Starting phenix.real_space_refine on Thu May 15 20:48:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dm0_46994/05_2025/9dm0_46994_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dm0_46994/05_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_46994/05_2025/9dm0_46994.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dm0_46994/05_2025/9dm0_46994.map" model { file = "/net/cci-nas-00/data/ceres_data/9dm0_46994/05_2025/9dm0_46994_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dm0_46994/05_2025/9dm0_46994_neut.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 10.56, per 1000 atoms: 0.77 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: 3.28 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.75 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: 4.28 Time building geometry restraints manager: 3.84 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: 6.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 34.290 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.060 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:11.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.600 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.035 0.002 TRP E 153 HIS 0.006 0.001 HIS C 35 PHE 0.020 0.002 PHE F 213 TYR 0.033 0.002 TYR I 94 ARG 0.017 0.001 ARG B 123 Details of bonding type rmsd link_NAG-ASN : bond 0.01050 ( 18) link_NAG-ASN : angle 5.74677 ( 54) link_BETA1-4 : bond 0.00409 ( 3) link_BETA1-4 : angle 1.71897 ( 9) hydrogen bonds : bond 0.19137 ( 516) hydrogen bonds : angle 8.00904 ( 1455) SS BOND : bond 0.00614 ( 20) SS BOND : angle 1.53879 ( 40) covalent geometry : bond 0.00455 (13960) covalent geometry : angle 0.75738 (18925) *********************** 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 : 1.496 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: 0.9845 time to fit residues: 257.0975 Evaluate side-chains 185 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 0.9990 chunk 125 optimal weight: 0.4980 chunk 69 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 ** E 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 282 GLN G 50 ASN 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 = 0.4097 r_free = 0.4097 target = 0.168177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.147253 restraints weight = 18037.717| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 2.26 r_work: 0.3782 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3663 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 14001 Z= 0.202 Angle : 0.656 15.712 19028 Z= 0.329 Chirality : 0.048 0.527 2098 Planarity : 0.005 0.077 2421 Dihedral : 5.695 46.847 2269 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.36 % Allowed : 9.71 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.19), residues: 1675 helix: 0.93 (0.25), residues: 378 sheet: -0.70 (0.26), residues: 360 loop : -0.90 (0.19), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 153 HIS 0.007 0.001 HIS C 35 PHE 0.019 0.002 PHE A 102 TYR 0.017 0.002 TYR G 24 ARG 0.005 0.001 ARG B 123 Details of bonding type rmsd link_NAG-ASN : bond 0.00758 ( 18) link_NAG-ASN : angle 4.39483 ( 54) link_BETA1-4 : bond 0.00436 ( 3) link_BETA1-4 : angle 1.59062 ( 9) hydrogen bonds : bond 0.04627 ( 516) hydrogen bonds : angle 5.73376 ( 1455) SS BOND : bond 0.00485 ( 20) SS BOND : angle 1.53381 ( 40) covalent geometry : bond 0.00474 (13960) covalent geometry : angle 0.60924 (18925) *********************** 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 233 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 213 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 55 THR cc_start: 0.7436 (m) cc_final: 0.7016 (p) REVERT: B 149 MET cc_start: 0.7553 (OUTLIER) cc_final: 0.7328 (mtp) REVERT: E 321 ARG cc_start: 0.6550 (OUTLIER) cc_final: 0.4516 (mtm180) REVERT: I 86 ASP cc_start: 0.8281 (m-30) cc_final: 0.8046 (m-30) outliers start: 20 outliers final: 13 residues processed: 220 average time/residue: 0.9831 time to fit residues: 241.5813 Evaluate side-chains 203 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 188 time to evaluate : 1.572 ------------------------------------------------------------------------------- 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 38 LEU 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 7 optimal weight: 8.9990 chunk 35 