Starting phenix.real_space_refine on Thu Sep 18 03:13:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dm0_46994/09_2025/9dm0_46994_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dm0_46994/09_2025/9dm0_46994.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dm0_46994/09_2025/9dm0_46994.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dm0_46994/09_2025/9dm0_46994.map" model { file = "/net/cci-nas-00/data/ceres_data/9dm0_46994/09_2025/9dm0_46994_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dm0_46994/09_2025/9dm0_46994_neut.cif" } resolution = 2.9 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= 0.015 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 57 5.16 5 C 8575 2.51 5 N 2321 2.21 5 O 2689 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13642 Number of models: 1 Model: "" Number of chains: 17 Chain: "D" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 832 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 100} Chain: "C" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 951 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 115} Chain: "A" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2529 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 19, 'TRANS': 304} Chain: "B" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1326 Classifications: {'peptide': 163} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 1, 'TRANS': 161} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2529 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 19, 'TRANS': 304} Chain: "G" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1326 Classifications: {'peptide': 163} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 1, 'TRANS': 161} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2529 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 19, 'TRANS': 304} Chain: "I" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1326 Classifications: {'peptide': 163} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 1, 'TRANS': 161} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.28, per 1000 atoms: 0.24 Number of scatterers: 13642 At special positions: 0 Unit cell: (96.212, 104.828, 164.422, 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 57 16.00 O 2689 8.00 N 2321 7.00 C 8575 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.04 Simple disulfide: pdb=" SG CYS E 14 " - pdb=" SG CYS G 137 " distance=2.03 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 277 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 76 " distance=2.03 Simple disulfide: pdb=" SG CYS E 97 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 305 " distance=2.03 Simple disulfide: pdb=" SG CYS G 144 " - pdb=" SG CYS G 148 " distance=2.03 Simple disulfide: pdb=" SG CYS F 14 " - pdb=" SG CYS I 137 " distance=2.05 Simple disulfide: pdb=" SG CYS F 52 " - pdb=" SG CYS F 277 " distance=2.04 Simple disulfide: pdb=" SG CYS F 64 " - pdb=" SG CYS F 76 " distance=2.03 Simple disulfide: pdb=" SG CYS F 97 " - pdb=" SG CYS F 139 " distance=2.03 Simple disulfide: pdb=" SG CYS F 281 " - pdb=" SG CYS F 305 " distance=2.03 Simple disulfide: pdb=" SG CYS I 144 " - pdb=" SG CYS I 148 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A 401 " - " ASN A 21 " " NAG A 402 " - " ASN A 33 " " NAG A 403 " - " ASN A 278 " " NAG A 404 " - " ASN A 289 " " NAG B 201 " - " ASN B 154 " " NAG E 401 " - " ASN E 21 " " NAG E 402 " - " ASN E 33 " " NAG E 403 " - " ASN E 278 " " NAG E 404 " - " ASN E 289 " " NAG F 401 " - " ASN F 21 " " NAG F 402 " - " ASN F 33 " " NAG F 403 " - " ASN F 278 " " NAG F 404 " - " ASN F 289 " " NAG G 201 " - " ASN G 154 " " NAG I 201 " - " ASN I 154 " " NAG S 1 " - " ASN A 94 " " NAG T 1 " - " ASN E 94 " " NAG U 1 " - " ASN F 94 " Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 632.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3122 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 38 sheets defined 23.9% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.781A pdb=" N ILE C 31 " --> pdb=" O THR C 28 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 28 through 32' Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.757A pdb=" N ALA C 87 " --> pdb=" O PRO C 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 77 removed outlier: 4.071A pdb=" N GLU A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 125 through 127 removed outlier: 4.601A pdb=" N TRP A 127 " --> pdb=" O LYS A 125A" (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'B' and resid 37 through 58 removed outlier: 3.591A pdb=" N LYS B 58 " --> pdb=" O SER B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 127 Processing helix chain 'B' and resid 145 through 155 removed outlier: 3.585A pdb=" N LYS B 153 " --> pdb=" O MET B 149 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN B 154 " --> pdb=" O GLU B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 171 removed outlier: 4.015A pdb=" N TYR B 162 " --> pdb=" O ASP B 158 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLU B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N GLU B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU B 171 " --> pdb=" O LYS B 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 104 through 112 Processing helix chain 'E' and resid 187 through 195 Processing helix chain 'G' and resid 37 through 58 removed outlier: 3.604A pdb=" N LYS G 58 " --> pdb=" O SER G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 127 Processing helix chain 'G' and resid 145 through 154 Processing helix chain 'G' and resid 158 through 169 removed outlier: 3.756A pdb=" N TYR G 162 " --> pdb=" O ASP G 158 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLU G 164 " --> pdb=" O PRO G 160 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N GLU G 165 " --> pdb=" O LYS G 