Starting phenix.real_space_refine on Wed Jul 30 19:19:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ut9_42534/07_2025/8ut9_42534.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ut9_42534/07_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_42534/07_2025/8ut9_42534.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ut9_42534/07_2025/8ut9_42534.map" model { file = "/net/cci-nas-00/data/ceres_data/8ut9_42534/07_2025/8ut9_42534.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ut9_42534/07_2025/8ut9_42534.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.98, per 1000 atoms: 0.71 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: 3.04 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.70 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: 4.07 Time building geometry restraints manager: 3.64 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: 8.800 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: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 31.960 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.020 ------------------------------------------------------------------------------- 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 : 5.53 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (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 TRP 0.018 0.002 TRP C 142 HIS 0.013 0.003 HIS D 159 PHE 0.030 0.004 PHE A 250 TYR 0.043 0.003 TYR F 119 ARG 0.014 0.001 ARG F 127 Details of bonding type rmsd link_NAG-ASN : bond 0.00550 ( 12) link_NAG-ASN : angle 3.51841 ( 36) link_BETA1-4 : bond 0.00070 ( 2) link_BETA1-4 : angle 2.20968 ( 6) hydrogen bonds : bond 0.13153 ( 520) hydrogen bonds : angle 7.11848 ( 1455) SS BOND : bond 0.01019 ( 15) SS BOND : angle 4.00523 ( 30) link_BETA1-3 : bond 0.00824 ( 1) link_BETA1-3 : angle 8.63223 ( 3) covalent geometry : bond 0.00684 (12909) covalent geometry : angle 1.16460 (17480) *********************** 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 : 1.381 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: 0.2730 time to fit residues: 61.7454 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 : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 0.8980 chunk 123 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 ASN C 239 ASN ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 HIS E 239 ASN F 106 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.181285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.160557 restraints weight = 16103.268| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 2.34 r_work: 0.3737 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 12939 Z= 0.163 Angle : 0.666 9.786 17555 Z= 0.348 Chirality : 0.044 0.300 1985 Planarity : 0.004 0.081 2315 Dihedral : 5.488 43.061 2117 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.22 % Allowed : 12.54 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.20), residues: 1438 helix: 1.39 (0.26), residues: 336 sheet: 0.60 (0.30), residues: 271 loop : -0.53 (0.19), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 142 HIS 0.008 0.001 HIS B 142 PHE 0.015 0.002 PHE C 92 TYR 0.017 0.001 TYR F 119 ARG 0.004 0.001 ARG F 25 Details of bonding type rmsd link_NAG-ASN : bond 0.00383 ( 12) link_NAG-ASN : angle 2.64497 ( 36) link_BETA1-4 : bond 0.00295 ( 2) link_BETA1-4 : angle 1.71445 ( 6) hydrogen bonds : bond 0.04830 ( 520) hydrogen bonds : angle 5.78460 ( 1455) SS BOND : bond 0.00550 ( 15) SS BOND : angle 1.97761 ( 30) link_BETA1-3 : bond 0.00597 ( 1) link_BETA1-3 : angle 6.44634 ( 3) covalent geometry : bond 0.00360 (12909) covalent geometry : angle 0.64505 (17480) *********************** 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: 15 poor density : 193 time to evaluate : 2.581 Fit side-chains revert: symmetry clash REVERT: A 232 ASP cc_start: 0.7552 (t0) cc_final: 0.7132 (t0) REVERT: A 247 ARG cc_start: 0.7765 (mtt180) cc_final: 0.7506 (mtt180) REVERT: B 25 ARG cc_start: 0.7892 (ttm170) cc_final: 0.7400 (tpp80) REVERT: B 39 LYS cc_start: 0.7356 (ttmt) cc_final: 0.6635 (ttpt) REVERT: E 232 ASP cc_start: 0.7003 (m-30) cc_final: 0.6767 (m-30) outliers start: 15 outliers final: 11 residues processed: 202 average time/residue: 0.3121 time to fit residues: 88.6568 Evaluate side-chains 168 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 157 time to evaluate : 1.825 ------------------------------------------------------------------------------- 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 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 272 CYS Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 144 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 130 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 128 optimal weight: 0.9990 chunk 137 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 124 optimal weight: 0.0170 overall best weight: 0.