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 8 optimal weight: 8.9990 chunk 114 optimal weight: 3.9990 chunk 50 optimal weight: 0.3980 chunk 21 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN B 43 ASN E 47 HIS I 135 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.165910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.145662 restraints weight = 18164.436| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 2.12 r_work: 0.3777 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3658 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 14001 Z= 0.272 Angle : 0.724 24.566 19028 Z= 0.358 Chirality : 0.050 0.494 2098 Planarity : 0.005 0.073 2421 Dihedral : 5.888 59.466 2269 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.78 % Allowed : 12.83 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.19), residues: 1675 helix: 0.95 (0.26), residues: 378 sheet: -0.77 (0.27), residues: 352 loop : -0.99 (0.18), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 100B HIS 0.008 0.002 HIS A 18 PHE 0.023 0.002 PHE A 102 TYR 0.018 0.002 TYR I 24 ARG 0.004 0.001 ARG I 76 Details of bonding type rmsd link_NAG-ASN : bond 0.00950 ( 18) link_NAG-ASN : angle 5.56582 ( 54) link_BETA1-4 : bond 0.00351 ( 3) link_BETA1-4 : angle 1.54409 ( 9) hydrogen bonds : bond 0.04879 ( 516) hydrogen bonds : angle 5.72906 ( 1455) SS BOND : bond 0.00928 ( 20) SS BOND : angle 1.79249 ( 40) covalent geometry : bond 0.00641 (13960) covalent geometry : angle 0.65683 (18925) *********************** 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 239 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 198 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 55 THR cc_start: 0.7429 (m) cc_final: 0.6996 (p) REVERT: C 100 TRP cc_start: 0.6638 (OUTLIER) cc_final: 0.5010 (m-10) REVERT: B 39 LYS cc_start: 0.8310 (ttpp) cc_final: 0.7918 (mppt) REVERT: B 149 MET cc_start: 0.7560 (OUTLIER) cc_final: 0.7259 (mtp) REVERT: E 15 ILE cc_start: 0.8171 (OUTLIER) cc_final: 0.7664 (pt) REVERT: E 190 ASP cc_start: 0.6441 (OUTLIER) cc_final: 0.6225 (m-30) REVERT: E 238 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.6680 (mp0) REVERT: I 86 ASP cc_start: 0.8387 (m-30) cc_final: 0.8073 (m-30) outliers start: 41 outliers final: 16 residues processed: 215 average time/residue: 0.9915 time to fit residues: 237.7319 Evaluate side-chains 199 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 178 time to evaluate : 1.392 ------------------------------------------------------------------------------- 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 A residue 29 VAL Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 190 ASP 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 139 GLU Chi-restraints excluded: chain G residue 145 ASP Chi-restraints excluded: chain G residue 154 ASN Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 128 ASN 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 114 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 158 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 129 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.4128 r_free = 0.4128 target = 0.167223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.147601 restraints weight = 18166.468| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 2.04 r_work: 0.3806 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3687 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 14001 Z= 0.189 Angle : 0.642 21.684 19028 Z= 0.315 Chirality : 0.047 0.490 2098 Planarity : 0.005 0.077 2421 Dihedral : 5.366 45.092 2269 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.78 % Allowed : 15.07 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.20), residues: 1675 helix: 1.32 (0.26), residues: 378 sheet: -0.82 (0.27), residues: 352 loop : -0.89 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 127 HIS 0.006 0.001 HIS A 18 PHE 0.012 0.002 PHE C 100E TYR 0.015 0.002 TYR E 98 ARG 0.002 0.000 ARG A 208 Details of bonding type rmsd link_NAG-ASN : bond 0.00758 ( 18) link_NAG-ASN : angle 5.47242 ( 54) link_BETA1-4 : bond 0.00081 ( 3) link_BETA1-4 : angle 1.39333 ( 9) hydrogen bonds : bond 0.04288 ( 516) hydrogen bonds : angle 5.41689 ( 1455) SS BOND : bond 0.00539 ( 20) SS BOND : angle 1.59602 ( 40) covalent geometry : bond 0.00447 (13960) covalent geometry : angle 0.56760 (18925) *********************** 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 231 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 190 time to evaluate : 1.