G 401 " -0.025 2.00e-02 2.50e+03 pdb=" N2 NAG G 401 " -0.128 2.00e-02 2.50e+03 pdb=" O7 NAG G 401 " 0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 95 " 0.075 2.00e-02 2.50e+03 7.74e-02 7.49e+01 pdb=" CG ASN C 95 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN C 95 " -0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN C 95 " -0.119 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " 0.093 2.00e-02 2.50e+03 ... (remaining 2464 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 4616 2.85 - 3.36: 12475 3.36 - 3.87: 24009 3.87 - 4.39: 28160 4.39 - 4.90: 45794 Nonbonded interactions: 115054 Sorted by model distance: nonbonded pdb=" NZ LYS D 83 " pdb=" OD1 ASP I 85 " model vdw 2.336 3.120 nonbonded pdb=" NZ LYS B 83 " pdb=" OD1 ASP D 85 " model vdw 2.342 3.120 nonbonded pdb=" OD1 ASP B 85 " pdb=" NZ LYS I 83 " model vdw 2.350 3.120 nonbonded pdb=" N ASP B 19 " pdb=" OD1 ASP B 19 " model vdw 2.380 3.120 nonbonded pdb=" N ASN H 76 " pdb=" N GLN H 77 " model vdw 2.396 2.560 ... (remaining 115049 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and resid 11 through 404) selection = chain 'G' } ncs_group { reference = (chain 'B' and resid 9 through 171) selection = chain 'D' selection = (chain 'I' and resid 9 through 171) } ncs_group { reference = chain 'E' selection = chain 'J' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 12.950 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 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 : 0.020 0.121 14060 Z= 1.068 Angle : 1.759 31.410 19132 Z= 1.160 Chirality : 0.110 0.520 2095 Planarity : 0.009 0.122 2451 Dihedral : 10.547 105.117 5402 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 0.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.07 % Allowed : 0.41 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.19), residues: 1684 helix: 0.86 (0.24), residues: 358 sheet: 0.89 (0.26), residues: 330 loop : 0.38 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 66 TYR 0.050 0.009 TYR D 157 PHE 0.052 0.007 PHE H 100J TRP 0.052 0.007 TRP D 21 HIS 0.010 0.003 HIS C 38 Details of bonding type rmsd covalent geometry : bond 0.01998 (14020) covalent geometry : angle 1.72001 (19032) SS BOND : bond 0.01239 ( 20) SS BOND : angle 7.33259 ( 40) hydrogen bonds : bond 0.16452 ( 574) hydrogen bonds : angle 7.83854 ( 1650) link_BETA1-4 : bond 0.06779 ( 4) link_BETA1-4 : angle 4.13060 ( 12) link_NAG-ASN : bond 0.07259 ( 16) link_NAG-ASN : angle 3.25146 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 488 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.8051 (mttt) cc_final: 0.7784 (mttm) REVERT: A 82 LYS cc_start: 0.7203 (mmtt) cc_final: 0.6594 (mmmt) REVERT: A 104 ASP cc_start: 0.9064 (m-30) cc_final: 0.8859 (m-30) REVERT: A 274 MET cc_start: 0.7445 (mtt) cc_final: 0.7240 (ttt) REVERT: B 46 ASN cc_start: 0.7856 (m-40) cc_final: 0.7608 (t0) REVERT: B 53 ASN cc_start: 0.6760 (m-40) cc_final: 0.5745 (t0) REVERT: C 82 LYS cc_start: 0.7522 (mmtt) cc_final: 0.6904 (tptp) REVERT: D 11 GLU cc_start: 0.7209 (tt0) cc_final: 0.6939 (pm20) REVERT: D 77 MET cc_start: 0.7521 (ttt) cc_final: 0.7132 (ttm) REVERT: D 142 HIS cc_start: 0.8256 (p90) cc_final: 0.7766 (p90) REVERT: G 75 GLU cc_start: 0.7041 (mm-30) cc_final: 0.6815 (mm-30) REVERT: G 107 GLU cc_start: 0.8307 (tp30) cc_final: 0.8093 (tp30) REVERT: G 148 TYR cc_start: 0.8047 (m-80) cc_final: 0.7523 (m-80) REVERT: G 201 TYR cc_start: 0.7945 (p90) cc_final: 0.7215 (p90) REVERT: G 224 ARG cc_start: 0.8435 (mtp85) cc_final: 0.6353 (mpt180) REVERT: G 256 TYR cc_start: 0.8342 (m-80) cc_final: 0.7914 (m-10) REVERT: I 34 TYR cc_start: 0.5419 (m-80) cc_final: 0.5104 (m-80) REVERT: I 109 ASP cc_start: 0.8289 (m-30) cc_final: 0.7824 (t70) REVERT: H 3 GLN cc_start: 0.7716 (mm-40) cc_final: 0.7478 (mm110) REVERT: H 36 TRP cc_start: 0.7984 (m100) cc_final: 0.7329 (m100) REVERT: H 100 PHE cc_start: 0.7508 (m-80) cc_final: 0.7215 (m-80) outliers start: 1 outliers final: 0 residues processed: 488 average time/residue: 0.1123 time to fit residues: 77.9561 Evaluate side-chains 238 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 HIS C 282 GLN C 295 GLN C 298 HIS ** D 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 298 HIS ** I 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 1 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.164685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.140558 restraints weight = 22272.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.144337 restraints weight = 13011.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.146850 restraints weight = 8929.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.148678 restraints weight = 6819.