Starting phenix.real_space_refine on Fri Jul 3 10:59:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8tp3_41465/07_2026/8tp3_41465.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tp3_41465/07_2026/8tp3_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8tp3_41465/07_2026/8tp3_41465.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8tp3_41465/07_2026/8tp3_41465.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tp3_41465/07_2026/8tp3_41465.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tp3_41465/07_2026/8tp3_41465.map" model { file = "/net/cci-nas-00/data/ceres_data/8tp3_41465/07_2026/8tp3_41465.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tp3_41465/07_2026/8tp3_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-dev-6108/lib/python3.11/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 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 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 chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "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 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 chiralities: 4 Time building chain proxies: 3.28, 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: 1.16 Conformation dependent library (CDL) restraints added in 498.6 milliseconds 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: 0.47 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: 2.41 Time building geometry restraints manager: 1.48 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 - 17.76: 7887 17.76 - 35.53: 203 35.53 - 53.29: 47 53.29 - 71.05: 24 71.05 - 88.81: 11 Dihedral angle restraints: 8172 sinusoidal: 3269 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 8169 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: 3.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 13.630 Find NCS groups from input model: 0.240 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 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 : 9.928 88.813 4984 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 are 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/Z covalent geometry : bond 0.01998 / 1.06 (14020) covalent geometry : angle 1.72001 / 1.15 (19032) SS BOND : bond 0.01239 / 0.82 ( 20) SS BOND : angle 7.33259 / 4.01 ( 40) hydrogen bonds : bond 0.16452 / 10.89 ( 574) hydrogen bonds : angle 7.83854 / 5.37 ( 1650) link_BETA1-4 : bond 0.06779 / 3.41 ( 4) link_BETA1-4 : angle 4.13060 / 1.95 ( 12) link_NAG-ASN : bond 0.07259 / 4.51 ( 16) link_NAG-ASN : angle 3.25146 / 2.05 ( 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 : 0.502 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: 0.7216 (p90) REVERT: G 224 ARG cc_start: 0.8435 (mtp85) cc_final: 0.6353 (mpt180) REVERT: G 256 TYR cc_start: 0.8343 (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: 0.1234 time to fit residues: 85.9952 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 : 0.399 ------------------------------------------------------------------------------- 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... ** 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 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** H 1 GLN ** 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 = 0.4272 r_free = 0.4272 target = 0.164971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.140804 restraints weight = 22303.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.144598 restraints weight = 13033.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.147142 restraints weight = 8956.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.148715 restraints weight = 6827.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.150044 restraints weight = 5654.964| |-----------------------------------------------------------------------------| r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 14060 Z= 0.187 Angle : 0.754 22.190 19132 Z= 0.394 Chirality : 0.049 0.441 2095 Planarity : 0.005 0.056 2451 Dihedral : 5.262 20.638 1835 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 3.38 % Allowed : 9.94 % Favored : 86.68 % 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 are not related in a simple way. whole: 0.80 (0.19), residues: 1684 helix: 1.85 (0.26), residues: 361 sheet: 1.13 (0.31), residues: 260 loop : -0.05 (0.18), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 321 TYR 0.020 0.002 TYR G 86 PHE 0.019 0.002 PHE G 118 TRP 0.012 0.002 TRP G 153 HIS 0.010 0.001 HIS A 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 (14020) covalent geometry : angle 0.71336 / 0.39 (19032) SS BOND : bond 0.00441 / 0.27 ( 20) SS BOND : angle 1.30516 / 0.83 ( 40) hydrogen bonds : bond 0.06515 / 4.21 ( 574) hydrogen bonds : angle 6.00121 / 4.17 ( 1650) link_BETA1-4 : bond 0.00140 / 0.07 ( 4) link_BETA1-4 : angle 2.40592 / 1.59 ( 12) link_NAG-ASN : bond 0.00743 / 0.45 ( 16) link_NAG-ASN : angle 4.67311 / 2.87 ( 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 321 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 271 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.8924 (m-30) cc_final: 