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 72 Processing helix chain 'F' and resid 73 through 77 removed outlier: 3.741A pdb=" N GLU F 77 " --> pdb=" O PRO F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 112 Processing helix chain 'F' 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 155 Processing helix chain 'I' and resid 159 through 171 removed outlier: 4.628A pdb=" N GLU I 164 " --> pdb=" O PRO I 160 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N GLU I 165 " --> pdb=" O LYS I 161 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU I 171 " --> pdb=" O LYS I 167 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.680A pdb=" N PHE D 71 " --> pdb=" O CYS D 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 10 through 13 removed outlier: 7.050A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ILE D 48 " --> pdb=" O TRP D 35 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N GLN D 37 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU D 46 " --> pdb=" O GLN D 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.608A pdb=" N LEU C 18 " --> pdb=" O MET C 82 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER C 70 " --> pdb=" O TYR C 79 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 11 through 12 Processing sheet with id=AA5, first strand: chain 'C' and resid 57 through 59 removed outlier: 3.525A pdb=" N TYR C 58 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N MET C 34 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA C 93 " --> pdb=" O HIS C 35 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 35 through 36 removed outlier: 3.764A pdb=" N ALA B 35 " --> pdb=" O TYR B 24 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY B 23 " --> pdb=" O GLY A 16 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY A 16 " --> pdb=" O GLY B 23 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N CYS B 137 " --> pdb=" O ILE B 133 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 24 through 26 removed outlier: 4.391A pdb=" N ASP A 24 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA9, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AB1, first strand: chain 'A' and resid 51 through 54 removed outlier: 5.556A pdb=" N LEU A 51 " --> pdb=" O HIS A 275 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N CYS A 277 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.524A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 115 through 122 removed outlier: 6.587A pdb=" N GLU A 261 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N PHE A 118 " --> pdb=" O ALA A 259 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ALA A 259 " --> pdb=" O PHE A 118 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ARG A 120 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ALA A 257 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 115 through 122 removed outlier: 6.587A pdb=" N GLU A 261 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N PHE A 118 " --> pdb=" O ALA A 259 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ALA A 259 " --> pdb=" O PHE A 118 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ARG A 120 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ALA A 257 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 136 through 141 removed outlier: 4.551A pdb=" N CYS A 139 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 164 through 169 removed outlier: 3.512A pdb=" N ALA A 247 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE A 243 " --> pdb=" O TYR A 168 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 281 through 282 removed outlier: 3.750A pdb=" N THR B 64 " --> pdb=" O GLY A 303 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 31 through 36 removed outlier: 3.524A pdb=" N GLY G 33 " --> pdb=" O HIS G 26 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N HIS G 26 " --> pdb=" O GLY G 33 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY G 23 " --> pdb=" O GLY E 16 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY E 16 " --> pdb=" O GLY G 23 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N CYS G 137 " --> pdb=" O ILE G 133 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE G 133 " --> pdb=" O CYS G 137 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 25 through 26 Processing sheet with id=AC1, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AC2, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AC3, first strand: chain 'E' and resid 51 through 54 removed outlier: 6.140A pdb=" N LEU E 51 " --> pdb=" O HIS E 275 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N CYS E 277 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 59 through 60 removed outlier: 6.537A pdb=" N LEU E 59 " --> pdb=" O VAL E 88 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 115 through 121 removed outlier: 6.781A pdb=" N GLU E 261 " --> pdb=" O SER E 116 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE E 118 " --> pdb=" O ALA E 259 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ALA E 259 " --> pdb=" O PHE E 118 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ARG E 120 " --> pdb=" O ALA E 257 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA E 257 " --> pdb=" O ARG E 120 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE E 258 " --> pdb=" O LEU E 177 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N LEU E 179 " --> pdb=" O PRO E 254 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 115 through 121 removed outlier: 6.781A pdb=" N GLU E 261 " --> pdb=" O SER E 116 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE E 118 " --> pdb=" O ALA E 259 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ALA E 259 " --> pdb=" O PHE E 118 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ARG E 120 " --> pdb=" O ALA E 257 