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 55 THR cc_start: 0.7426 (m) cc_final: 0.7006 (p) REVERT: C 82 MET cc_start: 0.7532 (OUTLIER) cc_final: 0.7316 (mpt) REVERT: C 100 TRP cc_start: 0.6661 (OUTLIER) cc_final: 0.4898 (m-10) REVERT: B 39 LYS cc_start: 0.8285 (ttpp) cc_final: 0.7953 (mppt) REVERT: B 149 MET cc_start: 0.7482 (OUTLIER) cc_final: 0.7253 (mtp) REVERT: E 15 ILE cc_start: 0.8141 (OUTLIER) cc_final: 0.7648 (pt) REVERT: E 238 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.6646 (mp0) REVERT: I 86 ASP cc_start: 0.8279 (m-30) cc_final: 0.7959 (m-30) outliers start: 41 outliers final: 21 residues processed: 211 average time/residue: 1.0233 time to fit residues: 240.5005 Evaluate side-chains 200 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 174 time to evaluate : 1.566 ------------------------------------------------------------------------------- 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 82 MET Chi-restraints excluded: chain C residue 100 TRP 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 A residue 323 ILE Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 149 MET 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 252 VAL Chi-restraints excluded: chain E residue 271 ASP 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 F residue 272 THR Chi-restraints excluded: chain F residue 277 CYS Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 118 LEU 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 158 optimal weight: 0.8980 chunk 157 optimal weight: 0.9990 chunk 151 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 25 optimal weight: 0.1980 chunk 136 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 139 optimal weight: 0.8980 chunk 161 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4158 r_free = 0.4158 target = 0.169836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.150422 restraints weight = 18064.472| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 2.03 r_work: 0.3828 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3711 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14001 Z= 0.131 Angle : 0.573 13.529 19028 Z= 0.288 Chirality : 0.044 0.482 2098 Planarity : 0.004 0.078 2421 Dihedral : 5.178 52.745 2269 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.58 % Allowed : 16.29 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.20), residues: 1675 helix: 1.63 (0.27), residues: 378 sheet: -0.76 (0.27), residues: 350 loop : -0.78 (0.19), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 127 HIS 0.005 0.001 HIS A 18 PHE 0.010 0.001 PHE C 100E TYR 0.014 0.001 TYR E 98 ARG 0.002 0.000 ARG A 208 Details of bonding type rmsd link_NAG-ASN : bond 0.00588 ( 18) link_NAG-ASN : angle 4.07486 ( 54) link_BETA1-4 : bond 0.00223 ( 3) link_BETA1-4 : angle 1.39384 ( 9) hydrogen bonds : bond 0.03912 ( 516) hydrogen bonds : angle 5.19310 ( 1455) SS BOND : bond 0.00443 ( 20) SS BOND : angle 1.90942 ( 40) covalent geometry : bond 0.00305 (13960) covalent geometry : angle 0.52306 (18925) *********************** 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 225 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 187 time to evaluate : 1.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 55 THR cc_start: 0.7374 (m) cc_final: 0.6960 (p) REVERT: C 82 MET cc_start: 0.7550 (OUTLIER) cc_final: 0.7309 (mpt) REVERT: C 100 TRP cc_start: 0.6588 (OUTLIER) cc_final: 0.4872 (m-10) REVERT: B 39 LYS cc_start: 0.8253 (ttpp) cc_final: 0.7938 (mppt) REVERT: E 15 ILE cc_start: 0.8063 (OUTLIER) cc_final: 0.7573 (pt) REVERT: E 238 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.6579 (mp0) REVERT: E 321 ARG cc_start: 0.6545 (OUTLIER) cc_final: 0.4442 (mtm180) REVERT: F 24 ASP cc_start: 0.8169 (m-30) cc_final: 0.7957 (m-30) REVERT: F 304 LYS cc_start: 0.7256 (ttmt) cc_final: 0.6357 (tppt) outliers start: 38 outliers final: 18 residues processed: 206 average time/residue: 1.0201 time to fit residues: 238.9051 Evaluate side-chains 198 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 175 time to evaluate : 1.445 ------------------------------------------------------------------------------- 