Starting phenix.real_space_refine on Sat Aug 23 14:29:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ut9_42534/08_2025/8ut9_42534.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ut9_42534/08_2025/8ut9_42534.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ut9_42534/08_2025/8ut9_42534.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ut9_42534/08_2025/8ut9_42534.map" model { file = "/net/cci-nas-00/data/ceres_data/8ut9_42534/08_2025/8ut9_42534.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ut9_42534/08_2025/8ut9_42534.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 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 66 5.16 5 C 7833 2.51 5 N 2266 2.21 5 O 2542 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12707 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2422 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 13, 'TRANS': 303} Chain: "B" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1359 Classifications: {'peptide': 167} Link IDs: {'TRANS': 166} Chain: "C" Number of atoms: 2414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2414 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 13, 'TRANS': 302} Chain: "D" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1359 Classifications: {'peptide': 167} Link IDs: {'TRANS': 166} Chain: "E" Number of atoms: 2414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2414 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 13, 'TRANS': 302} Chain: "F" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1359 Classifications: {'peptide': 167} Link IDs: {'TRANS': 166} Chain: "G" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 630 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 126} Link IDs: {'TRANS': 125} Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 378 Unresolved non-hydrogen dihedrals: 126 Planarities with less than four sites: {'UNK:plan-1': 126} Unresolved non-hydrogen planarities: 126 Chain: "H" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 540 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'TRANS': 107} Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 324 Unresolved non-hydrogen dihedrals: 108 Planarities with less than four sites: {'UNK:plan-1': 108} Unresolved non-hydrogen planarities: 108 Chain: "I" 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: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" 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: 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: "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: "C" 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: "D" 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 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: 2.63, per 1000 atoms: 0.21 Number of scatterers: 12707 At special positions: 0 Unit cell: (83.375, 107.3, 143.55, 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 66 16.00 O 2542 8.00 N 2266 7.00 C 7833 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 66 " distance=2.04 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 129 " distance=2.03 Simple disulfide: pdb=" SG CYS A 272 " - pdb=" SG CYS A 296 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.05 Simple disulfide: pdb=" SG CYS C 42 " - pdb=" SG CYS C 268 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 66 " distance=2.04 Simple disulfide: pdb=" SG CYS C 87 " - pdb=" SG CYS C 129 " distance=2.05 Simple disulfide: pdb=" SG CYS C 272 " - pdb=" SG CYS C 296 " distance=2.05 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS E 4 " - pdb=" SG CYS F 137 " distance=2.03 Simple disulfide: pdb=" SG CYS E 42 " - pdb=" SG CYS E 268 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 66 " distance=2.03 Simple disulfide: pdb=" SG CYS E 87 " - pdb=" SG CYS E 129 " distance=2.03 Simple disulfide: pdb=" SG CYS E 272 " - pdb=" SG CYS E 296 " distance=2.02 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-3 " NAG I 1 " - " NAG I 2 " BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " NAG-ASN " NAG A 401 " - " ASN A 28 " " NAG A 402 " - " ASN A 231 " " NAG B 301 " - " ASN B 154 " " NAG C 401 " - " ASN C 12 " " NAG C 402 " - " ASN C 28 " " NAG D 301 " - " ASN D 154 " " NAG E 401 " - " ASN E 28 " " NAG E 402 " - " ASN E 231 " " NAG F 301 " - " ASN F 154 " " NAG I 1 " - " ASN B 82 " " NAG J 1 " - " ASN D 82 " " NAG K 1 " - " ASN F 82 " Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 422.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3104 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 38 sheets defined 28.3% alpha, 29.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 57 through 62 removed outlier: 3.642A pdb=" N THR A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 70 removed outlier: 5.700A pdb=" N GLN A 68 " --> pdb=" O GLN A 65 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A 70 " --> pdb=" O ASP A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 104 Processing helix chain 'A' and resid 178 through 185 Processing helix chain 'B' and resid 37 through 56 Processing helix chain 'B' and resid 74 through 127 Processing helix chain 'B' and resid 146 through 154 removed outlier: 3.977A pdb=" N ALA B 150 " --> pdb=" O ASP B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 164 removed outlier: 4.400A pdb=" N GLU B 164 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 169 removed outlier: 3.569A pdb=" N ASN B 169 " --> pdb=" O GLU B 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 62 removed outlier: 4.277A pdb=" N THR C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 70 removed outlier: 3.916A pdb=" N ASP C 67 " --> pdb=" O PRO C 64 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N GLN C 68 " --> pdb=" O GLN C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 104 removed outlier: 3.638A pdb=" N GLU C 104 " --> pdb=" O GLN C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 186 Processing helix chain 'D' and resid 37 through 56 Processing helix chain 'D' and resid 74 through 127 Processing helix chain 'D' and resid 145 through 155 removed outlier: 3.680A pdb=" N MET D 149 " --> pdb=" O ASP