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA E 257 " --> pdb=" O ARG E 120 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE E 258 " --> pdb=" O LEU E 177 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 136 through 141 removed outlier: 4.459A pdb=" N CYS E 139 " --> pdb=" O SER E 146 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 164 through 169 Processing sheet with id=AC9, first strand: chain 'E' and resid 286 through 287 removed outlier: 3.539A pdb=" N THR E 283 " --> pdb=" O GLY E 286 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR G 64 " --> pdb=" O GLY E 303 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 31 through 32 Processing sheet with id=AD2, first strand: chain 'I' and resid 31 through 32 removed outlier: 3.699A pdb=" N GLY I 23 " --> pdb=" O GLY F 16 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU F 13 " --> pdb=" O PHE I 138 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE I 138 " --> pdb=" O LEU F 13 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N CYS I 137 " --> pdb=" O ILE I 133 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 25 through 26 Processing sheet with id=AD4, first strand: chain 'F' and resid 39 through 41 Processing sheet with id=AD5, first strand: chain 'F' and resid 43 through 44 Processing sheet with id=AD6, first strand: chain 'F' and resid 59 through 60 removed outlier: 6.424A pdb=" N LEU F 59 " --> pdb=" O VAL F 88 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE F 87 " --> pdb=" O ILE F 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'F' and resid 115 through 122 removed outlier: 3.807A pdb=" N SER F 117 " --> pdb=" O GLU F 261 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TYR F 256 " --> pdb=" O LEU F 179 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LEU F 179 " --> pdb=" O TYR F 256 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 136 through 141 removed outlier: 5.225A pdb=" N CYS F 139 " --> pdb=" O SER F 146 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER F 146 " --> pdb=" O CYS F 139 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 151 through 153 Processing sheet with id=AE1, first strand: chain 'F' and resid 164 through 170 removed outlier: 3.527A pdb=" N ASP F 241 " --> pdb=" O ASN F 170 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 286 through 288 removed outlier: 3.837A pdb=" N CYS F 281 " --> pdb=" O ILE F 288 " (cutoff:3.500A) 527 hydrogen bonds defined for protein. 1455 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: 2.07 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4410 1.35 - 1.47: 3550 1.47 - 1.60: 5925 1.60 - 1.73: 1 1.73 - 1.85: 74 Bond restraints: 13960 Sorted by residual: bond pdb=" C1 NAG G 201 " pdb=" O5 NAG G 201 " ideal model delta sigma weight residual 1.406 1.465 -0.059 2.00e-02 2.50e+03 8.66e+00 bond pdb=" C1 NAG A 402 " pdb=" O5 NAG A 402 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.96e+00 bond pdb=" C1 NAG I 201 " pdb=" O5 NAG I 201 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.28e+00 bond pdb=" CB PRO E 128 " pdb=" CG PRO E 128 " ideal model delta sigma weight residual 1.492 1.602 -0.110 5.00e-02 4.00e+02 4.80e+00 bond pdb=" C1 NAG E 403 " pdb=" O5 NAG E 403 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.69e+00 ... (remaining 13955 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 18579 2.45 - 4.89: 306 4.89 - 7.34: 24 7.34 - 9.79: 13 9.79 - 12.23: 3 Bond angle restraints: 18925 Sorted by residual: angle pdb=" N PRO C 99 " pdb=" CA PRO C 99 " pdb=" C PRO C 99 " ideal model delta sigma weight residual 110.70 115.87 -5.17 1.22e+00 6.72e-01 1.79e+01 angle pdb=" C LYS G 153 " pdb=" N ASN G 154 " pdb=" CA ASN G 154 " ideal model delta sigma weight residual 122.65 115.88 6.77 1.60e+00 3.91e-01 1.79e+01 angle pdb=" C CYS E 97 " pdb=" N TYR E 98 " pdb=" CA TYR E 98 " ideal model delta sigma weight residual 120.94 113.03 7.91 1.90e+00 2.77e-01 1.73e+01 angle pdb=" CA PRO E 128 " pdb=" N PRO E 128 " pdb=" CD PRO E 128 " ideal model delta sigma weight residual 112.00 106.82 5.18 1.40e+00 5.10e-01 1.37e+01 angle pdb=" CA LEU B 102 " pdb=" CB LEU B 102 " pdb=" CG LEU B 102 " ideal model delta sigma weight residual 116.30 128.53 -12.23 3.50e+00 8.16e-02 1.22e+01 ... (remaining 18920 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.49: 7775 18.49 - 36.99: 697 36.99 - 55.48: 114 55.48 - 73.97: 19 73.97 - 92.47: 12 Dihedral angle restraints: 8617 sinusoidal: 3729 harmonic: 4888 Sorted by residual: dihedral pdb=" CB CYS F 97 " pdb=" SG CYS F 97 " pdb=" SG CYS F 139 " pdb=" CB CYS F 139 " ideal model delta sinusoidal sigma weight residual -86.00 -2.35 -83.65 1 1.00e+01 1.00e-02 8.54e+01 dihedral pdb=" CA TRP D 94 " pdb=" C TRP D 94 " pdb=" N PRO D 95 " pdb=" CA PRO D 95 " ideal model delta harmonic sigma weight residual 180.00 135.13 44.87 0 5.00e+00 4.00e-02 8.05e+01 dihedral pdb=" CB CYS F 52 " pdb=" SG CYS F 52 " pdb=" SG CYS F 277 " pdb=" CB CYS F 277 " ideal model delta sinusoidal sigma weight residual -86.00 -13.28 -72.72 1 1.00e+01 1.00e-02 6.75e+01 ... (remaining 8614 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 2062 0.126 - 0.253: 33 0.253 - 0.379: 1 0.379 - 0.505: 1 0.505 - 0.632: 1 Chirality restraints: 2098 Sorted by residual: chirality pdb=" C1 NAG B 201 " pdb=" ND2 ASN B 154 " pdb=" C2 NAG B 201 " pdb=" O5 NAG B 201 " both_signs ideal model delta sigma weight residual False -2.40 -1.77 -0.63 2.00e-01 2.50e+01 9.98e+00 chirality pdb=" C1 NAG G 201 " pdb=" ND2 ASN G 154 " pdb=" C2 NAG G 201 " pdb=" O5 NAG G 201 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 2.43e+00 ... (remaining 2095 not shown) Planarity restraints: 2439 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN G 154 " 0.005 2.00e-02 2.50e+03 4.23e-02 2.24e+01 pdb=" CG ASN G 154 " -0.048 2.00e-02 2.50e+03 