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 82 MET 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 B residue 148 CYS Chi-restraints excluded: chain B residue 156 THR 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 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 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 65 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 42 optimal weight: 0.3980 chunk 156 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 152 optimal weight: 8.9990 chunk 154 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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 = 0.4123 r_free = 0.4123 target = 0.166863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.146762 restraints weight = 18356.614| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 2.12 r_work: 0.3771 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3651 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 14001 Z= 0.241 Angle : 0.650 11.923 19028 Z= 0.329 Chirality : 0.046 0.246 2098 Planarity : 0.005 0.074 2421 Dihedral : 6.466 94.730 2269 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.85 % Allowed : 16.63 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.20), residues: 1675 helix: 1.40 (0.27), residues: 372 sheet: -0.88 (0.27), residues: 352 loop : -0.94 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 100B HIS 0.008 0.001 HIS A 18 PHE 0.015 0.002 PHE A 118 TYR 0.017 0.002 TYR I 24 ARG 0.003 0.001 ARG E 321 Details of bonding type rmsd link_NAG-ASN : bond 0.00602 ( 18) link_NAG-ASN : angle 3.47171 ( 54) link_BETA1-4 : bond 0.00064 ( 3) link_BETA1-4 : angle 1.55869 ( 9) hydrogen bonds : bond 0.04489 ( 516) hydrogen bonds : angle 5.43940 ( 1455) SS BOND : bond 0.00623 ( 20) SS BOND : angle 1.80075 ( 40) covalent geometry : bond 0.00576 (13960) covalent geometry : angle 0.61799 (18925) *********************** 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 224 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 182 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 89 GLN cc_start: 0.7003 (OUTLIER) cc_final: 0.6527 (tp-100) REVERT: C 55 THR cc_start: 0.7445 (m) cc_final: 0.7028 (p) REVERT: C 82 MET cc_start: 0.7566 (OUTLIER) cc_final: 0.7332 (mpt) REVERT: C 100 TRP cc_start: 0.6680 (OUTLIER) cc_final: 0.5004 (m-10) REVERT: B 39 LYS cc_start: 0.8299 (ttpp) cc_final: 0.7917 (mppt) REVERT: E 15 ILE cc_start: 0.8161 (OUTLIER) cc_final: 0.7684 (pt) REVERT: E 238 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.6584 (mp0) REVERT: E 321 ARG cc_start: 0.6673 (OUTLIER) cc_final: 0.4550 (mtm180) REVERT: I 86 ASP cc_start: 0.8366 (m-30) cc_final: 0.8160 (m-30) outliers start: 42 outliers final: 24 residues processed: 206 average time/residue: 1.0364 time to fit residues: 237.6868 Evaluate side-chains 206 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 176 time to evaluate : 1.560 ------------------------------------------------------------------------------- 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 82 MET 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 A residue 323 ILE Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 90 THR 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 18 VAL 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 179 LEU Chi-restraints excluded: chain F residue 192 GLN Chi-restraints excluded: chain F residue 272 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 29 optimal weight: 0.7980 chunk 144 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 32 optimal weight: 0.9980 chunk 5 optimal weight: 0.1980 chunk 114 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 GLN I 135 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.170090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.150523 restraints weight = 18188.133| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 2.10 r_work: 0.3810 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3691 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14001 Z= 0.141 Angle : 0.575 10.444 19028 Z= 0.292 Chirality : 0.043 0.271 2098 Planarity : 0.004 0.080 2421 Dihedral : 6.024 84.754 2269 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.31 % Allowed : 17.99 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.20), residues: 1675 helix: 1.62 (0.27), residues: 375 sheet: -0.83 (0.27), residues: 352 