D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 171 removed outlier: 4.188A pdb=" N ALA D 166 " --> pdb=" O TYR D 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 62 Processing helix chain 'E' and resid 63 through 70 removed outlier: 5.507A pdb=" N GLN E 68 " --> pdb=" O GLN E 65 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU E 70 " --> pdb=" O ASP E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 104 Processing helix chain 'E' and resid 178 through 187 Processing helix chain 'F' and resid 38 through 56 Processing helix chain 'F' and resid 74 through 127 Processing helix chain 'F' and resid 145 through 154 Processing helix chain 'F' and resid 162 through 171 Processing helix chain 'G' and resid 61 through 65 removed outlier: 3.666A pdb=" N UNK G 65 " --> pdb=" O UNK G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 76 No H-bonds generated for 'chain 'G' and resid 74 through 76' Processing helix chain 'G' and resid 87 through 90 Processing helix chain 'G' and resid 109 through 113 removed outlier: 3.604A pdb=" N UNK G 113 " --> pdb=" O UNK G 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 32 No H-bonds generated for 'chain 'H' and resid 30 through 32' Processing helix chain 'H' and resid 80 through 84 removed outlier: 3.631A pdb=" N UNK H 84 " --> pdb=" O UNK H 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 32 through 36 removed outlier: 3.508A pdb=" N GLN B 27 " --> pdb=" O LYS A 2 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS A 2 " --> pdb=" O GLN B 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 17 Processing sheet with id=AA3, first strand: chain 'A' and resid 29 through 31 Processing sheet with id=AA4, first strand: chain 'A' and resid 33 through 34 Processing sheet with id=AA5, first strand: chain 'A' and resid 41 through 42 removed outlier: 6.089A pdb=" N ILE A 41 " --> pdb=" O ASP A 265 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 48 through 51 Processing sheet with id=AA7, first strand: chain 'A' and resid 90 through 92 removed outlier: 6.729A pdb=" N LYS A 91 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N TRP A 225 " --> pdb=" O LYS A 91 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N VAL A 170 " --> pdb=" O ARG A 247 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ARG A 247 " --> pdb=" O VAL A 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 90 through 92 removed outlier: 6.729A pdb=" N LYS A 91 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N TRP A 225 " --> pdb=" O LYS A 91 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N VAL A 170 " --> pdb=" O PRO A 245 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 155 through 160 Processing sheet with id=AB1, first strand: chain 'A' and resid 272 through 274 removed outlier: 4.031A pdb=" N CYS A 272 " --> pdb=" O ILE A 279 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 31 through 36 removed outlier: 3.805A pdb=" N GLN D 27 " --> pdb=" O LYS C 2 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS C 2 " --> pdb=" O GLN D 27 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 14 through 16 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 31 Processing sheet with id=AB5, first strand: chain 'C' and resid 33 through 34 Processing sheet with id=AB6, first strand: chain 'C' and resid 41 through 42 removed outlier: 5.695A pdb=" N ILE C 41 " --> pdb=" O ASP C 265 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 48 through 50 removed outlier: 3.744A pdb=" N ILE C 78 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ILE C 77 " --> pdb=" O ILE C 258 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 72 through 73 removed outlier: 3.889A pdb=" N PHE C 72 " --> pdb=" O ILE C 108 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ARG C 247 " --> pdb=" O VAL C 170 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N VAL C 170 " --> pdb=" O ARG C 247 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LYS C 91 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N TRP C 225 " --> pdb=" O LYS C 91 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 72 through 73 removed outlier: 3.889A pdb=" N PHE C 72 " --> pdb=" O ILE C 108 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ARG C 247 " --> pdb=" O VAL C 170 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N VAL C 170 " --> pdb=" O ARG C 247 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 120 through 121 Processing sheet with id=AC2, first strand: chain 'C' and resid 126 through 130 removed outlier: 3.689A pdb=" N SER C 135 " --> pdb=" O THR C 126 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 155 through 159 Processing sheet with id=AC4, first strand: chain 'C' and resid 272 through 274 removed outlier: 3.879A pdb=" N CYS C 272 " --> pdb=" O ILE C 279 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 14 through 15 removed outlier: 7.842A pdb=" N TRP F 14 " --> pdb=" O LEU E 5 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N HIS E 7 " --> pdb=" O TRP F 14 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS E 2 " --> pdb=" O GLN F 27 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 14 through 15 removed outlier: 7.842A pdb=" N TRP F 14 " --> pdb=" O LEU E 5 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N HIS E 7 " --> pdb=" O TRP F 14 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 14 through 16 Processing sheet with id=AC8, first strand: chain 'E' and resid 29 through 31 Processing sheet with id=AC9, first strand: chain 'E' and resid 33 through 34 Processing sheet with id=AD1, first strand: chain 'E' and resid 41 through 42 removed outlier: 5.469A pdb=" N ILE E 41 " --> pdb=" O ASP E 265 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'E' and resid 48 through 51 removed outlier: 6.666A pdb=" N VAL E 49 " --> pdb=" O ILE E 78 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ILE E 77 " --> pdb=" O ILE E 258 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'E' and resid 90 through 92 removed outlier: 6.716A pdb=" N LYS E 91 " --> pdb=" O PHE E 223 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N TRP E 225 " --> pdb=" O LYS E 91 