pdb=" OD1 ASN G 154 " 0.049 2.00e-02 2.50e+03 pdb=" ND2 ASN G 154 " -0.049 2.00e-02 2.50e+03 pdb=" C1 NAG G 201 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP D 94 " 0.063 5.00e-02 4.00e+02 9.57e-02 1.47e+01 pdb=" N PRO D 95 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO D 95 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO D 95 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR F 98 " -0.055 5.00e-02 4.00e+02 8.31e-02 1.11e+01 pdb=" N PRO F 99 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO F 99 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO F 99 " -0.045 5.00e-02 4.00e+02 ... (remaining 2436 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 643 2.73 - 3.27: 12109 3.27 - 3.81: 23439 3.81 - 4.36: 27919 4.36 - 4.90: 48673 Nonbonded interactions: 112783 Sorted by model distance: nonbonded pdb=" O TYR B 141 " pdb=" ND2 ASN B 169 " model vdw 2.184 3.120 nonbonded pdb=" OG1 THR A 28 " pdb=" O GLU A 31 " model vdw 2.292 3.040 nonbonded pdb=" O PRO E 125 " pdb=" OG SER E 126 " model vdw 2.300 3.040 nonbonded pdb=" O GLU I 103 " pdb=" OG1 THR I 107 " model vdw 2.324 3.040 nonbonded pdb=" OH TYR A 148 " pdb=" OH TYR A 232 " model vdw 2.340 3.040 ... (remaining 112778 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 'E' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.640 Find NCS groups from input model: 0.200 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:6.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 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 : 0.005 0.110 14001 Z= 0.209 Angle : 0.819 19.445 19028 Z= 0.411 Chirality : 0.053 0.632 2098 Planarity : 0.007 0.096 2421 Dihedral : 14.128 92.466 5435 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.19), residues: 1675 helix: -0.32 (0.23), residues: 360 sheet: -0.47 (0.27), residues: 352 loop : -1.05 (0.18), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 123 TYR 0.033 0.002 TYR I 94 PHE 0.020 0.002 PHE F 213 TRP 0.035 0.002 TRP E 153 HIS 0.006 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00455 (13960) covalent geometry : angle 0.75738 (18925) SS BOND : bond 0.00614 ( 20) SS BOND : angle 1.53879 ( 40) hydrogen bonds : bond 0.19137 ( 516) hydrogen bonds : angle 8.00904 ( 1455) link_BETA1-4 : bond 0.00409 ( 3) link_BETA1-4 : angle 1.71897 ( 9) link_NAG-ASN : bond 0.01050 ( 18) link_NAG-ASN : angle 5.74677 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 55 THR cc_start: 0.6948 (m) cc_final: 0.6718 (p) REVERT: C 91 TYR cc_start: 0.7361 (m-80) cc_final: 0.7159 (m-80) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.4952 time to fit residues: 128.3896 Evaluate side-chains 184 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 GLN A 196 GLN B 30 GLN B 43 ASN B 169 ASN ** E 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 282 GLN F 18 HIS F 282 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.166360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.145357 restraints weight = 18274.892| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 2.25 r_work: 0.3759 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3639 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 14001 Z= 0.240 Angle : 0.689 15.909 19028 Z= 0.346 Chirality : 0.049 0.527 2098 Planarity : 0.005 0.076 2421 Dihedral : 5.780 45.713 2269 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.43 % Allowed : 10.18 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.19), residues: 1675 helix: 0.82 (0.25), residues: 378 sheet: -0.71 (0.26), residues: 359 loop : -0.95 (0.19), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 123 TYR 0.019 0.002 TYR G 24 PHE 0.023 0.002 PHE A 102 TRP 0.017 0.002 TRP E 153 HIS 0.008 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00567 (13960) covalent geometry : angle 0.64165 (18925) SS BOND : bond 0.00529 ( 20) SS BOND : angle 1.64502 ( 40) hydrogen bonds : bond 0.04821 ( 516) hydrogen bonds : angle 5.81561 ( 1455) link_BETA1-4 : bond 0.00147 ( 3) link_BETA1-4 : angle 1.73567 ( 9) link_NAG-ASN : bond 0.00842 ( 18) link_NAG-ASN : angle 4.51068 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 213 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 55 THR cc_start: 0.7464 (m) cc_final: 0.7031 (p) REVERT: B 149 MET cc_start: 0.7602 (OUTLIER) cc_final: 0.7324 (mtp) REVERT: E 315 ARG cc_start: 0.8690 (ttm-80) cc_final: 0.8332 (tpt-90) REVERT: E 321 ARG cc_start: 0.6511 (OUTLIER) cc_final: 0.4486 (mtm180) REVERT: I 86 ASP cc_start: 0.8369 (m-30) cc_final: 0.8129 (m-30) outliers start: 21 outliers final: 12 residues processed: 220 average time/residue: 0.4725 time to fit residues: 115.9710 Evaluate side-chains 201 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 187 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 145 ASP Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain I residue 147 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 58 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 126 optimal weight: 0.9980 chunk 164 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 100DASN E 47 HIS I 135 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.173608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.153767 restraints weight = 18113.758| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 2.12 r_work: 0.3849 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3730 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14001 Z= 0.136 Angle : 0.606 25.923 19028 Z= 0.295 Chirality : 0.046 0.529 2098 Planarity : 0.004 0.077 2421 Dihedral : 5.437 54.762 2269 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.97 % Allowed : 13.17 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.20), residues: 1675 helix: 1.42 (0.26), residues: 378 sheet: -0.63 (0.27), residues: 353 loop : -0.79 