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 HIS A 123 ASN A 287 ASN ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN D 61 GLN D 159 HIS E 239 ASN E 263 GLN F 106 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.180687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.160067 restraints weight = 16412.013| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 2.34 r_work: 0.3736 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12939 Z= 0.144 Angle : 0.585 9.196 17555 Z= 0.306 Chirality : 0.043 0.282 1985 Planarity : 0.004 0.060 2315 Dihedral : 5.053 39.919 2117 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.12 % Allowed : 13.52 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.21), residues: 1438 helix: 1.47 (0.26), residues: 339 sheet: 0.48 (0.30), residues: 281 loop : -0.66 (0.20), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 142 HIS 0.005 0.001 HIS D 159 PHE 0.017 0.002 PHE C 238 TYR 0.013 0.001 TYR F 119 ARG 0.006 0.000 ARG C 291 Details of bonding type rmsd link_NAG-ASN : bond 0.00363 ( 12) link_NAG-ASN : angle 2.35096 ( 36) link_BETA1-4 : bond 0.00254 ( 2) link_BETA1-4 : angle 1.59671 ( 6) hydrogen bonds : bond 0.04382 ( 520) hydrogen bonds : angle 5.39499 ( 1455) SS BOND : bond 0.00383 ( 15) SS BOND : angle 1.57837 ( 30) link_BETA1-3 : bond 0.01013 ( 1) link_BETA1-3 : angle 6.04816 ( 3) covalent geometry : bond 0.00320 (12909) covalent geometry : angle 0.56644 (17480) *********************** 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 203 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 177 time to evaluate : 1.378 Fit side-chains revert: symmetry clash REVERT: A 121 ARG cc_start: 0.7723 (ptt180) cc_final: 0.7510 (ptt90) REVERT: A 238 PHE cc_start: 0.7547 (OUTLIER) cc_final: 0.7141 (m-10) REVERT: A 247 ARG cc_start: 0.7949 (mtt180) cc_final: 0.7689 (mtt180) REVERT: B 39 LYS cc_start: 0.7464 (ttmt) cc_final: 0.6742 (ttpt) REVERT: B 168 GLN cc_start: 0.7354 (mm110) cc_final: 0.6890 (pp30) REVERT: D 115 MET cc_start: 0.8703 (tpt) cc_final: 0.7756 (tpt) outliers start: 26 outliers final: 15 residues processed: 195 average time/residue: 0.2657 time to fit residues: 72.9454 Evaluate side-chains 185 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 169 time to evaluate : 1.241 ------------------------------------------------------------------------------- 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 238 PHE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain C residue 36 THR 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 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 272 CYS Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 110 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 10 optimal weight: 0.9990 chunk 132 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 chunk 145 optimal weight: 9.9990 chunk 140 optimal weight: 0.3980 chunk 119 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 chunk 154 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 229 ASN ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 GLN F 106 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.177143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.156360 restraints weight = 16464.344| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 2.35 r_work: 0.3708 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3570 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12939 Z= 0.159 Angle : 0.574 9.629 17555 Z= 0.300 Chirality : 0.042 0.291 1985 Planarity : 0.003 0.053 2315 Dihedral : 4.944 39.051 2117 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.52 % Allowed : 13.19 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.21), residues: 1438 helix: 1.56 (0.27), residues: 333 sheet: 0.33 (0.30), residues: 272 loop : -0.81 (0.19), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 142 HIS 0.004 0.001 HIS F 159 PHE 0.013 0.002 PHE C 136 TYR 0.014 0.001 TYR F 119 ARG 0.005 0.000 ARG F 25 Details of bonding type rmsd link_NAG-ASN : bond 0.00332 ( 12) link_NAG-ASN : angle 2.34344 ( 36) link_BETA1-4 : bond 0.00275 ( 2) link_BETA1-4 : angle 1.55272 ( 6) hydrogen bonds : bond 0.04228 ( 520) hydrogen bonds : angle 5.31526 ( 1455) SS BOND : bond 0.00434 ( 15) SS BOND : angle 1.81008 ( 30) link_BETA1-3 : bond 0.00325 ( 1) link_BETA1-3 : angle 6.17840 ( 3) covalent geometry : bond 0.00360 (12909) covalent geometry : angle 0.55413 (17480) *********************** 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 208 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 177 time to evaluate : 1.373 Fit side-chains revert: symmetry clash REVERT: A 121 ARG cc_start: 0.7768 (ptt180) cc_final: 0.7565 (ptt90) REVERT: A 238 PHE cc_start: 0.7855 (OUTLIER) cc_final: 0.7464 (m-10) REVERT: A 247 ARG cc_start: 0.8227 (mtt180) cc_final: 0.7921 (mtt180) REVERT: B 25 ARG cc_start: 0.8147 (ttm170) cc_final: 0.7890 (tpp80) REVERT: B 39 LYS cc_start: 0.7587 (ttmt) cc_final: 0.6847 (ttpt) REVERT: C 256 MET cc_start: 0.7460 (ttp) cc_final: 0.7023 (tmm) REVERT: D 115 MET cc_start: 0.8697 (tpt) cc_final: 0.8362 (mmm) REVERT: E 217 GLN cc_start: 0.7164 (tp40) cc_final: 0.6809 (mt0) outliers start: 31 outliers final: 21 residues processed: 198 average time/residue: 0.2878 time to fit residues: 80.3045 Evaluate side-chains 187 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 1.332 ------------------------------------------------------------------------------- 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 38 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain B residue 56 ILE 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 262 VAL 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 75 LYS Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 128 SER 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 17 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 124 optimal weight: 0.0980 chunk 136 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 