loop : -0.80 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 153 HIS 0.005 0.001 HIS F 18 PHE 0.013 0.001 PHE C 100E TYR 0.015 0.001 TYR D 36 ARG 0.003 0.000 ARG D 91 Details of bonding type rmsd link_NAG-ASN : bond 0.00390 ( 18) link_NAG-ASN : angle 3.09627 ( 54) link_BETA1-4 : bond 0.00192 ( 3) link_BETA1-4 : angle 1.36003 ( 9) hydrogen bonds : bond 0.03954 ( 516) hydrogen bonds : angle 5.24516 ( 1455) SS BOND : bond 0.00480 ( 20) SS BOND : angle 2.08463 ( 40) covalent geometry : bond 0.00332 (13960) covalent geometry : angle 0.54294 (18925) *********************** 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 218 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 184 time to evaluate : 1.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 55 THR cc_start: 0.7372 (m) cc_final: 0.6962 (p) REVERT: C 82 MET cc_start: 0.7568 (OUTLIER) cc_final: 0.7219 (mpt) REVERT: C 100 TRP cc_start: 0.6591 (OUTLIER) cc_final: 0.4859 (m-10) REVERT: B 39 LYS cc_start: 0.8278 (ttpp) cc_final: 0.7908 (mppt) REVERT: E 15 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7641 (pt) REVERT: E 238 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.6505 (mp0) REVERT: E 321 ARG cc_start: 0.6539 (OUTLIER) cc_final: 0.4441 (mtm180) REVERT: I 86 ASP cc_start: 0.8318 (m-30) cc_final: 0.8117 (m-30) outliers start: 34 outliers final: 18 residues processed: 201 average time/residue: 1.1018 time to fit residues: 245.6778 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 : 1.535 ------------------------------------------------------------------------------- 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 82 MET Chi-restraints excluded: chain C residue 100 TRP Chi-restraints excluded: chain A residue 23 THR 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 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 E residue 321 ARG Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 139 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 162 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 70 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 chunk 153 optimal weight: 0.8980 chunk 104 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 chunk 145 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 ** E 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.170167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.150611 restraints weight = 18169.601| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 2.09 r_work: 0.3810 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3692 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 14001 Z= 0.165 Angle : 0.824 59.200 19028 Z= 0.442 Chirality : 0.045 0.385 2098 Planarity : 0.004 0.079 2421 Dihedral : 6.058 85.151 2269 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.44 % Allowed : 18.13 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.20), residues: 1675 helix: 1.66 (0.27), residues: 375 sheet: -0.82 (0.27), residues: 352 loop : -0.79 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 127 HIS 0.005 0.001 HIS F 18 PHE 0.010 0.001 PHE C 100E TYR 0.014 0.001 TYR G 24 ARG 0.004 0.000 ARG B 106 Details of bonding type rmsd link_NAG-ASN : bond 0.01648 ( 18) link_NAG-ASN : angle 3.18421 ( 54) link_BETA1-4 : bond 0.00347 ( 3) link_BETA1-4 : angle 1.43160 ( 9) hydrogen bonds : bond 0.03961 ( 516) hydrogen bonds : angle 5.22195 ( 1455) SS BOND : bond 0.00467 ( 20) SS BOND : angle 2.25257 ( 40) covalent geometry : bond 0.00375 (13960) covalent geometry : angle 0.80174 (18925) *********************** 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 213 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 177 time to evaluate : 1.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 89 GLN cc_start: 0.7027 (OUTLIER) cc_final: 0.6447 (tp-100) REVERT: C 55 THR cc_start: 0.7374 (m) cc_final: 0.6966 (p) REVERT: C 82 MET cc_start: 0.7565 (OUTLIER) cc_final: 0.7188 (mpt) REVERT: C 100 TRP cc_start: 0.6585 (OUTLIER) cc_final: 0.4862 (m-10) REVERT: B 39 LYS cc_start: 0.8275 (ttpp) cc_final: 0.7900 (mppt) REVERT: E 15 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7634 (pt) REVERT: E 238 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.6526 (mp0) REVERT: E 321 ARG cc_start: 0.6531 (OUTLIER) cc_final: 0.4434 (mtm180) REVERT: I 86 ASP cc_start: 0.8313 (m-30) cc_final: 0.8107 (m-30) outliers start: 36 outliers final: 25 residues processed: 195 average time/residue: 1.0632 time to fit residues: 230.6900 Evaluate side-chains 203 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 172 time to evaluate : 1.516 ------------------------------------------------------------------------------- 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 48 VAL Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 100 TRP Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain A residue 23 THR 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 E residue 15 ILE Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 55 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 61 THR 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 61 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 150 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 159 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 164 optimal weight: 0.7980 chunk 140 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 154 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 GLN ** E 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.170189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.150760 restraints weight = 18005.746| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 2.07 r_work: 0.3814 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3695 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 14001 Z= 0.152 Angle : 0.780 45.156 19028 Z= 0.428 Chirality : 0.045 0.472 2098 Planarity : 0.005 0.078 2421 Dihedral : 5.929 80.717 2269 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.10 % Allowed : 18.67 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.20), residues: 1675 helix: 1.63 (0.27), residues: 378 sheet: -0.76 (0.27), residues: 350 loop : -0.79 (0.19), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 153 HIS 0.005 0.001 HIS A 18 PHE 0.009 0.001 PHE F 213 TYR 0.014 0.002 TYR E 98 ARG 0.003 0.000 ARG B 106 Details of bonding type rmsd link_NAG-ASN : bond 0.00685 ( 18) link_NAG-ASN : angle 4.52056 ( 54) link_BETA1-4 : bond 0.00192 ( 3) link_BETA1-4 : angle 1.39118 ( 9) hydrogen bonds : bond 0.03950 ( 516) hydrogen bonds : angle 5.19947 ( 1455) SS BOND : bond 0.00483 ( 20) SS BOND : angle 1.97591 ( 40) covalent geometry : bond 0.00357 (13960) covalent geometry : angle 0.73815 (18925) *********************** 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 213 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 182 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 89 GLN cc_start: 0.7007 (OUTLIER) cc_final: 0.6398 (tp-100) REVERT: C 55 THR cc_start: 0.7360 (m) cc_final: 0.6933 (p) REVERT: C 82 MET cc_start: 0.7537 (OUTLIER) cc_final: 0.7155 (mpt) REVERT: C 100 TRP cc_start: 0.6593 (OUTLIER) cc_final: 0.4853 (m-10) REVERT: B 39 LYS cc_start: 0.8275 (ttpp) cc_final: 0.7900 (mppt) REVERT: E 15 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7643 (pt) REVERT: E 238 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.6524 (mp0) REVERT: E 321 ARG cc_start: 0.6536 (OUTLIER) cc_final: 0.4419 (mtm180) REVERT: G 29 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.7701 (mm-30) REVERT: I 86 ASP cc_start: 0.8317 (m-30) cc_final: 0.8113 (m-30) outliers start: 31 outliers final: 19 residues processed: 197 average time/residue: 1.0619 time to fit residues: 232.5110 Evaluate side-chains 205 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 179 time to evaluate : 1.603 ------------------------------------------------------------------------------- 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 82 MET Chi-restraints excluded: chain C residue 100 TRP Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain A residue 23 THR 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 E residue 15 ILE 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 29 GLU Chi-restraints excluded: chain G residue 61 THR 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 61 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 78 optimal weight: 0.0570 chunk 99 optimal weight: 0.9990 chunk 159 optimal weight: 0.7980 chunk 136 optimal weight: 0.9990 chunk 110 optimal weight: 0.6980 chunk 145 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.7102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 ASN I 135 ASN 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 = 0.170113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.150721 restraints weight = 18130.580| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 2.07 r_work: 0.3812 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3695 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 14001 Z= 0.163 Angle : 0.918 59.166 19028 Z= 0.483 Chirality : 0.046 0.352 2098 Planarity : 0.005 0.118 2421 Dihedral : 5.644 59.792 2269 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.10 % Allowed : 18.94 % Favored : 78.95 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.20), residues: 1675 helix: 1.63 (0.27), residues: 378 sheet: -0.76 (0.27), residues: 350 loop : -0.79 (0.19), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 153 HIS 0.005 0.001 HIS A 18 PHE 0.009 0.001 PHE F 213 TYR 0.014 0.001 TYR G 24 ARG 0.005 0.000 ARG G 123 Details of bonding type rmsd link_NAG-ASN : bond 0.00709 ( 18) link_NAG-ASN : angle 4.87442 ( 54) link_BETA1-4 : bond 0.00213 ( 3) link_BETA1-4 : angle 1.63471 ( 9) hydrogen bonds : bond 0.03958 ( 516) hydrogen bonds : angle 5.20756 ( 1455) SS BOND : bond 0.00479 ( 20) SS BOND : angle 3.69585 ( 40) covalent geometry : bond 0.00367 (13960) covalent geometry : angle 0.86547 (18925) ********************** 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 211 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 180 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 55 THR cc_start: 0.7354 (m) cc_final: 0.6924 (p) REVERT: C 82 MET cc_start: 0.7529 (OUTLIER) cc_final: 0.7141 (mpt) REVERT: C 100 TRP cc_start: 0.6583 (OUTLIER) cc_final: 0.4850 (m-10) REVERT: B 39 LYS cc_start: 0.8275 (ttpp) cc_final: 0.7904 (mppt) REVERT: E 15 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7641 (pt) REVERT: E 238 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.6538 (mp0) REVERT: E 321 ARG cc_start: 0.6524 (OUTLIER) cc_final: 0.4417 (mtm180) REVERT: G 29 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.7707 (mm-30) outliers start: 31 outliers final: 21 residues processed: 195 average time/residue: 1.0575 time to fit residues: 229.5566 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 : 1.405 ------------------------------------------------------------------------------- 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 82 MET Chi-restraints excluded: chain C residue 100 TRP Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain A residue 23 THR 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 238 GLU Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain G residue 29 GLU Chi-restraints excluded: chain G residue 61 THR 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 61 THR Chi-restraints excluded: chain I residue 128 ASN 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 52 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 8 optimal weight: 9.9990 chunk 14 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 135 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.169541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.150011 restraints weight = 18235.244| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 2.08 r_work: 0.3805 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3688 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 14001 Z= 0.169 Angle : 0.606 10.480 19028 Z= 0.308 Chirality : 0.044 0.290 2098 Planarity : 0.004 0.077 2421 Dihedral : 6.390 101.129 2269 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.17 % Allowed : 18.60 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.20), residues: 1675 helix: 1.67 (0.27), residues: 369 sheet: -0.79 (0.27), residues: 352 loop : -0.85 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 153 HIS 0.005 0.001 HIS A 18 PHE 0.010 0.001 PHE C 100E TYR 0.014 0.002 TYR E 98 ARG 0.004 0.000 ARG B 106 Details of bonding type rmsd link_NAG-ASN : bond 0.00391 ( 18) link_NAG-ASN : angle 3.22605 ( 54) link_BETA1-4 : bond 0.00147 ( 3) link_BETA1-4 : angle 1.40990 ( 9) hydrogen bonds : bond 0.04034 ( 516) hydrogen bonds : angle 5.19821 ( 1455) SS BOND : bond 0.00491 ( 20) SS BOND : angle 2.06716 ( 40) covalent geometry : bond 0.00400 (13960) covalent geometry : angle 0.57455 (18925) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9595.37 seconds wall clock time: 166 minutes 31.16 seconds (9991.16 seconds total)