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 123 TYR 0.013 0.001 TYR E 98 PHE 0.011 0.001 PHE C 100E TRP 0.014 0.001 TRP A 127 HIS 0.005 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00312 (13960) covalent geometry : angle 0.52620 (18925) SS BOND : bond 0.00433 ( 20) SS BOND : angle 1.34095 ( 40) hydrogen bonds : bond 0.04146 ( 516) hydrogen bonds : angle 5.33624 ( 1455) link_BETA1-4 : bond 0.00233 ( 3) link_BETA1-4 : angle 1.22358 ( 9) link_NAG-ASN : bond 0.00931 ( 18) link_NAG-ASN : angle 5.56665 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 200 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 55 THR cc_start: 0.7367 (m) cc_final: 0.6940 (p) REVERT: C 100 TRP cc_start: 0.6428 (OUTLIER) cc_final: 0.4642 (m-10) REVERT: B 39 LYS cc_start: 0.8284 (ttpp) cc_final: 0.7931 (mppt) REVERT: E 15 ILE cc_start: 0.7976 (OUTLIER) cc_final: 0.7480 (pt) REVERT: E 238 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.6612 (mp0) outliers start: 29 outliers final: 10 residues processed: 215 average time/residue: 0.5016 time to fit residues: 120.3342 Evaluate side-chains 199 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 186 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain C residue 100 TRP Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain G residue 145 ASP Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 147 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 3 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 36 optimal weight: 5.9990 chunk 116 optimal weight: 0.7980 chunk 94 optimal weight: 0.6980 chunk 148 optimal weight: 0.2980 chunk 77 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 GLN G 50 ASN F 275 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.172624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.152602 restraints weight = 18090.229| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 2.14 r_work: 0.3836 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3717 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14001 Z= 0.142 Angle : 0.592 20.968 19028 Z= 0.288 Chirality : 0.045 0.476 2098 Planarity : 0.004 0.076 2421 Dihedral : 4.900 42.310 2269 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.51 % Allowed : 14.19 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.20), residues: 1675 helix: 1.69 (0.26), residues: 378 sheet: -0.67 (0.27), residues: 353 loop : -0.72 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 123 TYR 0.012 0.001 TYR I 24 PHE 0.011 0.001 PHE F 213 TRP 0.015 0.001 TRP E 153 HIS 0.005 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00333 (13960) covalent geometry : angle 0.51979 (18925) SS BOND : bond 0.00459 ( 20) SS BOND : angle 1.39431 ( 40) hydrogen bonds : bond 0.03966 ( 516) hydrogen bonds : angle 5.10019 ( 1455) link_BETA1-4 : bond 0.00162 ( 3) link_BETA1-4 : angle 1.28371 ( 9) link_NAG-ASN : bond 0.00675 ( 18) link_NAG-ASN : angle 5.18636 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 197 time to evaluate : 0.604 Fit side-chains revert: symmetry clash REVERT: C 55 THR cc_start: 0.7420 (m) cc_final: 0.6985 (p) REVERT: C 100 TRP cc_start: 0.6507 (OUTLIER) cc_final: 0.4810 (m-10) REVERT: B 39 LYS cc_start: 0.8260 (ttpp) cc_final: 0.7888 (mppt) REVERT: E 15 ILE cc_start: 0.8074 (OUTLIER) cc_final: 0.7583 (pt) REVERT: E 33 ASN cc_start: 0.8235 (t0) cc_final: 0.8007 (t160) REVERT: E 191 GLN cc_start: 0.7290 (OUTLIER) cc_final: 0.4481 (tm-30) REVERT: E 238 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.6554 (mp0) REVERT: E 321 ARG cc_start: 0.6662 (OUTLIER) cc_final: 0.4565 (mtm180) REVERT: F 24 ASP cc_start: 0.8129 (m-30) cc_final: 0.7916 (m-30) REVERT: F 31 GLU cc_start: 0.7577 (tp30) cc_final: 0.7263 (pt0) REVERT: F 304 LYS cc_start: 0.7212 (ttmt) cc_final: 0.6349 (tppt) REVERT: I 86 ASP cc_start: 0.8363 (m-30) cc_final: 0.7971 (m-30) outliers start: 37 outliers final: 18 residues processed: 221 average time/residue: 0.5182 time to fit residues: 127.3395 Evaluate side-chains 199 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 176 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 100 TRP Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 191 GLN Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 208 ARG Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 145 ASP Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 277 CYS Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 147 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 63 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 156 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 150 optimal weight: 0.0470 chunk 105 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 110 optimal weight: 1.9990 overall best weight: 0.8082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.172449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.152664 restraints weight = 18252.875| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 2.13 r_work: 0.3838 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3718 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14001 Z= 0.138 Angle : 0.572 12.152 19028 Z= 0.286 Chirality : 0.043 0.251 2098 Planarity : 0.004 0.077 2421 Dihedral : 6.078 90.283 2269 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.58 % Allowed : 15.07 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.20), residues: 1675 helix: 1.88 (0.27), residues: 372 sheet: -0.69 (0.27), residues: 355 loop : -0.68 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 106 TYR 0.013 0.001 TYR F 17 PHE 0.009 0.001 PHE F 213 TRP 0.015 0.001 TRP E 153 HIS 0.005 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00321 (13960) covalent geometry : angle 0.52913 (18925) SS BOND : bond 0.00430 ( 20) SS BOND : angle 1.81744 ( 40) hydrogen bonds : bond 0.03883 ( 516) hydrogen bonds : angle 5.05224 ( 