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.149844 restraints weight = 5544.688| |-----------------------------------------------------------------------------| r_work (final): 0.4102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 14060 Z= 0.188 Angle : 0.754 22.815 19132 Z= 0.396 Chirality : 0.048 0.461 2095 Planarity : 0.005 0.058 2451 Dihedral : 6.956 69.481 2253 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 3.31 % Allowed : 10.21 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.19), residues: 1684 helix: 1.91 (0.26), residues: 361 sheet: 1.22 (0.31), residues: 254 loop : -0.02 (0.18), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 310 TYR 0.018 0.002 TYR G 86 PHE 0.019 0.002 PHE G 118 TRP 0.012 0.002 TRP G 153 HIS 0.010 0.002 HIS A 196 Details of bonding type rmsd covalent geometry : bond 0.00419 (14020) covalent geometry : angle 0.71159 (19032) SS BOND : bond 0.00405 ( 20) SS BOND : angle 1.36552 ( 40) hydrogen bonds : bond 0.06636 ( 574) hydrogen bonds : angle 6.00478 ( 1650) link_BETA1-4 : bond 0.00137 ( 4) link_BETA1-4 : angle 2.48544 ( 12) link_NAG-ASN : bond 0.00669 ( 16) link_NAG-ASN : angle 4.76358 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 268 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.8917 (m-30) cc_final: 0.8684 (m-30) REVERT: A 274 MET cc_start: 0.7166 (mtt) cc_final: 0.6508 (ttt) REVERT: B 17 MET cc_start: 0.7482 (ttt) cc_final: 0.7254 (ttt) REVERT: B 19 ASP cc_start: 0.7455 (p0) cc_final: 0.6699 (t0) REVERT: B 53 ASN cc_start: 0.6070 (m-40) cc_final: 0.5516 (t0) REVERT: B 128 ASN cc_start: 0.7571 (m-40) cc_final: 0.7283 (t0) REVERT: B 141 TYR cc_start: 0.6271 (m-80) cc_final: 0.5288 (m-80) REVERT: C 226 GLN cc_start: 0.7918 (mm-40) cc_final: 0.7684 (mm-40) REVERT: D 50 ASN cc_start: 0.8124 (m-40) cc_final: 0.7873 (m-40) REVERT: D 142 HIS cc_start: 0.8218 (p90) cc_final: 0.7780 (p90) REVERT: G 45 ASP cc_start: 0.7998 (p0) cc_final: 0.7673 (p0) REVERT: G 224 ARG cc_start: 0.8184 (mtp85) cc_final: 0.6246 (mtt180) REVERT: I 109 ASP cc_start: 0.7906 (m-30) cc_final: 0.7325 (t70) REVERT: H 36 TRP cc_start: 0.8209 (m100) cc_final: 0.7354 (m100) REVERT: L 100 GLN cc_start: 0.7438 (pm20) cc_final: 0.7154 (pm20) outliers start: 49 outliers final: 24 residues processed: 302 average time/residue: 0.1016 time to fit residues: 45.3498 Evaluate side-chains 233 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 209 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 316 MET Chi-restraints excluded: chain D residue 26 HIS Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 118 PHE Chi-restraints excluded: chain G residue 158 ASN Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 92 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 162 optimal weight: 0.3980 chunk 165 optimal weight: 10.0000 chunk 156 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 126 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 147 optimal weight: 10.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 ASN C 282 GLN C 295 GLN D 27 GLN G 208 HIS ** I 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 129 ASN ** I 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.164092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.141117 restraints weight = 21669.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.144433 restraints weight = 13440.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.146726 restraints weight = 9555.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.148305 restraints weight = 7430.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.149233 restraints weight = 6156.043| |-----------------------------------------------------------------------------| r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14060 Z= 0.197 Angle : 0.703 20.948 19132 Z= 0.361 Chirality : 0.048 0.404 2095 Planarity : 0.005 0.050 2451 Dihedral : 6.086 54.977 2253 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.52 % Allowed : 12.37 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.19), residues: 1684 helix: 2.02 (0.26), residues: 361 sheet: 0.98 (0.32), residues: 240 loop : -0.26 (0.17), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 170 TYR 0.017 0.002 TYR H 59 PHE 0.024 0.002 PHE H 78 TRP 0.021 0.002 TRP L 96 HIS 0.013 0.002 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00446 (14020) covalent geometry : angle 0.66529 (19032) SS BOND : bond 0.00425 ( 20) SS BOND : angle 1.22600 ( 40) hydrogen bonds : bond 0.05718 ( 574) hydrogen bonds : angle 5.65503 ( 1650) link_BETA1-4 : bond 0.00356 ( 4) link_BETA1-4 : angle 2.08145 ( 12) link_NAG-ASN : bond 0.00853 ( 16) link_NAG-ASN : angle 4.40651 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 239 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.7690 (t0) cc_final: 0.7444 (t0) REVERT: A 32 LYS cc_start: 0.8501 (mttp) cc_final: 0.7814 (mmmt) REVERT: A 274 MET cc_start: 0.6961 (mtt) cc_final: 0.6525 (ttt) REVERT: B 53 ASN cc_start: 0.6218 (m-40) cc_final: 0.5648 (t0) REVERT: B 141 TYR