0.8688 (m-30) REVERT: A 274 MET cc_start: 0.7165 (mtt) cc_final: 0.6496 (ttt) REVERT: B 17 MET cc_start: 0.7502 (ttt) cc_final: 0.7269 (ttt) REVERT: B 19 ASP cc_start: 0.7447 (p0) cc_final: 0.6706 (t0) REVERT: B 53 ASN cc_start: 0.5920 (m-40) cc_final: 0.5496 (t0) REVERT: B 128 ASN cc_start: 0.7491 (m-40) cc_final: 0.7278 (t0) REVERT: B 141 TYR cc_start: 0.6264 (m-80) cc_final: 0.5360 (m-80) REVERT: C 82 LYS cc_start: 0.7135 (mmtt) cc_final: 0.6927 (tptp) REVERT: C 226 GLN cc_start: 0.7920 (mm-40) cc_final: 0.7686 (mm-40) REVERT: D 50 ASN cc_start: 0.8093 (m-40) cc_final: 0.7863 (m-40) REVERT: D 142 HIS cc_start: 0.8209 (p90) cc_final: 0.7768 (p90) REVERT: G 45 ASP cc_start: 0.7950 (p0) cc_final: 0.7647 (p0) REVERT: G 107 GLU cc_start: 0.7689 (tp30) cc_final: 0.7350 (tp30) REVERT: G 224 ARG cc_start: 0.8180 (mtp85) cc_final: 0.6236 (mtt180) REVERT: I 109 ASP cc_start: 0.7887 (m-30) cc_final: 0.7329 (t70) REVERT: H 36 TRP cc_start: 0.8221 (m100) cc_final: 0.7407 (m100) REVERT: L 1 GLU cc_start: 0.5508 (pp20) cc_final: 0.5057 (mp0) REVERT: L 48 ILE cc_start: 0.7901 (mp) cc_final: 0.7685 (mt) REVERT: L 100 GLN cc_start: 0.7471 (pm20) cc_final: 0.7192 (pm20) outliers start: 50 outliers final: 23 residues processed: 306 average time/residue: 0.1132 time to fit residues: 51.3004 Evaluate side-chains 235 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 212 time to evaluate : 0.415 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 140 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 162 optimal weight: 0.0770 chunk 165 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 147 optimal weight: 9.9990 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.165228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.142345 restraints weight = 21660.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.145660 restraints weight = 13382.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.147938 restraints weight = 9538.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.149340 restraints weight = 7424.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.150565 restraints weight = 6231.317| |-----------------------------------------------------------------------------| r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14060 Z= 0.172 Angle : 0.678 20.617 19132 Z= 0.348 Chirality : 0.047 0.382 2095 Planarity : 0.005 0.047 2451 Dihedral : 4.902 19.306 1835 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.52 % Allowed : 12.44 % Favored : 84.04 % 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 are not related in a simple way. whole: 0.67 (0.19), residues: 1684 helix: 2.09 (0.26), residues: 361 sheet: 0.95 (0.32), residues: 240 loop : -0.23 (0.18), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 170 TYR 0.016 0.002 TYR H 59 PHE 0.022 0.002 PHE H 78 TRP 0.018 0.002 TRP L 96 HIS 0.005 0.001 HIS A 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (14020) covalent geometry : angle 0.64207 / 0.34 (19032) SS BOND : bond 0.00361 / 0.21 ( 20) SS BOND : angle 1.13548 / 0.74 ( 40) hydrogen bonds : bond 0.05568 / 3.60 ( 574) hydrogen bonds : angle 5.58145 / 3.90 ( 1650) link_BETA1-4 : bond 0.00373 / 0.19 ( 4) link_BETA1-4 : angle 1.61633 / 0.97 ( 12) link_NAG-ASN : bond 0.00927 / 0.55 ( 16) link_NAG-ASN : angle 4.26687 / 2.80 ( 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 294 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 242 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.7699 (t0) cc_final: 0.7460 (t0) REVERT: A 274 MET cc_start: 0.6961 (mtt) cc_final: 0.6499 (ttt) REVERT: B 53 ASN cc_start: 0.6176 (m-40) cc_final: 0.5663 (t0) REVERT: B 125 GLN cc_start: 0.7350 (mm-40) cc_final: 0.7006 (tt0) REVERT: B 141 TYR cc_start: 0.6322 (m-80) cc_final: 0.5478 (m-80) REVERT: B 170 ARG cc_start: 0.6997 (ttm110) cc_final: 0.6623 (ttm110) REVERT: C 83 GLU cc_start: 0.6570 (mm-30) cc_final: 0.6236 (mm-30) REVERT: C 84 TRP cc_start: 0.5840 (m-10) cc_final: 0.5558 (m-10) REVERT: C 211 ARG cc_start: 0.6811 (mtp85) cc_final: 0.6526 (ttt90) REVERT: C 226 GLN cc_start: 0.7853 (mm-40) cc_final: 0.7582 (mm-40) REVERT: D 45 ILE cc_start: 0.7710 (OUTLIER) cc_final: 0.7496 (mp) REVERT: G 148 TYR cc_start: 0.7616 (m-80) cc_final: 0.7334 (m-80) REVERT: G 224 ARG cc_start: 0.7935 (mtp85) cc_final: 0.6265 (mtt180) REVERT: I 109 ASP cc_start: 0.7881 (m-30) cc_final: 0.7312 (t0) REVERT: H 36 TRP cc_start: 0.8354 (m100) cc_final: 0.7576 (m100) REVERT: H 103 TRP cc_start: 0.7500 (m-10) cc_final: 0.7287 (m-10) REVERT: L 100 GLN cc_start: 0.7722 (pm20) cc_final: 0.7300 (pm20) outliers start: 52 outliers final: 39 residues processed: 272 average time/residue: 0.1127 time to fit residues: 45.4939 Evaluate side-chains 247 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 207 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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 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 45 ILE 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: 7.9990 chunk 96 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 161 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 35 optimal weight: 0.0970 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 HIS D 43 ASN D 142 HIS ** I 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 142 HIS H 32 HIS ** 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 = 0.4326 r_free = 0.4326 target = 0.169343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.145530 restraints weight = 22343.