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N VAL E 170 " --> pdb=" O ARG E 247 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ARG E 247 " --> pdb=" O VAL E 170 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AD5, first strand: chain 'E' and resid 155 through 160 Processing sheet with id=AD6, first strand: chain 'E' and resid 277 through 278 Processing sheet with id=AD7, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AD8, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.598A pdb=" N UNK G 92 " --> pdb=" O UNK G 123 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N UNK G 33 " --> pdb=" O UNK G 99 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N UNK G 32 " --> pdb=" O UNK G 52 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N UNK G 52 " --> pdb=" O UNK G 32 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N UNK G 34 " --> pdb=" O UNK G 50 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N UNK G 50 " --> pdb=" O UNK G 34 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N UNK G 36 " --> pdb=" O UNK G 48 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AE1, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.655A pdb=" N UNK H 11 " --> pdb=" O UNK H 107 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N UNK H 38 " --> pdb=" O UNK H 47 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N UNK H 47 " --> pdb=" O UNK H 38 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.655A pdb=" N UNK H 11 " --> pdb=" O UNK H 107 " (cutoff:3.500A) 539 hydrogen bonds defined for protein. 1455 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.10 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4373 1.34 - 1.48: 3084 1.48 - 1.61: 5355 1.61 - 1.75: 5 1.75 - 1.88: 92 Bond restraints: 12909 Sorted by residual: bond pdb=" N CYS A 268 " pdb=" CA CYS A 268 " ideal model delta sigma weight residual 1.454 1.493 -0.039 1.17e-02 7.31e+03 1.12e+01 bond pdb=" CA UNK H 67 " pdb=" CB UNK H 67 " ideal model delta sigma weight residual 1.530 1.471 0.059 2.00e-02 2.50e+03 8.72e+00 bond pdb=" SD MET A 311 " pdb=" CE MET A 311 " ideal model delta sigma weight residual 1.791 1.722 0.069 2.50e-02 1.60e+03 7.65e+00 bond pdb=" CB PRO C 315 " pdb=" CG PRO C 315 " ideal model delta sigma weight residual 1.492 1.628 -0.136 5.00e-02 4.00e+02 7.37e+00 bond pdb=" N LYS B 161 " pdb=" CA LYS B 161 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.85e+00 ... (remaining 12904 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.56: 17126 3.56 - 7.12: 328 7.12 - 10.68: 22 10.68 - 14.24: 3 14.24 - 17.80: 1 Bond angle restraints: 17480 Sorted by residual: angle pdb=" CA PRO C 315 " pdb=" N PRO C 315 " pdb=" CD PRO C 315 " ideal model delta sigma weight residual 112.00 100.59 11.41 1.40e+00 5.10e-01 6.65e+01 angle pdb=" CA CYS C 296 " pdb=" CB CYS C 296 " pdb=" SG CYS C 296 " ideal model delta sigma weight residual 114.40 132.20 -17.80 2.30e+00 1.89e-01 5.99e+01 angle pdb=" N GLU B 164 " pdb=" CA GLU B 164 " pdb=" C GLU B 164 " ideal model delta sigma weight residual 111.33 103.52 7.81 1.21e+00 6.83e-01 4.16e+01 angle pdb=" CA CYS A 42 " pdb=" CB CYS A 42 " pdb=" SG CYS A 42 " ideal model delta sigma weight residual 114.40 128.33 -13.93 2.30e+00 1.89e-01 3.67e+01 angle pdb=" CA CYS F 144 " pdb=" CB CYS F 144 " pdb=" SG CYS F 144 " ideal model delta sigma weight residual 114.40 124.46 -10.06 2.30e+00 1.89e-01 1.91e+01 ... (remaining 17475 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 7301 17.98 - 35.96: 464 35.96 - 53.93: 133 53.93 - 71.91: 42 71.91 - 89.89: 19 Dihedral angle restraints: 7959 sinusoidal: 3137 harmonic: 4822 Sorted by residual: dihedral pdb=" CB CYS D 144 " pdb=" SG CYS D 144 " pdb=" SG CYS D 148 " pdb=" CB CYS D 148 " ideal model delta sinusoidal sigma weight residual -86.00 -172.54 86.54 1 1.00e+01 1.00e-02 9.02e+01 dihedral pdb=" CD ARG B 163 " pdb=" NE ARG B 163 " pdb=" CZ ARG B 163 " pdb=" NH1 ARG B 163 " ideal model delta sinusoidal sigma weight residual 0.00 -82.06 82.06 1 1.00e+01 1.00e-02 8.27e+01 dihedral pdb=" CB CYS C 87 " pdb=" SG CYS C 87 " pdb=" SG CYS C 129 " pdb=" CB CYS C 129 " ideal model delta sinusoidal sigma weight residual 93.00 13.54 79.46 1 1.00e+01 1.00e-02 7.84e+01 ... (remaining 7956 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1641 0.075 - 0.151: 303 0.151 - 0.226: 30 0.226 - 0.301: 7 0.301 - 0.377: 4 Chirality restraints: 1985 Sorted by residual: chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN B 82 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" CB THR D 49 " pdb=" CA THR D 49 " pdb=" OG1 THR D 49 " pdb=" CG2 THR D 49 " both_signs ideal model delta sigma weight residual False 2.55 2.22 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CA CYS C 296 " pdb=" N CYS C 296 " pdb=" C CYS C 296 " pdb=" CB CYS C 296 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.65e+00 ... (remaining 1982 not shown) Planarity restraints: 2327 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 163 " 1.089 9.50e-02 1.11e+02 4.88e-01 1.44e+02 pdb=" NE ARG B 163 " -0.065 2.00e-02 2.50e+03 pdb=" CZ ARG B 163 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG B 163 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG B 163 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL E 314 " -0.097 5.00e-02 4.00e+02 1.45e-01 3.38e+01 pdb=" N PRO E 315 " 0.251 5.00e-02 4.00e+02 pdb=" CA PRO E 315 " -0.080 5.00e-02 4.00e+02 pdb=" CD PRO E 315 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 314 " -0.089 5.00e-02 4.00e+02 1.26e-01 2.55e+01 pdb=" N PRO C 315 " 0.218 5.00e-02 4.00e+02 pdb=" CA PRO C 315 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO C 315 " -0.066 5.00e-02 4.00e+02 ... (remaining 2324 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.33: 17 2.33 - 2.97: 6042 2.97 - 3.61: 18152 3.61 - 4.26: 28471 4.26 - 4.90: 48837 Nonbonded interactions: 101519 Sorted by model distance: nonbonded pdb=" NE2 GLN A 201 " pdb=" OD1 ASP E 222 " model vdw 1.682 3.120 nonbonded pdb=" OD2 ASP B 67 " pdb=" NH2 ARG B 85 " model vdw 1.886 3.120 nonbonded pdb=" OG SER E 43 " pdb=" OG1 THR E 48 " model vdw 2.062 3.040 nonbonded pdb=" NE2 HIS E 