cc_start: 0.6346 (m-80) cc_final: 0.5553 (m-80) REVERT: B 170 ARG cc_start: 0.7001 (ttm110) cc_final: 0.6648 (ttm110) REVERT: C 83 GLU cc_start: 0.6648 (mm-30) cc_final: 0.6375 (mm-30) REVERT: G 148 TYR cc_start: 0.7696 (m-80) cc_final: 0.7364 (m-80) REVERT: G 224 ARG cc_start: 0.7985 (mtp85) cc_final: 0.6304 (mtt180) REVERT: I 109 ASP cc_start: 0.7913 (m-30) cc_final: 0.7570 (t70) REVERT: H 36 TRP cc_start: 0.8426 (m100) cc_final: 0.7595 (m100) REVERT: H 103 TRP cc_start: 0.7527 (m-10) cc_final: 0.7285 (m-10) REVERT: L 100 GLN cc_start: 0.7739 (pm20) cc_final: 0.7324 (pm20) outliers start: 52 outliers final: 40 residues processed: 270 average time/residue: 0.1033 time to fit residues: 41.3163 Evaluate side-chains 244 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 204 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 282 GLN Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 316 MET Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 118 PHE Chi-restraints excluded: chain G residue 158 ASN Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 92 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 130 optimal weight: 9.9990 chunk 96 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 161 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 118 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 HIS C 38 HIS C 141 HIS C 282 GLN ** C 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 ASN D 62 GLN D 142 HIS ** I 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 142 HIS ** I 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 HIS L 32 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.165124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.141089 restraints weight = 22604.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.144705 restraints weight = 13408.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.147103 restraints weight = 9326.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.148789 restraints weight = 7203.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.149940 restraints weight = 5957.370| |-----------------------------------------------------------------------------| r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.4609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 14060 Z= 0.251 Angle : 0.748 21.070 19132 Z= 0.381 Chirality : 0.049 0.403 2095 Planarity : 0.005 0.060 2451 Dihedral : 5.775 54.435 2253 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 5.00 % Allowed : 13.66 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.19), residues: 1684 helix: 1.83 (0.26), residues: 363 sheet: 0.42 (0.32), residues: 246 loop : -0.54 (0.18), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 310 TYR 0.027 0.002 TYR C 201 PHE 0.031 0.003 PHE G 118 TRP 0.025 0.002 TRP L 96 HIS 0.007 0.002 HIS G 183 Details of bonding type rmsd covalent geometry : bond 0.00586 (14020) covalent geometry : angle 0.71521 (19032) SS BOND : bond 0.00470 ( 20) SS BOND : angle 1.20325 ( 40) hydrogen bonds : bond 0.05565 ( 574) hydrogen bonds : angle 5.62437 ( 1650) link_BETA1-4 : bond 0.00213 ( 4) link_BETA1-4 : angle 1.97142 ( 12) link_NAG-ASN : bond 0.00850 ( 16) link_NAG-ASN : angle 4.21513 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 220 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: A 27 ASP cc_start: 0.7931 (t0) cc_final: 0.7654 (t0) REVERT: A 32 LYS cc_start: 0.8521 (mttp) cc_final: 0.7258 (mmmt) REVERT: B 125 GLN cc_start: 0.7653 (mm-40) cc_final: 0.7115 (tt0) REVERT: B 141 TYR cc_start: 0.6527 (m-80) cc_final: 0.5652 (m-80) REVERT: C 108 LEU cc_start: 0.9237 (tp) cc_final: 0.9022 (tp) REVERT: C 225 ASP cc_start: 0.7529 (t0) cc_final: 0.6857 (t0) REVERT: D 45 ILE cc_start: 0.7834 (OUTLIER) cc_final: 0.7552 (mp) REVERT: D 125 GLN cc_start: 0.8309 (tp40) cc_final: 0.7463 (tp-100) REVERT: G 224 ARG cc_start: 0.8145 (mtp85) cc_final: 0.6449 (mtt180) REVERT: G 314 LEU cc_start: 0.6611 (OUTLIER) cc_final: 0.6378 (mm) REVERT: G 320 LEU cc_start: 0.8666 (mp) cc_final: 0.8314 (mt) REVERT: I 109 ASP cc_start: 0.8019 (m-30) cc_final: 0.7636 (t70) REVERT: H 100 PHE cc_start: 0.6971 (m-80) cc_final: 0.6245 (m-80) outliers start: 74 outliers final: 57 residues processed: 268 average time/residue: 0.0888 time to fit residues: 36.3452 Evaluate side-chains 262 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 203 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 282 GLN Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 316 MET Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 118 PHE Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 158 ASN Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 225 ASP Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 92 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 34 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 167 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 146 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 GLN C 322 ASN D 25 HIS D 43 ASN ** I 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.168664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.143210 restraints weight = 23123.