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.149299 restraints weight = 13000.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.151784 restraints weight = 8917.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.153565 restraints weight = 6813.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.154555 restraints weight = 5561.893| |-----------------------------------------------------------------------------| r_work (final): 0.4143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14060 Z= 0.182 Angle : 0.674 20.593 19132 Z= 0.341 Chirality : 0.046 0.393 2095 Planarity : 0.005 0.051 2451 Dihedral : 4.782 18.601 1835 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 4.19 % Allowed : 13.59 % Favored : 82.22 % 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 are not related in a simple way. whole: 0.50 (0.20), residues: 1684 helix: 2.10 (0.26), residues: 363 sheet: 0.71 (0.32), residues: 246 loop : -0.38 (0.18), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 170 TYR 0.026 0.002 TYR C 201 PHE 0.023 0.002 PHE H 78 TRP 0.029 0.002 TRP L 96 HIS 0.006 0.001 HIS D 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 (14020) covalent geometry : angle 0.64099 / 0.33 (19032) SS BOND : bond 0.00371 / 0.23 ( 20) SS BOND : angle 1.09992 / 0.72 ( 40) hydrogen bonds : bond 0.05222 / 3.39 ( 574) hydrogen bonds : angle 5.40192 / 3.80 ( 1650) link_BETA1-4 : bond 0.00212 / 0.11 ( 4) link_BETA1-4 : angle 1.60774 / 1.00 ( 12) link_NAG-ASN : bond 0.00740 / 0.41 ( 16) link_NAG-ASN : angle 4.09140 / 2.54 ( 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 279 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 217 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.7822 (t0) cc_final: 0.7568 (t0) REVERT: A 32 LYS cc_start: 0.8507 (mttp) cc_final: 0.7696 (mmmt) REVERT: A 104 ASP cc_start: 0.8960 (m-30) cc_final: 0.8642 (m-30) REVERT: B 125 GLN cc_start: 0.7595 (mm-40) cc_final: 0.7104 (tt0) REVERT: B 141 TYR cc_start: 0.6399 (m-80) cc_final: 0.5470 (m-80) REVERT: C 211 ARG cc_start: 0.7049 (mtp85) cc_final: 0.6819 (ttt90) REVERT: C 225 ASP cc_start: 0.7259 (t0) cc_final: 0.6892 (t0) REVERT: C 226 GLN cc_start: 0.7881 (mm-40) cc_final: 0.7599 (mm-40) REVERT: D 58 LYS cc_start: 0.7302 (mmmt) cc_final: 0.6889 (mmtt) REVERT: D 142 HIS cc_start: 0.7868 (p90) cc_final: 0.7520 (p90) REVERT: G 32 LYS cc_start: 0.6968 (mmmm) cc_final: 0.6616 (mmtt) REVERT: G 148 TYR cc_start: 0.7815 (m-80) cc_final: 0.7491 (m-80) REVERT: G 224 ARG cc_start: 0.8037 (mtp85) cc_final: 0.6363 (mtt180) REVERT: G 314 LEU cc_start: 0.6306 (OUTLIER) cc_final: 0.5992 (mm) REVERT: G 320 LEU cc_start: 0.8565 (mp) cc_final: 0.8182 (mt) REVERT: I 109 ASP cc_start: 0.7969 (m-30) cc_final: 0.7335 (t0) REVERT: H 100 PHE cc_start: 0.7075 (m-80) cc_final: 0.6309 (m-80) REVERT: L 89 GLN cc_start: 0.6961 (OUTLIER) cc_final: 0.6613 (tp40) outliers start: 62 outliers final: 45 residues processed: 254 average time/residue: 0.0994 time to fit residues: 38.5496 Evaluate side-chains 249 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 202 time to evaluate : 0.572 ------------------------------------------------------------------------------- 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 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 242 THR Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 302 ILE 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 D residue 118 LEU Chi-restraints excluded: chain D residue 122 VAL 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 158 ASN 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 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 H residue 86 ASP Chi-restraints excluded: chain L residue 30 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 34 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 167 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 146 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 42 GLN C 141 HIS C 282 GLN ** C 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 90 GLN ** 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 = 0.4280 r_free = 0.4280 target = 0.165031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.141349 restraints weight = 22596.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.144954 restraints weight = 13413.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.147353 restraints weight = 9299.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.148977 restraints weight = 7142.