1455) link_BETA1-4 : bond 0.00257 ( 3) link_BETA1-4 : angle 1.32026 ( 9) link_NAG-ASN : bond 0.00414 ( 18) link_NAG-ASN : angle 3.82305 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 177 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 89 GLN cc_start: 0.6969 (OUTLIER) cc_final: 0.6545 (tp-100) REVERT: C 55 THR cc_start: 0.7398 (m) cc_final: 0.6956 (p) REVERT: C 100 TRP cc_start: 0.6528 (OUTLIER) cc_final: 0.4804 (m-10) REVERT: B 39 LYS cc_start: 0.8261 (ttpp) cc_final: 0.7857 (mppt) REVERT: E 15 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7591 (pt) REVERT: E 191 GLN cc_start: 0.7357 (OUTLIER) cc_final: 0.4637 (tm-30) REVERT: E 238 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.6456 (mp0) REVERT: E 321 ARG cc_start: 0.6597 (OUTLIER) cc_final: 0.4516 (mtm180) REVERT: F 24 ASP cc_start: 0.8122 (m-30) cc_final: 0.7916 (m-30) REVERT: F 304 LYS cc_start: 0.7124 (ttmt) cc_final: 0.6239 (tppt) REVERT: I 86 ASP cc_start: 0.8351 (m-30) cc_final: 0.7989 (m-30) outliers start: 38 outliers final: 20 residues processed: 197 average time/residue: 0.5343 time to fit residues: 116.9898 Evaluate side-chains 198 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 172 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain C residue 100 TRP Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 191 GLN Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 208 ARG Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 271 ASP Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 145 ASP Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 277 CYS Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 147 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 89 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 165 optimal weight: 0.0870 chunk 104 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 126 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 GLN D 100 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.173093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.153586 restraints weight = 18203.610| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 2.12 r_work: 0.3847 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3728 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14001 Z= 0.124 Angle : 0.544 10.265 19028 Z= 0.275 Chirality : 0.043 0.278 2098 Planarity : 0.004 0.077 2421 Dihedral : 5.600 76.882 2269 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.10 % Allowed : 16.50 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.20), residues: 1675 helix: 1.90 (0.26), residues: 378 sheet: -0.65 (0.27), residues: 354 loop : -0.60 (0.20), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 120 TYR 0.014 0.001 TYR D 36 PHE 0.009 0.001 PHE F 213 TRP 0.015 0.001 TRP E 153 HIS 0.004 0.001 HIS F 18 Details of bonding type rmsd covalent geometry : bond 0.00287 (13960) covalent geometry : angle 0.51098 (18925) SS BOND : bond 0.00400 ( 20) SS BOND : angle 1.98514 ( 40) hydrogen bonds : bond 0.03777 ( 516) hydrogen bonds : angle 4.98997 ( 1455) link_BETA1-4 : bond 0.00223 ( 3) link_BETA1-4 : angle 1.28537 ( 9) link_NAG-ASN : bond 0.00422 ( 18) link_NAG-ASN : angle 3.07638 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 186 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 55 THR cc_start: 0.7376 (m) cc_final: 0.6931 (p) REVERT: C 100 TRP cc_start: 0.6510 (OUTLIER) cc_final: 0.4799 (m-10) REVERT: B 39 LYS cc_start: 0.8259 (ttpp) cc_final: 0.7885 (mppt) REVERT: E 15 ILE cc_start: 0.8057 (OUTLIER) cc_final: 0.7545 (pt) REVERT: E 52 CYS cc_start: 0.5652 (m) cc_final: 0.5304 (m) REVERT: E 238 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.6453 (mp0) REVERT: E 321 ARG cc_start: 0.6580 (OUTLIER) cc_final: 0.4524 (mtm180) REVERT: F 24 ASP cc_start: 0.8101 (m-30) cc_final: 0.7892 (m-30) REVERT: F 31 GLU cc_start: 0.7533 (tp30) cc_final: 0.7158 (pt0) REVERT: F 304 LYS cc_start: 0.7120 (ttmt) cc_final: 0.6245 (tppt) REVERT: I 86 ASP cc_start: 0.8326 (m-30) cc_final: 0.7903 (m-30) outliers start: 31 outliers final: 19 residues processed: 201 average time/residue: 0.5262 time to fit residues: 117.6899 Evaluate side-chains 200 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 177 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain C residue 100 TRP Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 208 ARG Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 271 ASP Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 145 ASP Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 277 CYS Chi-restraints excluded: chain I residue 147 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 143 optimal weight: 2.9990 chunk 81 optimal weight: 0.0570 chunk 4 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 68 optimal weight: 0.9980 chunk 42 optimal weight: 0.2980 chunk 121 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 GLN D 100 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.173235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.153707 restraints weight = 18115.632| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 2.12 r_work: 0.3851 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3732 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14001 Z= 0.120 Angle : 0.534 10.153 19028 Z= 0.271 Chirality : 0.042 0.289 2098 Planarity : 0.004 0.076 2421 Dihedral : 5.216 58.443 2269 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.44 % Allowed : 16.50 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.20), residues: 1675 helix: 1.93 (0.26), residues: 378 sheet: -0.61 (0.27), residues: 360 loop : -0.58 (0.20), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 120 TYR 0.013 0.001 TYR B 157 PHE 0.019 0.001 PHE A 121 TRP 0.016 0.001 TRP E 153 HIS 0.004 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00280 (13960) covalent