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.146879 restraints weight = 13913.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.149371 restraints weight = 9754.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.151082 restraints weight = 7577.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.152126 restraints weight = 6276.694| |-----------------------------------------------------------------------------| r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.4879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14060 Z= 0.172 Angle : 0.676 20.599 19132 Z= 0.342 Chirality : 0.046 0.400 2095 Planarity : 0.005 0.054 2451 Dihedral : 5.595 55.353 2253 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.19 % Allowed : 15.62 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.19), residues: 1684 helix: 1.96 (0.27), residues: 363 sheet: 0.35 (0.32), residues: 256 loop : -0.62 (0.18), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 170 TYR 0.026 0.002 TYR B 119 PHE 0.023 0.002 PHE G 118 TRP 0.015 0.002 TRP L 96 HIS 0.006 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00398 (14020) covalent geometry : angle 0.63519 (19032) SS BOND : bond 0.00358 ( 20) SS BOND : angle 1.08625 ( 40) hydrogen bonds : bond 0.05139 ( 574) hydrogen bonds : angle 5.44456 ( 1650) link_BETA1-4 : bond 0.00283 ( 4) link_BETA1-4 : angle 1.68096 ( 12) link_NAG-ASN : bond 0.00728 ( 16) link_NAG-ASN : angle 4.50515 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 225 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.7995 (t0) cc_final: 0.7648 (t0) REVERT: A 32 LYS cc_start: 0.8186 (mttp) cc_final: 0.7287 (mmmt) REVERT: B 125 GLN cc_start: 0.7522 (mm-40) cc_final: 0.7007 (tt0) REVERT: B 141 TYR cc_start: 0.6542 (m-80) cc_final: 0.5575 (m-80) REVERT: C 225 ASP cc_start: 0.7462 (OUTLIER) cc_final: 0.6855 (t0) REVERT: D 45 ILE cc_start: 0.7773 (OUTLIER) cc_final: 0.7520 (mp) REVERT: D 58 LYS cc_start: 0.7262 (mmmt) cc_final: 0.7006 (mmtt) REVERT: D 125 GLN cc_start: 0.8319 (tp40) cc_final: 0.7449 (tp-100) REVERT: G 179 LEU cc_start: 0.5569 (OUTLIER) cc_final: 0.5231 (mt) REVERT: G 224 ARG cc_start: 0.8247 (mtp85) cc_final: 0.6468 (mtt180) REVERT: I 109 ASP cc_start: 0.8029 (m-30) cc_final: 0.7734 (t70) REVERT: H 77 GLN cc_start: 0.7468 (OUTLIER) cc_final: 0.7187 (pp30) REVERT: H 100 PHE cc_start: 0.6951 (m-80) cc_final: 0.6149 (m-80) outliers start: 62 outliers final: 50 residues processed: 263 average time/residue: 0.0977 time to fit residues: 39.0330 Evaluate side-chains 254 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 200 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain D residue 17 MET Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 118 PHE Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 158 ASN Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 92 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 113 optimal weight: 1.9990 chunk 159 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 153 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 15 optimal weight: 0.0060 chunk 4 optimal weight: 0.3980 chunk 123 optimal weight: 7.9990 overall best weight: 0.8198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS B 53 ASN C 282 GLN I 142 HIS ** I 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.169533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.144102 restraints weight = 22861.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.147781 restraints weight = 13727.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.150227 restraints weight = 9622.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.151843 restraints weight = 7473.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.153130 restraints weight = 6231.707| |-----------------------------------------------------------------------------| r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.5052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14060 Z= 0.149 Angle : 0.639 20.314 19132 Z= 0.323 Chirality : 0.045 0.396 2095 Planarity : 0.004 0.051 2451 Dihedral : 5.405 54.969 2253 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.87 % Allowed : 15.75 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.20), residues: 1684 helix: 2.10 (0.27), residues: 363 sheet: 0.37 (0.31), residues: 260 loop : -0.66 (0.18), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 170 TYR 0.027 0.002 TYR B 119 PHE 0.021 0.002 PHE G 118 TRP 0.018 0.001 TRP H 36 HIS 0.006 0.001 HIS D 142 Details of bonding type rmsd covalent geometry : bond 0.00342 (14020) covalent geometry : angle 0.60604 (19032) SS BOND : bond 0.00350 ( 20) SS BOND : angle 1.04139 ( 40) hydrogen bonds : bond 0.04853 ( 574) hydrogen bonds : angle 5.33121 ( 1650) link_BETA1-4 : bond 0.00272 ( 4) link_BETA1-4 : angle 1.50947 ( 12) link_NAG-ASN : bond 0.00791 ( 16) link_NAG-ASN : angle 3.92948 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 217 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8054 (t0) cc_final: 0.7840 (t0) REVERT: A 32 LYS cc_start: 0.8273 (mttp) cc_final: 0.7377 (mmmt) REVERT: B 125 GLN cc_start: 0.7601 (mm-40) cc_final: 0.7203 (tt0) REVERT: B 137 CYS cc_start: 0.5087 (m) cc_final: 0.4748 (m) REVERT: B 141 TYR cc_start: 0.6596 (m-80) cc_final: 0.5497 (m-80) REVERT: C 225 ASP cc_start: 0.7368 (OUTLIER) cc_final: 0.6811 (t0) REVERT: D 45 ILE cc_start: 0.7775 (OUTLIER) cc_final: 0.7536 (mp) REVERT: D 58 LYS cc_start: 0.7203 (mmmt) cc_final: 0.6892 (mmtt) REVERT: D 125 GLN cc_start: 0.8314 (tp40) cc_final: 0.7480 (tp-100) REVERT: G 179 LEU cc_start: 0.5491 (OUTLIER) cc_final: 0.5178 (mt) REVERT: G 187 ASN cc_start: 0.7269 (p0) cc_final: 0.7065 (p0) REVERT: G 224 ARG cc_start: 0.8251 (mtp85) cc_final: 0.6471 (mtt180) REVERT: I 109 ASP cc_start: 0.8035 (m-30) cc_final: 0.7435 (t0) REVERT: H 45 LEU cc_start: 0.7697 (mm) cc_final: 0.7441 (mm) REVERT: H 77 GLN cc_start: 0.7495 (OUTLIER) cc_final: 0.7245 (pp30) REVERT: H 100 PHE cc_start: 0.6983 (m-80) cc_final: 0.6208 (m-80) REVERT: L 48 ILE cc_start: 0.7736 (mp) cc_final: 0.7491 (mt) REVERT: L 89 GLN cc_start: 0.6789 (OUTLIER) cc_final: 0.6374 (tp40) outliers start: 72 outliers final: 54 residues processed: 260 average time/residue: 0.0939 time to fit residues: 37.4613 Evaluate side-chains 261 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 202 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 282 GLN Chi-restraints excluded: chain D residue 17 MET Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 33 ASN Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 118 PHE Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 158 ASN Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 92 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 75 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 167 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 282 GLN G 271 ASN ** I 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.164905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.141174 restraints weight = 22284.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.144752 restraints weight = 13251.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.147143 restraints weight = 9213.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.148804 restraints weight = 7105.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.149950 restraints weight = 5853.694| |-----------------------------------------------------------------------------| r_work (final): 0.4099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.5224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14060 Z= 0.151 Angle : 0.641 20.094 19132 Z= 0.322 Chirality : 0.046 0.391 2095 Planarity : 0.004 0.057 2451 Dihedral : 5.333 54.754 2253 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 4.80 % Allowed : 16.23 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.20), residues: 1684 helix: 2.15 (0.27), residues: 363 sheet: 0.31 (0.31), residues: 260 loop : -0.71 (0.18), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 170 TYR 0.028 0.002 TYR B 119 PHE 0.021 0.002 PHE G 118 TRP 0.017 0.001 TRP H 36 HIS 0.005 0.001 HIS D 142 Details of bonding type rmsd covalent geometry : bond 0.00352 (14020) covalent geometry : angle 0.60623 (19032) SS BOND : bond 0.00369 ( 20) SS BOND : angle 1.75516 ( 40) hydrogen bonds : bond 0.04777 ( 574) hydrogen bonds : angle 5.32565 ( 1650) link_BETA1-4 : bond 0.00317 ( 4) link_BETA1-4 : angle 1.52346 ( 12) link_NAG-ASN : bond 0.00724 ( 16) link_NAG-ASN : angle 3.88077 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 216 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8065 (t0) cc_final: 0.7772 (t0) REVERT: A 32 LYS cc_start: 0.8276 (mttp) cc_final: 0.7423 (mmmt) REVERT: B 59 MET cc_start: 0.6955 (tpp) cc_final: 0.6454 (tpp) REVERT: B 125 GLN cc_start: 0.7644 (mm-40) cc_final: 0.7261 (tt0) REVERT: B 137 CYS cc_start: 0.5111 (m) cc_final: 0.4730 (m) REVERT: B 141 TYR cc_start: 0.6635 (m-80) cc_final: 0.5600 (m-80) REVERT: C 18 HIS cc_start: 0.7479 (OUTLIER) cc_final: 0.7147 (p-80) REVERT: C 225 ASP cc_start: 0.7306 (OUTLIER) cc_final: 0.6948 (t70) REVERT: C 282 GLN cc_start: 0.7132 (OUTLIER) cc_final: 0.6873 (tt0) REVERT: D 45 ILE cc_start: 0.7836 (OUTLIER) cc_final: 0.7567 (mp) REVERT: D 58 LYS cc_start: 0.7220 (mmmt) cc_final: 0.6958 (mmtt) REVERT: G 179 LEU cc_start: 0.5490 (OUTLIER) cc_final: 0.5190 (mt) REVERT: G 224 ARG cc_start: 0.8261 (mtp85) cc_final: 0.6440 (mtt180) REVERT: I 