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.150030 restraints weight = 5899.025| |-----------------------------------------------------------------------------| r_work (final): 0.4099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.4800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14060 Z= 0.178 Angle : 0.658 20.303 19132 Z= 0.334 Chirality : 0.046 0.393 2095 Planarity : 0.004 0.052 2451 Dihedral : 4.732 24.909 1835 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.67 % Allowed : 14.20 % Favored : 81.14 % 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 are not related in a simple way. whole: 0.33 (0.20), residues: 1684 helix: 2.07 (0.27), residues: 363 sheet: 0.48 (0.32), residues: 256 loop : -0.51 (0.18), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 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 103 HIS 0.007 0.001 HIS D 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (14020) covalent geometry : angle 0.62099 / 0.33 (19032) SS BOND : bond 0.00405 / 0.24 ( 20) SS BOND : angle 1.03169 / 0.66 ( 40) hydrogen bonds : bond 0.04969 / 3.23 ( 574) hydrogen bonds : angle 5.35979 / 3.79 ( 1650) link_BETA1-4 : bond 0.00364 / 0.18 ( 4) link_BETA1-4 : angle 1.42894 / 0.85 ( 12) link_NAG-ASN : bond 0.00742 / 0.42 ( 16) link_NAG-ASN : angle 4.30357 / 2.91 ( 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 294 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 225 time to evaluate : 0.532 Fit side-chains revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8565 (mttp) cc_final: 0.7727 (mmmt) REVERT: B 125 GLN cc_start: 0.7479 (mm-40) cc_final: 0.7108 (tt0) REVERT: B 141 TYR cc_start: 0.6493 (m-80) cc_final: 0.5649 (m-80) REVERT: C 226 GLN cc_start: 0.7945 (mm-40) cc_final: 0.7382 (mm-40) REVERT: D 45 ILE cc_start: 0.7911 (OUTLIER) cc_final: 0.7673 (mp) REVERT: D 58 LYS cc_start: 0.7319 (mmmt) cc_final: 0.6946 (mmtt) REVERT: D 142 HIS cc_start: 0.7712 (p90) cc_final: 0.7446 (p90) REVERT: G 32 LYS cc_start: 0.6868 (mmmm) cc_final: 0.6274 (tppt) REVERT: G 148 TYR cc_start: 0.7907 (m-80) cc_final: 0.7511 (m-80) REVERT: G 224 ARG cc_start: 0.8039 (mtp85) cc_final: 0.6401 (mtt180) REVERT: G 314 LEU cc_start: 0.6237 (OUTLIER) cc_final: 0.5972 (mm) REVERT: I 109 ASP cc_start: 0.8020 (m-30) cc_final: 0.7749 (t70) REVERT: H 77 GLN cc_start: 0.7435 (OUTLIER) cc_final: 0.7187 (pp30) REVERT: H 100 PHE cc_start: 0.7011 (m-80) cc_final: 0.6368 (m-80) REVERT: L 89 GLN cc_start: 0.7116 (OUTLIER) cc_final: 0.6631 (tp40) outliers start: 69 outliers final: 49 residues processed: 268 average time/residue: 0.1058 time to fit residues: 42.4446 Evaluate side-chains 254 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 201 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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 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 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 235 THR 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 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 66 VAL 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 40 VAL Chi-restraints excluded: chain G residue 54 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 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 55 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 74 THR Chi-restraints excluded: chain L residue 89 GLN 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: 3.9990 chunk 159 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 71 optimal weight: 0.7980 chunk 153 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 282 GLN ** C 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 HIS D 27 GLN D 43 ASN I 125 GLN I 142 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.163081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.139049 restraints weight = 22549.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.142618 restraints weight = 13503.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.144999 restraints weight = 9438.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.146587 restraints weight = 7305.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.147721 restraints weight = 6073.719| |-----------------------------------------------------------------------------| r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.5001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 14060 Z= 0.184 Angle : 0.665 20.267 19132 Z= 0.336 Chirality : 0.047 0.394 2095 Planarity : 0.004 0.053 2451 Dihedral : 4.703 18.556 1835 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 4.60 % Allowed : 15.35 % Favored : 80.05 % 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 are not related in a simple way. whole: 0.18 (0.20), residues: 1684 helix: 2.02 (0.27), residues: 363 sheet: 0.32 (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 0.029 0.002 TYR B 119 PHE 0.024 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/Z covalent geometry : bond 0.00433 / 0.18 (14020) covalent geometry : angle 0.62948 / 0.33 (19032) SS BOND : bond 0.00511 / 0.28 ( 20) SS BOND : angle 1.34804 / 0.92 ( 40) hydrogen bonds : bond 0.04914 / 3.21 ( 574) hydrogen bonds : angle 5.37397 / 3.79 ( 1650) link_BETA1-4 : bond 0.00288 / 0.14 ( 4) link_BETA1-4 : angle 1.56074 / 0.98 ( 