175 " pdb=" OD2 ASP E 222 " model vdw 2.141 3.120 nonbonded pdb=" OE2 GLU A 34 " pdb=" OG1 THR A 36 " model vdw 2.166 3.040 ... (remaining 101514 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' and (resid 1 through 316 or resid 401 through 402)) selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = (chain 'G' and resid 20 through 127) selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' } 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: 8.450 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 11.200 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 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 : 0.007 0.136 12939 Z= 0.314 Angle : 1.191 17.797 17555 Z= 0.639 Chirality : 0.060 0.377 1985 Planarity : 0.012 0.488 2315 Dihedral : 14.131 89.890 4810 Min Nonbonded Distance : 1.682 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 12.70 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.20), residues: 1438 helix: 1.00 (0.25), residues: 329 sheet: 0.78 (0.30), residues: 262 loop : -0.35 (0.19), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 127 TYR 0.043 0.003 TYR F 119 PHE 0.030 0.004 PHE A 250 TRP 0.018 0.002 TRP C 142 HIS 0.013 0.003 HIS D 159 Details of bonding type rmsd covalent geometry : bond 0.00684 (12909) covalent geometry : angle 1.16460 (17480) SS BOND : bond 0.01019 ( 15) SS BOND : angle 4.00523 ( 30) hydrogen bonds : bond 0.13153 ( 520) hydrogen bonds : angle 7.11848 ( 1455) link_BETA1-3 : bond 0.00824 ( 1) link_BETA1-3 : angle 8.63223 ( 3) link_BETA1-4 : bond 0.00070 ( 2) link_BETA1-4 : angle 2.20968 ( 6) link_NAG-ASN : bond 0.00550 ( 12) link_NAG-ASN : angle 3.51841 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.311 Fit side-chains REVERT: A 42 CYS cc_start: 0.5936 (m) cc_final: 0.5717 (m) REVERT: B 39 LYS cc_start: 0.7346 (ttmt) cc_final: 0.6690 (ttpt) REVERT: B 167 MET cc_start: 0.6540 (tmm) cc_final: 0.6056 (ttp) REVERT: B 168 GLN cc_start: 0.7363 (mm-40) cc_final: 0.7126 (mm-40) REVERT: C 185 LEU cc_start: 0.7320 (mp) cc_final: 0.7120 (mt) REVERT: C 303 ARG cc_start: 0.7471 (mtp-110) cc_final: 0.7070 (ptm-80) REVERT: D 135 THR cc_start: 0.7938 (t) cc_final: 0.7714 (t) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.1086 time to fit residues: 24.6071 Evaluate side-chains 142 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.3980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 9.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 HIS A 287 ASN B 60 ASN ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN D 159 HIS E 239 ASN F 106 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.175905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.154651 restraints weight = 16400.794| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 2.39 r_work: 0.3680 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 12939 Z= 0.207 Angle : 0.704 10.322 17555 Z= 0.367 Chirality : 0.046 0.311 1985 Planarity : 0.005 0.084 2315 Dihedral : 5.579 42.977 2117 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.55 % Allowed : 12.38 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.20), residues: 1438 helix: 1.24 (0.26), residues: 339 sheet: 0.48 (0.30), residues: 271 loop : -0.64 (0.19), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 25 TYR 0.016 0.002 TYR F 119 PHE 0.017 0.002 PHE C 92 TRP 0.013 0.001 TRP C 142 HIS 0.007 0.002 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00470 (12909) covalent geometry : angle 0.68280 (17480) SS BOND : bond 0.00494 ( 15) SS BOND : angle 2.08614 ( 30) hydrogen bonds : bond 0.04828 ( 520) hydrogen bonds : angle 5.82928 ( 1455) link_BETA1-3 : bond 0.00382 ( 1) link_BETA1-3 : angle 6.80986 ( 3) link_BETA1-4 : bond 0.00204 ( 2) link_BETA1-4 : angle 1.90883 ( 6) link_NAG-ASN : bond 0.00449 ( 12) link_NAG-ASN : angle 2.65417 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 189 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: A 232 ASP cc_start: 0.7597 (t0) cc_final: 0.7174 (t0) REVERT: A 247 ARG cc_start: 0.7975 (mtt180) cc_final: 0.7705 (mtt180) REVERT: B 25 ARG cc_start: 0.7921 (ttm170) cc_final: 0.7499 (tpp80) REVERT: B 39 LYS cc_start: 0.7402 (ttmt) cc_final: 0.6670 (ttpt) REVERT: B 167 MET cc_start: 0.6290 (tmm) cc_final: 0.6057 (tmm) outliers start: 19 outliers final: 13 residues processed: 199 average time/residue: 0.1067 time to fit residues: 29.9642 Evaluate side-chains 175 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 162 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain F residue 110 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 149 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 85 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 101 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 123 ASN ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 ASN ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 GLN E 263 GLN F 106 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.177100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.156031 restraints weight = 16667.007| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.37 r_work: 0.3698 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3561 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12939 Z= 0.168 Angle : 0.610 9.460 17555 Z= 0.318 Chirality : 0.043 0.294 1985 Planarity : 0.004 0.062 2315 Dihedral : 5.217 39.349 2117 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.93 % Allowed : 13.03 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.20), residues: 1438 helix: 1.35 (0.27), residues: 333 sheet: 0.30 (0.29), residues: 276 loop : -0.81 (0.19), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 291 TYR 0.014 0.002 TYR F 119 PHE 0.022 0.002 PHE C 238 TRP 0.009 0.001 TRP C 142 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00382 (12909) covalent geometry : angle 0.59098 (17480) SS BOND : bond 0.00439 ( 15) SS BOND : angle 1.65048 ( 30) hydrogen bonds : bond 0.04466 ( 520) hydrogen bonds : angle 5.53380 ( 1455) link_BETA1-3 : bond 0.00918 ( 1) link_BETA1-3 : angle 6.16308 ( 3) link_BETA1-4 : bond 0.00438 ( 2) link_BETA1-4 : angle 1.68282 ( 6) link_NAG-ASN : bond 