109 ASP cc_start: 0.8006 (m-30) cc_final: 0.7542 (t0) REVERT: H 45 LEU cc_start: 0.7547 (mm) cc_final: 0.7335 (mm) REVERT: H 100 PHE cc_start: 0.6760 (m-80) cc_final: 0.6084 (m-80) REVERT: L 89 GLN cc_start: 0.6870 (OUTLIER) cc_final: 0.5569 (tp40) outliers start: 71 outliers final: 53 residues processed: 260 average time/residue: 0.0845 time to fit residues: 34.1304 Evaluate side-chains 252 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 193 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 282 GLN Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain D residue 17 MET Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 118 PHE Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 158 ASN Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 92 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 16 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 165 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 76 optimal weight: 7.9990 chunk 84 optimal weight: 7.9990 chunk 15 optimal weight: 0.9980 chunk 157 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS C 282 GLN G 271 ASN ** I 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.168474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.143060 restraints weight = 22881.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.146632 restraints weight = 13889.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.149021 restraints weight = 9792.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.150752 restraints weight = 7660.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.151635 restraints weight = 6347.111| |-----------------------------------------------------------------------------| r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.5352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 14060 Z= 0.171 Angle : 0.669 20.131 19132 Z= 0.332 Chirality : 0.048 0.565 2095 Planarity : 0.004 0.060 2451 Dihedral : 5.625 59.637 2253 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.73 % Allowed : 16.29 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.20), residues: 1684 helix: 2.10 (0.27), residues: 363 sheet: 0.27 (0.30), residues: 289 loop : -0.76 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 170 TYR 0.028 0.002 TYR B 119 PHE 0.022 0.002 PHE G 118 TRP 0.017 0.002 TRP H 36 HIS 0.005 0.001 HIS D 142 Details of bonding type rmsd covalent geometry : bond 0.00397 (14020) covalent geometry : angle 0.61978 (19032) SS BOND : bond 0.00406 ( 20) SS BOND : angle 1.67651 ( 40) hydrogen bonds : bond 0.04766 ( 574) hydrogen bonds : angle 5.33944 ( 1650) link_BETA1-4 : bond 0.00333 ( 4) link_BETA1-4 : angle 1.55547 ( 12) link_NAG-ASN : bond 0.00870 ( 16) link_NAG-ASN : angle 4.78958 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 212 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8123 (t0) cc_final: 0.7765 (t0) REVERT: A 32 LYS cc_start: 0.8332 (mttp) cc_final: 0.7420 (mmmt) REVERT: B 59 MET cc_start: 0.6934 (tpp) cc_final: 0.6483 (tpp) REVERT: B 125 GLN cc_start: 0.7600 (mm-40) cc_final: 0.7208 (tt0) REVERT: B 137 CYS cc_start: 0.4972 (m) cc_final: 0.4619 (m) REVERT: B 141 TYR cc_start: 0.6661 (m-80) cc_final: 0.5664 (m-80) REVERT: C 18 HIS cc_start: 0.7653 (OUTLIER) cc_final: 0.7336 (p-80) REVERT: C 110 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7494 (mm-30) REVERT: C 225 ASP cc_start: 0.7286 (OUTLIER) cc_final: 0.6733 (t0) REVERT: D 45 ILE cc_start: 0.7840 (OUTLIER) cc_final: 0.7584 (mp) REVERT: D 58 LYS cc_start: 0.7253 (mmmt) cc_final: 0.7008 (mmtt) REVERT: D 162 TYR cc_start: 0.8174 (m-80) cc_final: 0.7607 (m-10) REVERT: G 179 LEU cc_start: 0.5576 (OUTLIER) cc_final: 0.5253 (mt) REVERT: G 187 ASN cc_start: 0.7319 (p0) cc_final: 0.7116 (p0) REVERT: G 224 ARG cc_start: 0.8371 (mtp85) cc_final: 0.6536 (mtt180) REVERT: G 245 PHE cc_start: 0.6154 (m-80) cc_final: 0.5923 (m-10) REVERT: I 109 ASP cc_start: 0.8009 (m-30) cc_final: 0.7493 (t0) REVERT: H 45 LEU cc_start: 0.7571 (mm) cc_final: 0.7359 (mm) REVERT: H 100 PHE cc_start: 0.6855 (m-80) cc_final: 0.6454 (m-80) REVERT: L 11 LEU cc_start: 0.8858 (mm) cc_final: 0.7923 (tt) REVERT: L 48 ILE cc_start: 0.7693 (mp) cc_final: 0.7459 (mt) REVERT: L 89 GLN cc_start: 0.6938 (OUTLIER) cc_final: 0.5962 (tp40) outliers start: 70 outliers final: 56 residues processed: 258 average time/residue: 0.0868 time to fit residues: 34.6935 Evaluate side-chains 261 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 200 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain D residue 17 MET Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 118 PHE Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 158 ASN Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 92 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 64 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 129 optimal weight: 8.9990 chunk 108 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 148 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 282 GLN G 271 ASN ** I 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.159759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.135687 restraints weight = 22787.