12) link_NAG-ASN : bond 0.00730 / 0.40 ( 16) link_NAG-ASN : angle 4.11476 / 2.62 ( 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 290 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 222 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8679 (mttp) cc_final: 0.7617 (mmmt) REVERT: B 125 GLN cc_start: 0.7573 (mm-40) cc_final: 0.7234 (tt0) REVERT: B 137 CYS cc_start: 0.5179 (m) cc_final: 0.4826 (m) REVERT: B 141 TYR cc_start: 0.6595 (m-80) cc_final: 0.5757 (m-80) REVERT: C 225 ASP cc_start: 0.6964 (t0) cc_final: 0.6320 (t0) REVERT: D 45 ILE cc_start: 0.7873 (OUTLIER) cc_final: 0.7636 (mp) REVERT: D 58 LYS cc_start: 0.7304 (mmmt) cc_final: 0.6982 (mmtt) REVERT: D 142 HIS cc_start: 0.7774 (p90) cc_final: 0.7520 (p90) REVERT: G 224 ARG cc_start: 0.8172 (mtp85) cc_final: 0.6483 (mtt180) REVERT: G 314 LEU cc_start: 0.6331 (OUTLIER) cc_final: 0.6030 (mm) REVERT: I 109 ASP cc_start: 0.8099 (m-30) cc_final: 0.7515 (t0) REVERT: H 100 PHE cc_start: 0.6856 (m-80) cc_final: 0.6527 (m-80) REVERT: L 48 ILE cc_start: 0.7735 (mp) cc_final: 0.7487 (mt) REVERT: L 89 GLN cc_start: 0.7130 (OUTLIER) cc_final: 0.6454 (tp40) outliers start: 68 outliers final: 56 residues processed: 266 average time/residue: 0.0935 time to fit residues: 38.1714 Evaluate side-chains 266 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 207 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 107 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 13 ILE 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 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 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 89 LEU Chi-restraints excluded: chain D residue 122 VAL 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 112 LEU Chi-restraints excluded: chain G residue 118 PHE Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 158 ASN Chi-restraints excluded: chain G residue 164 LEU 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 32 SER 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 23 CYS Chi-restraints excluded: chain L residue 30 SER 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: 1.9990 chunk 43 optimal weight: 0.7980 chunk 33 optimal weight: 0.0370 chunk 85 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 282 GLN ** C 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN ** I 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.164460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.140721 restraints weight = 22202.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.144289 restraints weight = 13251.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.146702 restraints weight = 9219.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.148318 restraints weight = 7084.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.149326 restraints weight = 5866.551| |-----------------------------------------------------------------------------| r_work (final): 0.4105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.5187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14060 Z= 0.138 Angle : 0.625 19.974 19132 Z= 0.315 Chirality : 0.045 0.393 2095 Planarity : 0.004 0.052 2451 Dihedral : 4.569 18.722 1835 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 4.46 % Allowed : 15.62 % Favored : 79.92 % 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 are not related in a simple way. whole: 0.21 (0.20), residues: 1684 helix: 2.18 (0.27), residues: 363 sheet: 0.31 (0.32), residues: 249 loop : -0.64 (0.18), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 170 TYR 0.028 0.002 TYR B 119 PHE 0.034 0.002 PHE L 71 TRP 0.017 0.001 TRP H 36 HIS 0.005 0.001 HIS D 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (14020) covalent geometry : angle 0.59163 / 0.31 (19032) SS BOND : bond 0.00464 / 0.26 ( 20) SS BOND : angle 1.43758 / 0.94 ( 40) hydrogen bonds : bond 0.04693 / 3.06 ( 574) hydrogen bonds : angle 5.26900 / 3.72 ( 1650) link_BETA1-4 : bond 0.00251 / 0.13 ( 4) link_BETA1-4 : angle 1.32821 / 0.83 ( 12) link_NAG-ASN : bond 0.00705 / 0.38 ( 16) link_NAG-ASN : angle 3.87247 / 2.38 ( 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 284 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 218 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8225 (mttp) cc_final: 0.7656 (mmmt) REVERT: B 125 GLN cc_start: 0.7613 (mm-40) cc_final: 0.7264 (tt0) REVERT: B 137 CYS cc_start: 0.5129 (m) cc_final: 0.4780 (m) REVERT: B 141 TYR cc_start: 0.6581 (m-80) cc_final: 0.5607 (m-80) REVERT: C 225 ASP cc_start: 0.7077 (t0) cc_final: 0.6100 (t0) REVERT: D 45 ILE cc_start: 0.7879 (OUTLIER) cc_final: 0.7602 (mp) REVERT: D 58 LYS cc_start: 0.7248 (mmmt) cc_final: 0.6924 (mmtt) REVERT: D 119 TYR cc_start: 0.8419 (t80) cc_final: 0.8109 (t80) REVERT: D 142 HIS cc_start: 0.7777 (p90) cc_final: 0.7500 (p90) REVERT: G 187 ASN cc_start: 0.7218 (p0) cc_final: 0.6996 (p0) REVERT: G 224 ARG cc_start: 0.8260 (mtp85) cc_final: 0.6425 (mtt180) REVERT: G 314 LEU cc_start: 0.6284 (OUTLIER) cc_final: 0.5954 (mm) REVERT: I 109 ASP cc_start: 0.8079 (m-30) cc_final: 0.7532 (t0) REVERT: H 100 PHE