0.00345 ( 12) link_NAG-ASN : angle 2.50002 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 179 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: A 185 LEU cc_start: 0.6187 (OUTLIER) cc_final: 0.5986 (tp) REVERT: A 238 PHE cc_start: 0.7910 (OUTLIER) cc_final: 0.7524 (m-10) REVERT: A 247 ARG cc_start: 0.8248 (mtt180) cc_final: 0.7948 (mtt180) REVERT: B 25 ARG cc_start: 0.8174 (ttm170) cc_final: 0.7894 (tpp80) REVERT: B 39 LYS cc_start: 0.7582 (ttmt) cc_final: 0.6838 (ttpt) REVERT: C 27 VAL cc_start: 0.8725 (p) cc_final: 0.8284 (t) REVERT: D 115 MET cc_start: 0.8733 (tpt) cc_final: 0.7830 (tpt) REVERT: E 217 GLN cc_start: 0.7148 (tp40) cc_final: 0.6812 (mt0) outliers start: 36 outliers final: 21 residues processed: 200 average time/residue: 0.1102 time to fit residues: 31.1483 Evaluate side-chains 187 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 225 TRP Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain C residue 311 MET Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 113 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 36 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 97 optimal weight: 0.9990 chunk 127 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 139 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 ASN C 229 ASN C 239 ASN ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 GLN ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 GLN E 201 GLN E 239 ASN F 106 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.171900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.152248 restraints weight = 16517.449| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.17 r_work: 0.3659 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3528 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12939 Z= 0.210 Angle : 0.638 9.920 17555 Z= 0.330 Chirality : 0.044 0.315 1985 Planarity : 0.004 0.055 2315 Dihedral : 5.206 38.884 2117 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.09 % Allowed : 13.84 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.20), residues: 1438 helix: 1.27 (0.27), residues: 333 sheet: -0.08 (0.30), residues: 270 loop : -1.05 (0.19), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 25 TYR 0.012 0.002 TYR D 119 PHE 0.026 0.002 PHE C 238 TRP 0.028 0.002 TRP C 142 HIS 0.005 0.001 HIS A 7 Details of bonding type rmsd covalent geometry : bond 0.00484 (12909) covalent geometry : angle 0.61799 (17480) SS BOND : bond 0.00740 ( 15) SS BOND : angle 1.87455 ( 30) hydrogen bonds : bond 0.04400 ( 520) hydrogen bonds : angle 5.54418 ( 1455) link_BETA1-3 : bond 0.00378 ( 1) link_BETA1-3 : angle 6.35837 ( 3) link_BETA1-4 : bond 0.00068 ( 2) link_BETA1-4 : angle 1.74568 ( 6) link_NAG-ASN : bond 0.00279 ( 12) link_NAG-ASN : angle 2.53198 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 185 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 247 ARG cc_start: 0.8370 (mtt180) cc_final: 0.8011 (mtt180) REVERT: B 25 ARG cc_start: 0.8105 (ttm170) cc_final: 0.7842 (tpp80) REVERT: B 39 LYS cc_start: 0.7650 (ttmt) cc_final: 0.6936 (ttpt) REVERT: B 168 GLN cc_start: 0.7422 (mm110) cc_final: 0.6851 (pp30) REVERT: C 37 ASN cc_start: 0.8553 (OUTLIER) cc_final: 0.8214 (p0) REVERT: C 256 MET cc_start: 0.7538 (ttp) cc_final: 0.7076 (tmm) REVERT: D 67 ASP cc_start: 0.8095 (m-30) cc_final: 0.7854 (m-30) REVERT: D 115 MET cc_start: 0.8725 (tpt) cc_final: 0.8410 (mmm) REVERT: E 217 GLN cc_start: 0.7313 (tp40) cc_final: 0.6841 (mt0) outliers start: 38 outliers final: 27 residues processed: 211 average time/residue: 0.1072 time to fit residues: 31.8160 Evaluate side-chains 198 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 170 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 225 TRP Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain C residue 311 MET Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 110 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 72 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 78 optimal weight: 0.3980 chunk 71 optimal weight: 2.9990 chunk 150 optimal weight: 8.9990 chunk 11 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 134 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 GLN ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 239 ASN ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 47 GLN ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.174086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.153343 restraints weight = 16581.564| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 2.34 r_work: 0.3673 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3538 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12939 Z= 0.141 Angle : 0.570 9.346 17555 Z= 0.295 Chirality : 0.042 0.304 1985 Planarity : 0.003 0.050 2315 Dihedral : 5.012 37.927 2117 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.69 % Allowed : 15.15 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.20), residues: 1438 helix: 1.45 (0.27), residues: 333 sheet: -0.06 (0.30), residues: 270 loop : -1.06 (0.19), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 47 TYR 0.015 0.001 TYR C 274 PHE 0.020 0.001 PHE C 238 TRP 0.021 0.001 TRP C 142 HIS 0.003 0.001 HIS E 7 Details of bonding type rmsd covalent geometry : bond 0.00317 (12909) covalent geometry : angle 0.55009 (17480) SS BOND : bond 0.00400 ( 15) SS BOND : angle 1.66804 ( 30) hydrogen bonds : bond 0.04140 ( 520) hydrogen bonds : angle 5.32607 ( 1455) link_BETA1-3 : bond 0.00662 ( 1) link_BETA1-3 : angle 5.93835 ( 3) link_BETA1-4 : bond 0.00160 ( 2) link_BETA1-4 : angle 1.52555 ( 6) link_NAG-ASN : bond 0.00287 ( 12) link_NAG-ASN : angle 2.36751 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 183 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8037 (ptt180) cc_final: 0.7767 (ptt90) REVERT: A 185 LEU cc_start: 0.6342 (OUTLIER) cc_final: 0.5123 (mp) REVERT: A 238 PHE cc_start: 0.8181 (OUTLIER) cc_final: 0.7735 (m-80) REVERT: A 247 ARG cc_start: 0.8342 (mtt180) cc_final: 0.7997 (mtt180) REVERT: B 25 ARG cc_start: 0.8143 (ttm170) cc_final: 0.7901 (tpp80) REVERT: B 39 LYS cc_start: 0.7694 (ttmt) cc_final: 0.6971 (ttpt) REVERT: D 61 GLN cc_start: 0.8497 (tp40) cc_final: 0.8191 (tp40) REVERT: D 115 MET cc_start: 0.8681 (tpt) cc_final: 0.8423 (mmm) REVERT: D 120 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7693 (mp0) REVERT: E 217 GLN cc_start: 0.7297 (tp40) cc_final: 0.6859 (mt0) outliers start: 33 outliers final: 21 residues processed: 205 average time/residue: 0.1116 time to fit residues: 32.1557 Evaluate side-chains 192 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 168 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 225 TRP Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain C residue 311 MET Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 110 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 116 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 90 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 102 optimal weight: 0.0070 chunk 83 optimal weight: 5.9990 chunk 128 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 153 optimal weight: 10.0000 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN B 159 HIS ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 ASN E 239 ASN ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 12 ASN ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.174150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.153387 restraints weight = 16465.761| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 2.35 r_work: 0.3682 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3544 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12939 Z= 0.132 Angle : 0.546 8.995 17555 Z= 0.284 Chirality : 0.041 0.301 1985 Planarity : 0.003 0.049 2315 Dihedral : 4.822 37.242 2117 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.69 % Allowed : 16.45 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.21), residues: 1438 helix: 1.71 (0.27), residues: 327 sheet: -0.08 (0.31), residues: 270 loop : -1.04 (0.19), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 47 TYR 0.014 0.001 TYR C 186 PHE 0.016 0.001 PHE C 238 TRP 0.019 0.001 TRP C 142 HIS 0.004 0.001 HIS C 174 Details of bonding type rmsd covalent geometry : bond 0.00296 (12909) covalent geometry : angle 0.52793 (17480) SS BOND : bond 0.00367 ( 15) SS BOND : angle 1.47221 ( 30) hydrogen bonds : bond 0.04001 ( 520) hydrogen bonds : angle 5.19714 ( 1455) link_BETA1-3 : bond 0.00819 ( 1) link_BETA1-3 : angle 5.72155 ( 3) link_BETA1-4 : bond 0.00290 ( 2) link_BETA1-4 : angle 1.48590 ( 6) link_NAG-ASN : bond 0.00284 ( 12) link_NAG-ASN : angle 2.26683 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 176 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8000 (ptt180) cc_final: 0.7714 (ptt90) REVERT: A 185 LEU cc_start: 0.6396 (OUTLIER) cc_final: 0.5139 (mp) REVERT: A 238 PHE cc_start: 0.8144 (OUTLIER) cc_final: 0.7708 (m-80) REVERT: A 247 ARG cc_start: 0.8348 (mtt180) cc_final: 0.8037 (mtt180) REVERT: A 256 MET cc_start: 0.8027 (ptm) cc_final: 0.7703 (ttp) REVERT: B 25 ARG cc_start: 0.8147 (ttm170) cc_final: 0.7903 (tpp80) REVERT: B 39 LYS cc_start: 0.7711 (ttmt) cc_final: 0.6987 (ttpt) REVERT: C 27 VAL cc_start: 0.8813 (p) cc_final: 0.8402 (t) REVERT: C 256 MET cc_start: 0.7526 (ttp) cc_final: 0.7310 (tmm) REVERT: D 115 MET cc_start: 0.8659 (tpt) cc_final: 0.8431 (mmm) REVERT: D 120 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7684 (mp0) REVERT: E 217 GLN cc_start: 0.7276 (tp40) cc_final: 0.6839 (mt0) REVERT: F 53 ASN cc_start: 0.8961 (t0) cc_final: 0.8491 (t0) REVERT: F 157 TYR cc_start: 0.6452 (t80) cc_final: 0.5998 (t80) outliers start: 33 outliers final: 22 residues processed: 199 average time/residue: 0.1078 time to fit residues: 30.5347 Evaluate side-chains 188 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 163 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 225 TRP Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain C residue 311 MET Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain F residue 12 ASN Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 113 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 30 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 154 optimal weight: 9.9990 chunk 160 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 74 optimal weight: 0.0270 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 110 optimal weight: 0.0980 chunk 9 optimal weight: 0.9990 chunk 120 optimal weight: 0.7980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN C 239 ASN ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 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 = 0.4034 r_free = 0.4034 target = 0.175691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.156319 restraints weight = 16297.350| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 2.16 r_work: 0.3706 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3575 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12939 Z= 0.122 Angle : 0.538 9.016 17555 Z= 0.280 Chirality : 0.041 0.298 1985 Planarity : 0.003 0.047 2315 Dihedral : 4.675 31.487 2117 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.44 % Allowed : 16.94 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.21), residues: 1438 helix: 1.81 (0.27), residues: 327 sheet: -0.09 (0.31), residues: 272 loop : -1.01 (0.19), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 220 TYR 0.011 0.001 TYR C 186 PHE 0.016 0.001 PHE C 238 TRP 0.017 0.001 TRP C 142 HIS 0.003 0.001 HIS E 7 Details of bonding type rmsd covalent geometry : bond 0.00272 (12909) covalent geometry : angle 0.51826 (17480) SS BOND : bond 0.00347 ( 15) SS BOND : angle 1.36065 ( 30) hydrogen bonds : bond 0.03937 ( 520) hydrogen bonds : angle 5.11887 ( 1455) link_BETA1-3 : bond 0.00633 ( 1) link_BETA1-3 : angle 5.67943 ( 3) link_BETA1-4 : bond 0.00148 ( 2) link_BETA1-4 : angle 1.42823 ( 6) link_NAG-ASN : bond 0.00232 ( 12) link_NAG-ASN : angle 2.45963 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 170 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 ARG cc_start: 0.7957 (ptt180) cc_final: 0.7721 (ptt90) REVERT: A 185 LEU cc_start: 0.6380 (OUTLIER) cc_final: 0.5141 (mp) REVERT: A 238 PHE cc_start: 0.8094 (OUTLIER) cc_final: 0.7673 (m-80) REVERT: A 247 ARG cc_start: 0.8324 (mtt180) cc_final: 0.8025 (mtt180) REVERT: B 25 ARG cc_start: 0.8108 (ttm170) cc_final: 0.7864 (tpp80) REVERT: B 39 LYS cc_start: 0.7720 (ttmt) cc_final: 0.6999 (ttpt) REVERT: B 168 GLN cc_start: 0.7444 (mm-40) cc_final: 0.6805 (pp30) REVERT: C 27 VAL cc_start: 0.8772 (p) cc_final: 0.8345 (t) REVERT: C 256 MET cc_start: 0.7461 (ttp) cc_final: 0.7214 (tmm) REVERT: D 120 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7624 (mp0) REVERT: E 217 GLN cc_start: 0.7202 (tp40) cc_final: 0.6782 (mt0) REVERT: F 157 TYR cc_start: 0.6445 (t80) cc_final: 0.6016 (t80) outliers start: 30 outliers final: 22 residues processed: 192 average time/residue: 0.1002 time to fit residues: 27.0390 Evaluate side-chains 186 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 225 TRP Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 311 MET Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 113 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 47 optimal weight: 8.9990 chunk 157 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 142 optimal weight: 9.9990 chunk 87 optimal weight: 0.7980 chunk 144 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN B 26 HIS C 37 ASN ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 12 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.171279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.150404 restraints weight = 16440.934| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.34 r_work: 0.3642 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3505 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12939 Z= 0.185 Angle : 0.594 9.348 17555 Z= 0.308 Chirality : 0.043 0.318 1985 Planarity : 0.004 0.049 2315 Dihedral : 4.887 41.796 2117 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.26 % Allowed : 16.78 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.21), residues: 1438 helix: 1.53 (0.27), residues: 333 sheet: -0.23 (0.32), residues: 262 loop : -1.14 (0.19), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 47 TYR 0.012 0.002 TYR D 119 PHE 0.020 0.002 PHE C 238 TRP 0.021 0.001 TRP C 142 HIS 0.004 0.001 HIS C 224 Details of bonding type rmsd covalent geometry : bond 0.00423 (12909) covalent geometry : angle 0.57675 (17480) SS BOND : bond 0.00533 ( 15) SS BOND : angle 1.50879 ( 30) hydrogen bonds : bond 0.04106 ( 520) hydrogen bonds : angle 5.28760 ( 1455) link_BETA1-3 : bond 0.00383 ( 1) link_BETA1-3 : angle 5.89044 ( 3) link_BETA1-4 : bond 0.00184 ( 2) link_BETA1-4 : angle 1.56614 ( 6) link_NAG-ASN : bond 0.00196 ( 12) link_NAG-ASN : angle 2.33972 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 175 time to evaluate : 0.462 Fit side-chains revert: symmetry clash REVERT: A 37 ASN cc_start: 0.6963 (OUTLIER) cc_final: 0.6556 (p0) REVERT: A 121 ARG cc_start: 0.8119 (ptt180) cc_final: 0.7864 (ptt90) REVERT: A 185 LEU cc_start: 0.6501 (OUTLIER) cc_final: 0.5182 (mp) REVERT: A 238 PHE cc_start: 0.8195 (OUTLIER) cc_final: 0.7725 (m-80) REVERT: A 247 ARG cc_start: 0.8515 (mtt180) cc_final: 0.8275 (mtt180) REVERT: B 25 ARG cc_start: 0.8159 (ttm170) cc_final: 0.7912 (tpp80) REVERT: B 39 LYS cc_start: 0.7770 (ttmt) cc_final: 0.7047 (ttpt) REVERT: C 34 GLU cc_start: 0.8081 (tp30) cc_final: 0.7879 (tp30) REVERT: C 256 MET cc_start: 0.7557 (ttp) cc_final: 0.7189 (tmm) REVERT: D 61 GLN cc_start: 0.8423 (tp40) cc_final: 0.8221 (tp40) REVERT: D 120 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7689 (mp0) REVERT: D 149 MET cc_start: 0.5997 (OUTLIER) cc_final: 0.5383 (ttm) REVERT: E 217 GLN cc_start: 0.7378 (tp40) cc_final: 0.6927 (mt0) REVERT: F 53 ASN cc_start: 0.9005 (t0) cc_final: 0.8529 (t0) REVERT: F 157 TYR cc_start: 0.6625 (t80) cc_final: 0.6173 (t80) outliers start: 40 outliers final: 26 residues processed: 201 average time/residue: 0.1065 time to fit residues: 30.5627 Evaluate side-chains 199 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 168 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 37 ASN Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 225 TRP Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain C residue 311 MET Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain F residue 12 ASN Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 113 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 92 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 123 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 162 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN C 313 ASN ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.171099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.150207 restraints weight = 16584.281| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.35 r_work: 0.3638 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3502 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12939 Z= 0.177 Angle : 0.591 9.339 17555 Z= 0.305 Chirality : 0.043 0.315 1985 Planarity : 0.003 0.048 2315 Dihedral : 4.875 33.369 2117 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.09 % Allowed : 16.61 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.21), residues: 1438 helix: 1.67 (0.27), residues: 327 sheet: -0.30 (0.32), residues: 264 loop : -1.20 (0.19), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 47 TYR 0.013 0.002 TYR F 119 PHE 0.019 0.002 PHE C 238 TRP 0.018 0.001 TRP C 142 HIS 0.004 0.001 HIS A 7 Details of bonding type rmsd covalent geometry : bond 0.00406 (12909) covalent geometry : angle 0.56889 (17480) SS BOND : bond 0.00462 ( 15) SS BOND : angle 1.43904 ( 30) hydrogen bonds : bond 0.04104 ( 520) hydrogen bonds : angle 5.29701 ( 1455) link_BETA1-3 : bond 0.00396 ( 1) link_BETA1-3 : angle 5.84893 ( 3) link_BETA1-4 : bond 0.00178 ( 2) link_BETA1-4 : angle 1.47914 ( 6) link_NAG-ASN : bond 0.00403 ( 12) link_NAG-ASN : angle 2.90187 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 173 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8159 (ptt180) cc_final: 0.7871 (ptt90) REVERT: A 185 LEU cc_start: 0.6549 (OUTLIER) cc_final: 0.5254 (mp) REVERT: A 238 PHE cc_start: 0.8161 (OUTLIER) cc_final: 0.7693 (m-80) REVERT: A 247 ARG cc_start: 0.8526 (mtt180) cc_final: 0.8280 (mtt180) REVERT: A 256 