geometry : angle 0.50417 (18925) SS BOND : bond 0.00401 ( 20) SS BOND : angle 1.67837 ( 40) hydrogen bonds : bond 0.03733 ( 516) hydrogen bonds : angle 4.91796 ( 1455) link_BETA1-4 : bond 0.00209 ( 3) link_BETA1-4 : angle 1.26302 ( 9) link_NAG-ASN : bond 0.00381 ( 18) link_NAG-ASN : angle 3.01607 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 190 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 89 GLN cc_start: 0.6954 (OUTLIER) cc_final: 0.6350 (tp-100) REVERT: C 2 VAL cc_start: 0.8110 (OUTLIER) cc_final: 0.7746 (m) REVERT: C 100 TRP cc_start: 0.6502 (OUTLIER) cc_final: 0.4816 (m-10) REVERT: B 39 LYS cc_start: 0.8307 (ttpp) cc_final: 0.7955 (mppt) REVERT: E 15 ILE cc_start: 0.8054 (OUTLIER) cc_final: 0.7559 (pt) REVERT: E 52 CYS cc_start: 0.5718 (m) cc_final: 0.5486 (m) REVERT: E 321 ARG cc_start: 0.6604 (OUTLIER) cc_final: 0.4560 (mtm180) REVERT: F 24 ASP cc_start: 0.8121 (m-30) cc_final: 0.7915 (m-30) REVERT: F 31 GLU cc_start: 0.7575 (tp30) cc_final: 0.7249 (pt0) REVERT: F 304 LYS cc_start: 0.7134 (ttmt) cc_final: 0.6288 (tppt) REVERT: I 86 ASP cc_start: 0.8272 (m-30) cc_final: 0.7932 (m-30) outliers start: 36 outliers final: 19 residues processed: 211 average time/residue: 0.5361 time to fit residues: 125.7376 Evaluate side-chains 203 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 179 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 100 GLN Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 100 TRP Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 208 ARG Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 277 CYS Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 147 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 147 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 93 optimal weight: 0.8980 chunk 82 optimal weight: 9.9990 chunk 89 optimal weight: 4.9990 chunk 126 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 GLN B 43 ASN I 135 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.170591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.151608 restraints weight = 18038.143| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 2.00 r_work: 0.3832 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3716 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14001 Z= 0.181 Angle : 0.642 25.979 19028 Z= 0.311 Chirality : 0.047 0.732 2098 Planarity : 0.004 0.075 2421 Dihedral : 6.091 80.786 2269 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.31 % Allowed : 17.18 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.20), residues: 1675 helix: 1.75 (0.26), residues: 378 sheet: -0.71 (0.27), residues: 359 loop : -0.68 (0.19), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 120 TYR 0.014 0.002 TYR I 24 PHE 0.014 0.002 PHE A 121 TRP 0.019 0.001 TRP E 153 HIS 0.006 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00430 (13960) covalent geometry : angle 0.56969 (18925) SS BOND : bond 0.00517 ( 20) SS BOND : angle 1.66346 ( 40) hydrogen bonds : bond 0.04020 ( 516) hydrogen bonds : angle 5.06678 ( 1455) link_BETA1-4 : bond 0.00128 ( 3) link_BETA1-4 : angle 1.35318 ( 9) link_NAG-ASN : bond 0.00411 ( 18) link_NAG-ASN : angle 5.39118 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 176 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 2 VAL cc_start: 0.8147 (OUTLIER) cc_final: 0.7783 (m) REVERT: C 55 THR cc_start: 0.7309 (m) cc_final: 0.6893 (p) REVERT: C 82 MET cc_start: 0.7361 (mpt) cc_final: 0.7081 (mpt) REVERT: C 100 TRP cc_start: 0.6620 (OUTLIER) cc_final: 0.4891 (m-10) REVERT: B 39 LYS cc_start: 0.8267 (ttpp) cc_final: 0.7969 (mppt) REVERT: E 15 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7619 (pt) REVERT: E 52 CYS cc_start: 0.5662 (m) cc_final: 0.5429 (m) REVERT: E 238 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.6446 (mp0) REVERT: E 321 ARG cc_start: 0.6760 (OUTLIER) cc_final: 0.4703 (mtm180) REVERT: F 24 ASP cc_start: 0.8147 (m-30) cc_final: 0.7907 (m-30) REVERT: I 86 ASP cc_start: 0.8251 (m-30) cc_final: 0.7998 (m-30) outliers start: 34 outliers final: 18 residues processed: 194 average time/residue: 0.5448 time to fit residues: 117.3147 Evaluate side-chains 193 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 170 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 100 TRP Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 271 ASP Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 145 ASP Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 192 GLN Chi-restraints excluded: chain F residue 277 CYS Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 147 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 0.7980 chunk 135 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 128 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 121 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 GLN B 43 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.172393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.153553 restraints weight = 18075.416| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 1.99 r_work: 0.3853 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3737 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14001 Z= 0.133 Angle : 0.591 22.938 19028 Z= 0.290 Chirality : 0.045 0.570 2098 Planarity : 0.004 0.078 2421 Dihedral : 6.197 98.815 2269 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.83 % Allowed : 18.06 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.20), residues: 1675 helix: 1.93 (0.27), residues: 369 sheet: -0.70 (0.27), residues: 360 loop : -0.63 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 120 TYR 0.013 0.001 TYR B 157 PHE 0.017 0.001 PHE A 121 TRP 0.020 0.001 TRP E 153 HIS 0.005 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00311 (13960) covalent geometry : angle 0.53224 (18925) SS BOND : bond 0.00424 ( 20) SS BOND : angle 