cc_start: 0.6840 (m-80) cc_final: 0.6505 (m-80) REVERT: L 89 GLN cc_start: 0.7187 (OUTLIER) cc_final: 0.6480 (tp40) outliers start: 66 outliers final: 51 residues processed: 264 average time/residue: 0.0906 time to fit residues: 37.0741 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 : 0.532 ------------------------------------------------------------------------------- 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 35 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 112 LEU 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 235 THR Chi-restraints excluded: chain C residue 242 THR 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 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 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 155 THR Chi-restraints excluded: chain G residue 158 ASN Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain I residue 32 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 23 CYS Chi-restraints excluded: chain L residue 30 SER 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: 5.9990 chunk 41 optimal weight: 0.9990 chunk 165 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 76 optimal weight: 0.0770 chunk 84 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 282 GLN C 285 GLN 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 = 0.4262 r_free = 0.4262 target = 0.163958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.140146 restraints weight = 22434.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.143692 restraints weight = 13517.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.146060 restraints weight = 9465.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.147694 restraints weight = 7316.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.148637 restraints weight = 6060.869| |-----------------------------------------------------------------------------| r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.5307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14060 Z= 0.156 Angle : 0.641 19.906 19132 Z= 0.321 Chirality : 0.046 0.395 2095 Planarity : 0.004 0.050 2451 Dihedral : 4.568 19.507 1835 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 4.26 % Allowed : 16.36 % 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 are not related in a simple way. whole: 0.15 (0.20), residues: 1684 helix: 2.18 (0.27), residues: 363 sheet: 0.33 (0.32), residues: 253 loop : -0.72 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 170 TYR 0.030 0.002 TYR B 119 PHE 0.026 0.002 PHE L 71 TRP 0.016 0.001 TRP H 36 HIS 0.006 0.001 HIS C 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (14020) covalent geometry : angle 0.60899 / 0.31 (19032) SS BOND : bond 0.00480 / 0.28 ( 20) SS BOND : angle 1.39125 / 0.92 ( 40) hydrogen bonds : bond 0.04668 / 3.05 ( 574) hydrogen bonds : angle 5.26523 / 3.72 ( 1650) link_BETA1-4 : bond 0.00231 / 0.12 ( 4) link_BETA1-4 : angle 1.35644 / 0.85 ( 12) link_NAG-ASN : bond 0.00718 / 0.39 ( 16) link_NAG-ASN : angle 3.81810 / 2.31 ( 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 271 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 208 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8264 (mttp) cc_final: 0.7701 (mmmt) REVERT: B 125 GLN cc_start: 0.7578 (mm-40) cc_final: 0.7318 (tt0) REVERT: B 137 CYS cc_start: 0.5112 (m) cc_final: 0.4725 (m) REVERT: B 141 TYR cc_start: 0.6606 (m-80) cc_final: 0.5756 (m-80) REVERT: D 45 ILE cc_start: 0.7904 (OUTLIER) cc_final: 0.7669 (mp) REVERT: D 58 LYS cc_start: 0.7334 (mmmt) cc_final: 0.6985 (mmtt) REVERT: D 142 HIS cc_start: 0.7702 (p90) cc_final: 0.7488 (p90) REVERT: G 224 ARG cc_start: 0.8277 (mtp85) cc_final: 0.6456 (mtt180) REVERT: G 245 PHE cc_start: 0.6117 (m-80) cc_final: 0.5897 (m-10) REVERT: G 314 LEU cc_start: 0.6260 (OUTLIER) cc_final: 0.5873 (mm) REVERT: I 109 ASP cc_start: 0.8026 (m-30) cc_final: 0.7536 (t0) REVERT: H 45 LEU cc_start: 0.7560 (mm) cc_final: 0.7352 (mm) REVERT: L 89 GLN cc_start: 0.7190 (OUTLIER) cc_final: 0.6476 (tp40) outliers start: 63 outliers final: 51 residues processed: 250 average time/residue: 0.0986 time to fit residues: 38.4920 Evaluate side-chains 252 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 198 time to evaluate : 0.477 ------------------------------------------------------------------------------- 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 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 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 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 68 LYS Chi-restraints excluded: chain D residue 89 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 314 LEU Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain I residue 32 SER 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 23 CYS Chi-restraints excluded: chain L residue 30 SER 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: 0.8980 chunk 55 optimal weight: 0.6980 chunk 129 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 148 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 282 GLN D 60 ASN ** I 142 HIS ** 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 = 0.4266 r_free = 0.4266 target = 0.164424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.140716 restraints weight = 22465.