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.139085 restraints weight = 13911.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.141379 restraints weight = 9852.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.142915 restraints weight = 7681.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.144053 restraints weight = 6429.223| |-----------------------------------------------------------------------------| r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.5558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 14060 Z= 0.238 Angle : 0.736 20.431 19132 Z= 0.369 Chirality : 0.049 0.513 2095 Planarity : 0.005 0.062 2451 Dihedral : 5.842 54.893 2253 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.60 % Allowed : 16.90 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.20), residues: 1684 helix: 1.79 (0.27), residues: 363 sheet: -0.06 (0.31), residues: 271 loop : -0.91 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 170 TYR 0.032 0.002 TYR C 105 PHE 0.030 0.003 PHE G 118 TRP 0.018 0.002 TRP H 36 HIS 0.006 0.002 HIS D 142 Details of bonding type rmsd covalent geometry : bond 0.00558 (14020) covalent geometry : angle 0.69567 (19032) SS BOND : bond 0.00507 ( 20) SS BOND : angle 1.54609 ( 40) hydrogen bonds : bond 0.05078 ( 574) hydrogen bonds : angle 5.54252 ( 1650) link_BETA1-4 : bond 0.00232 ( 4) link_BETA1-4 : angle 1.80853 ( 12) link_NAG-ASN : bond 0.00941 ( 16) link_NAG-ASN : angle 4.61618 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 202 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8226 (t0) cc_final: 0.7887 (t0) REVERT: A 32 LYS cc_start: 0.8386 (mttp) cc_final: 0.7523 (mmmt) REVERT: B 59 MET cc_start: 0.6939 (tpp) cc_final: 0.6443 (tpp) REVERT: B 89 LEU cc_start: 0.8518 (tp) cc_final: 0.8167 (tp) REVERT: B 125 GLN cc_start: 0.7711 (mm-40) cc_final: 0.7422 (tt0) REVERT: B 137 CYS cc_start: 0.4944 (m) cc_final: 0.4638 (m) REVERT: B 141 TYR cc_start: 0.6600 (m-80) cc_final: 0.5598 (m-80) REVERT: C 18 HIS cc_start: 0.7764 (OUTLIER) cc_final: 0.7398 (p-80) REVERT: C 105 TYR cc_start: 0.7227 (t80) cc_final: 0.6859 (t80) REVERT: C 225 ASP cc_start: 0.7267 (OUTLIER) cc_final: 0.6693 (t0) REVERT: D 45 ILE cc_start: 0.7843 (OUTLIER) cc_final: 0.7609 (mp) REVERT: D 125 GLN cc_start: 0.8310 (tp40) cc_final: 0.7501 (tp-100) REVERT: D 162 TYR cc_start: 0.8079 (m-80) cc_final: 0.7724 (m-10) REVERT: G 175 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7438 (mp0) REVERT: G 179 LEU cc_start: 0.5750 (OUTLIER) cc_final: 0.5431 (mt) REVERT: G 187 ASN cc_start: 0.7276 (p0) cc_final: 0.7056 (p0) REVERT: G 195 TYR cc_start: 0.8258 (m-10) cc_final: 0.7863 (m-10) REVERT: G 224 ARG cc_start: 0.8361 (mtp85) cc_final: 0.6581 (mtt180) REVERT: G 245 PHE cc_start: 0.6296 (m-80) cc_final: 0.5971 (m-10) REVERT: I 109 ASP cc_start: 0.8060 (m-30) cc_final: 0.7584 (t0) REVERT: H 45 LEU cc_start: 0.7724 (mm) cc_final: 0.7522 (mm) REVERT: H 100 PHE cc_start: 0.6797 (m-80) cc_final: 0.6240 (m-80) REVERT: L 11 LEU cc_start: 0.8816 (mm) cc_final: 0.7948 (tt) outliers start: 68 outliers final: 56 residues processed: 246 average time/residue: 0.0914 time to fit residues: 34.3583 Evaluate side-chains 252 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 191 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 282 GLN Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain D residue 17 MET Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 33 ASN Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 118 PHE Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 158 ASN Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 175 GLU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 35 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN G 271 ASN ** I 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.166533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.141244 restraints weight = 23000.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.144809 restraints weight = 13931.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.147169 restraints weight = 9829.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.148844 restraints weight = 7701.