MET cc_start: 0.8108 (ptm) cc_final: 0.7763 (ttp) REVERT: B 25 ARG cc_start: 0.8178 (ttm170) cc_final: 0.7930 (tpp80) REVERT: B 39 LYS cc_start: 0.7738 (ttmt) cc_final: 0.7214 (mtpt) REVERT: B 168 GLN cc_start: 0.7555 (mm-40) cc_final: 0.6886 (pp30) REVERT: C 34 GLU cc_start: 0.8090 (tp30) cc_final: 0.7883 (tp30) REVERT: C 256 MET cc_start: 0.7579 (ttp) cc_final: 0.7200 (tmm) REVERT: D 120 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7642 (mp0) REVERT: D 149 MET cc_start: 0.5977 (OUTLIER) cc_final: 0.5389 (ttm) REVERT: E 217 GLN cc_start: 0.7395 (tp40) cc_final: 0.6934 (mt0) REVERT: F 53 ASN cc_start: 0.9003 (t0) cc_final: 0.8522 (t0) REVERT: F 157 TYR cc_start: 0.6670 (t80) cc_final: 0.6234 (t80) outliers start: 38 outliers final: 30 residues processed: 200 average time/residue: 0.1030 time to fit residues: 29.3749 Evaluate side-chains 207 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 173 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 225 TRP Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain C residue 311 MET Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 213 GLN Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain F residue 12 ASN Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 113 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 49 optimal weight: 0.5980 chunk 100 optimal weight: 0.0010 chunk 31 optimal weight: 0.0030 chunk 63 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 148 optimal weight: 6.9990 chunk 58 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 157 optimal weight: 6.9990 chunk 121 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.174142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.153181 restraints weight = 16607.595| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.39 r_work: 0.3663 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12939 Z= 0.119 Angle : 0.544 8.758 17555 Z= 0.284 Chirality : 0.041 0.297 1985 Planarity : 0.003 0.047 2315 Dihedral : 4.706 31.804 2117 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.52 % Allowed : 17.75 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.21), residues: 1438 helix: 1.82 (0.27), residues: 333 sheet: -0.13 (0.32), residues: 252 loop : -1.13 (0.19), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 47 TYR 0.011 0.001 TYR D 119 PHE 0.017 0.001 PHE C 238 TRP 0.015 0.001 TRP C 142 HIS 0.003 0.001 HIS E 7 Details of bonding type rmsd covalent geometry : bond 0.00264 (12909) covalent geometry : angle 0.52318 (17480) SS BOND : bond 0.00352 ( 15) SS BOND : angle 1.28651 ( 30) hydrogen bonds : bond 0.03947 ( 520) hydrogen bonds : angle 5.12213 ( 1455) link_BETA1-3 : bond 0.00889 ( 1) link_BETA1-3 : angle 5.46430 ( 3) link_BETA1-4 : bond 0.00137 ( 2) link_BETA1-4 : angle 1.36714 ( 6) link_NAG-ASN : bond 0.00245 ( 12) link_NAG-ASN : angle 2.72465 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 177 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: A 37 ASN cc_start: 0.6905 (OUTLIER) cc_final: 0.6478 (p0) REVERT: A 185 LEU cc_start: 0.6398 (OUTLIER) cc_final: 0.5186 (mp) REVERT: A 238 PHE cc_start: 0.7916 (OUTLIER) cc_final: 0.7521 (m-80) REVERT: A 247 ARG cc_start: 0.8283 (mtt180) cc_final: 0.7949 (mtt180) REVERT: B 25 ARG cc_start: 0.7909 (ttm170) cc_final: 0.7665 (tpp80) REVERT: B 39 LYS cc_start: 0.7688 (ttmt) cc_final: 0.6984 (ttpt) REVERT: B 168 GLN cc_start: 0.7513 (mm-40) cc_final: 0.6899 (pp30) REVERT: C 256 MET cc_start: 0.7330 (ttp) cc_final: 0.7046 (tmm) REVERT: D 120 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7448 (mp0) REVERT: D 149 MET cc_start: 0.5817 (OUTLIER) cc_final: 0.5201 (ttm) REVERT: E 213 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.7952 (tp40) REVERT: E 217 GLN cc_start: 0.7133 (tp40) cc_final: 0.6822 (mt0) REVERT: F 157 TYR cc_start: 0.6509 (t80) cc_final: 0.6108 (t80) outliers start: 31 outliers final: 22 residues processed: 195 average time/residue: 0.1068 time to fit residues: 29.6832 Evaluate side-chains 198 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 170 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 37 ASN Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 225 TRP Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 311 MET Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 213 GLN Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 113 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 106 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 141 optimal weight: 8.9990 chunk 138 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 160 optimal weight: 9.9990 chunk 71 optimal weight: 0.8980 chunk 148 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN A 182 GLN ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 ASN F 12 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.165193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.144165 restraints weight = 16674.415| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.33 r_work: 0.3567 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 12939 Z= 0.308 Angle : 0.734 9.941 17555 Z= 0.378 Chirality : 0.048 0.364 1985 Planarity : 0.004 0.049 2315 Dihedral : 5.362 35.137 2117 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.77 % Allowed : 17.67 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.21), residues: 1438 helix: 1.28 (0.27), residues: 327 sheet: -0.70 (0.32), residues: 264 loop : -1.44 (0.19), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 220 TYR 0.017 0.003 TYR D 157 PHE 0.032 0.003 PHE C 238 TRP 0.022 0.002 TRP C 142 HIS 0.006 0.002 HIS C 7 Details of bonding type rmsd covalent geometry : bond 0.00714 (12909) covalent geometry : angle 0.71495 (17480) SS BOND : bond 0.00756 ( 15) SS BOND : angle 1.74226 ( 30) hydrogen bonds : bond 0.04606 ( 520) hydrogen bonds : angle 5.71980 ( 1455) link_BETA1-3 : bond 0.00069 ( 1) link_BETA1-3 : angle 6.24497 ( 3) link_BETA1-4 : bond 0.00140 ( 2) link_BETA1-4 : angle 1.85754 ( 6) link_NAG-ASN : bond 0.00233 ( 12) link_NAG-ASN : angle 2.83607 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2470.60 seconds wall clock time: 43 minutes 13.45 seconds (2593.45 seconds total)