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.144271 restraints weight = 13490.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.146584 restraints weight = 9437.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.148227 restraints weight = 7320.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.149191 restraints weight = 6055.417| |-----------------------------------------------------------------------------| r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.5462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14060 Z= 0.144 Angle : 0.648 19.745 19132 Z= 0.319 Chirality : 0.047 0.631 2095 Planarity : 0.004 0.048 2451 Dihedral : 4.508 18.858 1835 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.06 % Allowed : 16.43 % Favored : 79.51 % 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 are not related in a simple way. whole: 0.15 (0.20), residues: 1684 helix: 2.21 (0.27), residues: 363 sheet: 0.34 (0.32), residues: 253 loop : -0.74 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 170 TYR 0.030 0.002 TYR B 119 PHE 0.022 0.002 PHE L 71 TRP 0.017 0.001 TRP H 36 HIS 0.008 0.001 HIS C 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (14020) covalent geometry : angle 0.60770 / 0.31 (19032) SS BOND : bond 0.00361 / 0.23 ( 20) SS BOND : angle 1.38965 / 1.01 ( 40) hydrogen bonds : bond 0.04516 / 2.95 ( 574) hydrogen bonds : angle 5.20718 / 3.68 ( 1650) link_BETA1-4 : bond 0.00267 / 0.13 ( 4) link_BETA1-4 : angle 1.27831 / 0.79 ( 12) link_NAG-ASN : bond 0.00970 / 0.56 ( 16) link_NAG-ASN : angle 4.32103 / 2.46 ( 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 267 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 207 time to evaluate : 0.541 Fit side-chains revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8300 (mttp) cc_final: 0.7732 (mmmt) REVERT: A 323 ILE cc_start: 0.8152 (mp) cc_final: 0.7563 (tt) REVERT: B 125 GLN cc_start: 0.7603 (mm-40) cc_final: 0.7382 (tt0) REVERT: B 137 CYS cc_start: 0.5042 (m) cc_final: 0.4712 (m) REVERT: B 141 TYR cc_start: 0.6619 (m-80) cc_final: 0.5757 (m-80) REVERT: C 105 TYR cc_start: 0.6934 (t80) cc_final: 0.6554 (t80) REVERT: D 45 ILE cc_start: 0.7866 (OUTLIER) cc_final: 0.7637 (mp) REVERT: D 58 LYS cc_start: 0.7285 (mmmt) cc_final: 0.7034 (mmtt) REVERT: D 125 GLN cc_start: 0.8170 (tp40) cc_final: 0.7555 (tp-100) REVERT: D 142 HIS cc_start: 0.7725 (p90) cc_final: 0.7444 (p90) REVERT: G 187 ASN cc_start: 0.7289 (p0) cc_final: 0.7070 (p0) REVERT: G 224 ARG cc_start: 0.8271 (mtp85) cc_final: 0.6493 (mtt180) REVERT: G 245 PHE cc_start: 0.6061 (m-80) cc_final: 0.5829 (m-10) REVERT: G 314 LEU cc_start: 0.6304 (OUTLIER) cc_final: 0.5933 (mm) REVERT: I 109 ASP cc_start: 0.8001 (m-30) cc_final: 0.7513 (t0) REVERT: L 11 LEU cc_start: 0.8872 (mm) cc_final: 0.7998 (tt) REVERT: L 89 GLN cc_start: 0.7221 (OUTLIER) cc_final: 0.6596 (tp40) outliers start: 60 outliers final: 54 residues processed: 249 average time/residue: 0.0980 time to fit residues: 37.9913 Evaluate side-chains 255 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 198 time to evaluate : 0.534 ------------------------------------------------------------------------------- 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 316 MET 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 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 235 THR Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 282 GLN Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 24 TYR 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 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 155 THR Chi-restraints excluded: chain G residue 158 ASN Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 302 ILE Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 317 VAL 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 23 CYS Chi-restraints excluded: chain L residue 30 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 35 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 119 optimal weight: 0.9980 chunk 161 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 HIS ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 271 ASN ** I 142 HIS ** 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 = 0.4199 r_free = 0.4199 target = 0.163748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.140329 restraints weight = 21863.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.143417 restraints weight = 13932.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.145558 restraints weight = 10080.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.147089 restraints weight = 7961.