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.150019 restraints weight = 6414.035| |-----------------------------------------------------------------------------| r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.5649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14060 Z= 0.154 Angle : 0.679 19.980 19132 Z= 0.338 Chirality : 0.047 0.454 2095 Planarity : 0.004 0.064 2451 Dihedral : 5.646 55.328 2253 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.92 % Allowed : 17.51 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.20), residues: 1684 helix: 1.99 (0.27), residues: 363 sheet: -0.01 (0.31), residues: 265 loop : -0.89 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 170 TYR 0.030 0.002 TYR B 119 PHE 0.022 0.002 PHE G 118 TRP 0.017 0.002 TRP H 36 HIS 0.005 0.001 HIS D 142 Details of bonding type rmsd covalent geometry : bond 0.00358 (14020) covalent geometry : angle 0.63738 (19032) SS BOND : bond 0.00328 ( 20) SS BOND : angle 1.50846 ( 40) hydrogen bonds : bond 0.04736 ( 574) hydrogen bonds : angle 5.39158 ( 1650) link_BETA1-4 : bond 0.00289 ( 4) link_BETA1-4 : angle 1.72629 ( 12) link_NAG-ASN : bond 0.00866 ( 16) link_NAG-ASN : angle 4.44802 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 207 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8212 (t0) cc_final: 0.7824 (t0) REVERT: B 59 MET cc_start: 0.6915 (tpp) cc_final: 0.6464 (tpp) REVERT: B 125 GLN cc_start: 0.7672 (mm-40) cc_final: 0.7348 (tt0) REVERT: B 137 CYS cc_start: 0.4931 (m) cc_final: 0.4586 (m) REVERT: B 141 TYR cc_start: 0.6622 (m-80) cc_final: 0.5587 (m-80) REVERT: C 18 HIS cc_start: 0.7764 (OUTLIER) cc_final: 0.7371 (p-80) REVERT: C 105 TYR cc_start: 0.7092 (t80) cc_final: 0.6736 (t80) REVERT: C 225 ASP cc_start: 0.7235 (OUTLIER) cc_final: 0.6809 (t0) REVERT: D 45 ILE cc_start: 0.7762 (OUTLIER) cc_final: 0.7530 (mp) REVERT: D 125 GLN cc_start: 0.8303 (tp40) cc_final: 0.7654 (tp-100) REVERT: D 162 TYR cc_start: 0.8126 (m-80) cc_final: 0.7896 (m-10) REVERT: D 168 LEU cc_start: 0.8848 (tp) cc_final: 0.8617 (mt) REVERT: G 175 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7508 (mp0) REVERT: G 179 LEU cc_start: 0.5680 (OUTLIER) cc_final: 0.5436 (mt) REVERT: G 187 ASN cc_start: 0.7199 (p0) cc_final: 0.6975 (p0) REVERT: G 224 ARG cc_start: 0.8408 (mtp85) cc_final: 0.6606 (mtt180) REVERT: G 245 PHE cc_start: 0.6160 (m-80) cc_final: 0.5883 (m-10) REVERT: I 109 ASP cc_start: 0.7989 (m-30) cc_final: 0.7516 (t0) REVERT: I 126 LEU cc_start: 0.5176 (OUTLIER) cc_final: 0.4796 (mp) REVERT: H 45 LEU cc_start: 0.7622 (mm) cc_final: 0.7413 (mm) REVERT: H 100 PHE cc_start: 0.6871 (m-80) cc_final: 0.6509 (m-80) REVERT: L 11 LEU cc_start: 0.8821 (mm) cc_final: 0.7945 (tt) REVERT: L 48 ILE cc_start: 0.7616 (mp) cc_final: 0.7363 (mt) outliers start: 58 outliers final: 50 residues processed: 247 average time/residue: 0.0889 time to fit residues: 34.0111 Evaluate side-chains 256 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 200 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 33 ASN Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 118 PHE Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 158 ASN Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 175 GLU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 12 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 94 optimal weight: 7.9990 chunk 130 optimal weight: 4.9990 chunk 139 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 282 GLN ** C 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN I 142 HIS ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.159804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.135624 restraints weight = 22539.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.138615 restraints weight = 14678.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.140743 restraints weight = 10817.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.142287 restraints weight = 8634.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.143285 restraints weight = 7260.250| |-----------------------------------------------------------------------------| r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.5823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14060 Z= 0.229 Angle : 0.735 20.354 19132 Z= 0.369 Chirality : 0.049 0.431 2095 Planarity : 0.005 0.060 2451 Dihedral : 5.777 54.489 2253 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.99 % Allowed : 17.92 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.20), residues: 1684 helix: 1.80 (0.27), residues: 363 sheet: -0.22 (0.29), residues: 301 loop : -0.99 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 170 TYR 0.031 0.002 TYR B 119 PHE 0.030 0.002 PHE G 118 TRP 0.018 0.002 TRP H 103 HIS 0.006 0.001 HIS G 183 Details of bonding type rmsd covalent geometry : bond 0.00539 (14020) covalent geometry : angle 0.69557 (19032) SS BOND : bond 0.00506 ( 20) SS BOND : angle 1.49635 ( 40) hydrogen bonds : bond 0.05020 ( 574) hydrogen bonds : angle 5.55388 ( 1650) link_BETA1-4 : bond 0.00251 ( 4) link_BETA1-4 : angle 1.85485 ( 12) link_NAG-ASN : bond 0.00900 ( 16) link_NAG-ASN : angle 4.54642 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2019.93 seconds wall clock time: 35 minutes 53.68 seconds (2153.68 seconds total)