1.50293 ( 40) hydrogen bonds : bond 0.03815 ( 516) hydrogen bonds : angle 4.95085 ( 1455) link_BETA1-4 : bond 0.00159 ( 3) link_BETA1-4 : angle 1.28141 ( 9) link_NAG-ASN : bond 0.00534 ( 18) link_NAG-ASN : angle 4.69454 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 174 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 82 MET cc_start: 0.7246 (mpt) cc_final: 0.7022 (mpt) REVERT: C 100 TRP cc_start: 0.6539 (OUTLIER) cc_final: 0.4848 (m-10) REVERT: B 39 LYS cc_start: 0.8305 (ttpp) cc_final: 0.7973 (mppt) REVERT: E 15 ILE cc_start: 0.8061 (OUTLIER) cc_final: 0.7568 (pt) REVERT: E 238 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.6315 (mp0) REVERT: E 321 ARG cc_start: 0.6674 (OUTLIER) cc_final: 0.4631 (mtm180) REVERT: F 24 ASP cc_start: 0.8140 (m-30) cc_final: 0.7939 (m-30) REVERT: F 304 LYS cc_start: 0.7229 (ttmt) cc_final: 0.6345 (tppt) REVERT: I 86 ASP cc_start: 0.8190 (m-30) cc_final: 0.7904 (m-30) outliers start: 27 outliers final: 20 residues processed: 192 average time/residue: 0.5355 time to fit residues: 114.4773 Evaluate side-chains 188 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 100 TRP Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 145 ASP Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 277 CYS Chi-restraints excluded: chain I residue 37 ASP Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 147 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 88 optimal weight: 0.5980 chunk 87 optimal weight: 0.7980 chunk 118 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 163 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.172099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.153210 restraints weight = 18039.736| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 1.99 r_work: 0.3852 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3737 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14001 Z= 0.141 Angle : 0.594 22.029 19028 Z= 0.293 Chirality : 0.045 0.537 2098 Planarity : 0.004 0.077 2421 Dihedral : 6.298 106.445 2269 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.77 % Allowed : 18.33 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.20), residues: 1675 helix: 1.90 (0.27), residues: 369 sheet: -0.66 (0.27), residues: 360 loop : -0.65 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 120 TYR 0.014 0.001 TYR A 105 PHE 0.016 0.001 PHE A 121 TRP 0.025 0.001 TRP E 153 HIS 0.005 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00330 (13960) covalent geometry : angle 0.53757 (18925) SS BOND : bond 0.00434 ( 20) SS BOND : angle 1.49608 ( 40) hydrogen bonds : bond 0.03829 ( 516) hydrogen bonds : angle 4.96688 ( 1455) link_BETA1-4 : bond 0.00119 ( 3) link_BETA1-4 : angle 1.30131 ( 9) link_NAG-ASN : bond 0.00501 ( 18) link_NAG-ASN : angle 4.57487 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 170 time to evaluate : 0.573 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: D 89 GLN cc_start: 0.6880 (OUTLIER) cc_final: 0.6415 (tp-100) REVERT: C 82 MET cc_start: 0.7492 (mpt) cc_final: 0.7211 (mpt) REVERT: C 100 TRP cc_start: 0.6527 (OUTLIER) cc_final: 0.4833 (m-10) REVERT: B 39 LYS cc_start: 0.8264 (ttpp) cc_final: 0.7986 (mppt) REVERT: E 15 ILE cc_start: 0.8069 (OUTLIER) cc_final: 0.7587 (pt) REVERT: E 238 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.6334 (mp0) REVERT: E 321 ARG cc_start: 0.6671 (OUTLIER) cc_final: 0.4609 (mtm180) REVERT: F 24 ASP cc_start: 0.8114 (m-30) cc_final: 0.7913 (m-30) REVERT: F 304 LYS cc_start: 0.7168 (ttmt) cc_final: 0.6301 (tppt) REVERT: I 86 ASP cc_start: 0.8203 (m-30) cc_final: 0.7916 (m-30) outliers start: 26 outliers final: 21 residues processed: 186 average time/residue: 0.5545 time to fit residues: 114.2655 Evaluate side-chains 192 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 100 TRP Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 191 GLN Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 145 ASP Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 192 GLN Chi-restraints excluded: chain F residue 277 CYS Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 147 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 48 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 147 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 29 optimal weight: 0.0670 chunk 73 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 overall best weight: 1.3922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 GLN D 100 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.169749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.150412 restraints weight = 18318.153| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 2.07 r_work: 0.3806 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3689 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 14001 Z= 0.194 Angle : 0.633 21.767 19028 Z= 0.314 Chirality : 0.046 0.497 2098 Planarity : 0.004 0.074 2421 Dihedral : 6.468 108.380 2269 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.97 % Allowed : 18.40 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.20), residues: 1675 helix: 1.70 (0.27), residues: 369 sheet: -0.79 (0.26), residues: 382 loop : -0.81 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 120 TYR 0.017 0.002 TYR A 105 PHE 0.013 0.002 PHE C 100E TRP 0.028 0.002 TRP E 153 HIS 0.006 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00461 (13960) covalent geometry : angle 0.58042 (18925) SS BOND : bond 0.00540 ( 20) SS BOND : angle 1.62457 ( 40) hydrogen bonds : bond 0.04115 ( 516) hydrogen bonds : angle 5.12703 ( 1455) link_BETA1-4 : bond 0.00330 ( 3) link_BETA1-4 : angle 1.47810 ( 9) link_NAG-ASN : bond 0.00536 ( 18) link_NAG-ASN : angle 4.58401 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4983.24 seconds wall clock time: 86 minutes 9.89 seconds (5169.89 seconds total)