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.148001 restraints weight = 6687.330| |-----------------------------------------------------------------------------| r_work (final): 0.4020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.5532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14060 Z= 0.147 Angle : 0.656 19.699 19132 Z= 0.324 Chirality : 0.047 0.545 2095 Planarity : 0.004 0.055 2451 Dihedral : 4.494 18.935 1835 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.92 % Allowed : 16.84 % Favored : 79.24 % 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 are not related in a simple way. whole: 0.11 (0.20), residues: 1684 helix: 2.22 (0.27), residues: 363 sheet: 0.33 (0.32), residues: 253 loop : -0.78 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 170 TYR 0.043 0.002 TYR G 195 PHE 0.021 0.002 PHE L 71 TRP 0.020 0.001 TRP H 36 HIS 0.014 0.001 HIS C 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (14020) covalent geometry : angle 0.61595 / 0.31 (19032) SS BOND : bond 0.00361 / 0.23 ( 20) SS BOND : angle 1.44956 / 1.04 ( 40) hydrogen bonds : bond 0.04486 / 2.93 ( 574) hydrogen bonds : angle 5.20229 / 3.68 ( 1650) link_BETA1-4 : bond 0.00239 / 0.12 ( 4) link_BETA1-4 : angle 1.26762 / 0.79 ( 12) link_NAG-ASN : bond 0.00830 / 0.47 ( 16) link_NAG-ASN : angle 4.35456 / 2.44 ( 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 261 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 203 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8315 (mttp) cc_final: 0.7723 (mmmt) REVERT: A 323 ILE cc_start: 0.8151 (mp) cc_final: 0.7530 (tt) REVERT: B 137 CYS cc_start: 0.5010 (m) cc_final: 0.4676 (m) REVERT: B 141 TYR cc_start: 0.6638 (m-80) cc_final: 0.5884 (m-80) REVERT: C 105 TYR cc_start: 0.6871 (t80) cc_final: 0.6484 (t80) REVERT: D 45 ILE cc_start: 0.7851 (OUTLIER) cc_final: 0.7629 (mp) REVERT: D 125 GLN cc_start: 0.8099 (tp40) cc_final: 0.7680 (tp-100) REVERT: D 142 HIS cc_start: 0.7722 (p90) cc_final: 0.7502 (p90) REVERT: G 32 LYS cc_start: 0.6772 (mmmm) cc_final: 0.6319 (tppt) REVERT: G 187 ASN cc_start: 0.7190 (p0) cc_final: 0.6961 (p0) REVERT: G 224 ARG cc_start: 0.8156 (mtp85) cc_final: 0.6524 (mtt180) REVERT: G 245 PHE cc_start: 0.6028 (m-80) cc_final: 0.5791 (m-10) REVERT: G 314 LEU cc_start: 0.6368 (OUTLIER) cc_final: 0.5910 (mm) REVERT: I 109 ASP cc_start: 0.7992 (m-30) cc_final: 0.7565 (t0) REVERT: L 11 LEU cc_start: 0.8823 (mm) cc_final: 0.7957 (tt) REVERT: L 89 GLN cc_start: 0.7246 (OUTLIER) cc_final: 0.6687 (tp40) outliers start: 58 outliers final: 52 residues processed: 242 average time/residue: 0.0868 time to fit residues: 32.4155 Evaluate side-chains 250 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 195 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 HIS 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 316 MET 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 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 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 24 TYR 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 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 155 THR Chi-restraints excluded: chain G residue 158 ASN Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 302 ILE 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 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 23 CYS Chi-restraints excluded: chain L residue 30 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 139 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 HIS C 282 GLN D 62 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.160515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.136517 restraints weight = 22494.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.139537 restraints weight = 14537.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.141667 restraints weight = 10638.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.143081 restraints weight = 8454.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.143973 restraints weight = 7199.546| |-----------------------------------------------------------------------------| r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.5654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14060 Z= 0.227 Angle : 0.713 19.943 19132 Z= 0.358 Chirality : 0.049 0.501 2095 Planarity : 0.005 0.054 2451 Dihedral : 4.718 19.134 1835 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.12 % Allowed : 16.77 % Favored : 79.11 % 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 are not related in a simple way. whole: -0.16 (0.20), residues: 1684 helix: 1.87 (0.27), residues: 363 sheet: -0.03 (0.29), residues: 295 loop : -0.89 (0.18), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 170 TYR 0.032 0.002 TYR G 195 PHE 0.028 0.002 PHE G 118 TRP 0.018 0.002 TRP H 36 HIS 0.017 0.002 HIS A 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.23 (14020) covalent geometry : angle 0.67379 / 0.35 (19032) SS BOND : bond 0.00474 / 0.30 ( 20) SS BOND : angle 1.36949 / 0.95 ( 40) hydrogen bonds : bond 0.04850 / 3.19 ( 574) hydrogen bonds : angle 5.40102 / 3.83 ( 1650) link_BETA1-4 : bond 0.00247 / 0.12 ( 4) link_BETA1-4 : angle 1.66624 / 0.98 ( 12) link_NAG-ASN : bond 0.00860 / 0.49 ( 16) link_NAG-ASN : angle 4.48802 / 2.56 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2257.21 seconds wall clock time: 40 minutes 0.51 seconds (2400.51 seconds total)