GLN E 53 GLN F 106 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.171004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.150056 restraints weight = 16682.176| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.36 r_work: 0.3638 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3499 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12939 Z= 0.222 Angle : 0.642 9.737 17555 Z= 0.331 Chirality : 0.045 0.321 1985 Planarity : 0.004 0.052 2315 Dihedral : 5.124 37.531 2117 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.18 % Allowed : 14.41 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.21), residues: 1438 helix: 1.32 (0.27), residues: 333 sheet: 0.01 (0.31), residues: 270 loop : -1.01 (0.19), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 142 HIS 0.006 0.002 HIS A 7 PHE 0.022 0.002 PHE C 238 TYR 0.016 0.002 TYR F 119 ARG 0.009 0.001 ARG C 291 Details of bonding type rmsd link_NAG-ASN : bond 0.00325 ( 12) link_NAG-ASN : angle 2.53382 ( 36) link_BETA1-4 : bond 0.00010 ( 2) link_BETA1-4 : angle 1.67876 ( 6) hydrogen bonds : bond 0.04359 ( 520) hydrogen bonds : angle 5.49468 ( 1455) SS BOND : bond 0.00773 ( 15) SS BOND : angle 1.97254 ( 30) link_BETA1-3 : bond 0.00407 ( 1) link_BETA1-3 : angle 6.33008 ( 3) covalent geometry : bond 0.00515 (12909) covalent geometry : angle 0.62111 (17480) *********************** 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 224 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 185 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8100 (ptt180) cc_final: 0.7853 (ptt90) REVERT: A 139 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7811 (mm-30) REVERT: A 222 ASP cc_start: 0.8386 (m-30) cc_final: 0.8158 (m-30) REVERT: A 238 PHE cc_start: 0.8111 (OUTLIER) cc_final: 0.7711 (m-80) REVERT: A 247 ARG cc_start: 0.8417 (mtt180) cc_final: 0.8024 (mtt180) REVERT: B 25 ARG cc_start: 0.8189 (ttm170) cc_final: 0.7940 (tpp80) REVERT: B 39 LYS cc_start: 0.7695 (ttmt) cc_final: 0.6992 (ttpt) REVERT: C 37 ASN cc_start: 0.8518 (OUTLIER) cc_final: 0.8169 (p0) REVERT: D 120 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7751 (mp0) REVERT: D 163 ARG cc_start: 0.6365 (mmt90) cc_final: 0.6080 (mtm180) REVERT: E 217 GLN cc_start: 0.7393 (tp40) cc_final: 0.6964 (mt0) REVERT: E 271 ASP cc_start: 0.8088 (p0) cc_final: 0.7302 (t0) outliers start: 39 outliers final: 25 residues processed: 215 average time/residue: 0.2884 time to fit residues: 87.4098 Evaluate side-chains 192 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 164 time to evaluate : 1.295 ------------------------------------------------------------------------------- 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 185 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain B residue 56 ILE 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 160 LYS 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 311 MET Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 71 THR 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 14 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 128 SER 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 115 optimal weight: 0.0980 chunk 86 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 157 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 142 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 135 optimal weight: 0.6980 chunk 125 optimal weight: 0.3980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 ASN E 201 GLN ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.174891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.155617 restraints weight = 16484.410| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 2.15 r_work: 0.3699 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3568 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12939 Z= 0.130 Angle : 0.557 9.292 17555 Z= 0.289 Chirality : 0.042 0.299 1985 Planarity : 0.003 0.049 2315 Dihedral : 4.857 33.489 2117 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.44 % Allowed : 15.80 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.21), residues: 1438 helix: 1.56 (0.27), residues: 333 sheet: 0.04 (0.32), residues: 256 loop : -1.01 (0.19), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 142 HIS 0.003 0.001 HIS D 142 PHE 0.019 0.001 PHE C 238 TYR 0.013 0.001 TYR C 274 ARG 0.003 0.000 ARG E 22 Details of bonding type rmsd link_NAG-ASN : bond 0.00261 ( 12) link_NAG-ASN : angle 2.59996 ( 36) link_BETA1-4 : bond 0.00090 ( 2) link_BETA1-4 : angle 1.45804 ( 6) hydrogen bonds : bond 0.04059 ( 520) hydrogen bonds : angle 5.24834 ( 1455) SS BOND : bond 0.00390 ( 15) SS BOND : angle 1.49205 ( 30) link_BETA1-3 : bond 0.00643 ( 1) link_BETA1-3 : angle 5.91123 ( 3) covalent geometry : bond 0.00289 (12909) covalent geometry : angle 0.53588 (17480) *********************** 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 211 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 181 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.8057 (OUTLIER) cc_final: 0.7702 (m-80) REVERT: A 247 ARG cc_start: 0.8258 (mtt180) cc_final: 0.7941 (mtt180) REVERT: B 25 ARG cc_start: 0.8078 (ttm170) cc_final: 0.7822 (tpp80) REVERT: B 39 LYS cc_start: 0.7588 (ttmt) cc_final: 0.6867 (ttpt) REVERT: C 256 MET cc_start: 0.7504 (ttp) cc_final: 0.7179 (tmm) REVERT: D 61 GLN cc_start: 0.8393 (tp40) cc_final: 0.8166 (tp40) REVERT: D 115 MET cc_start: 0.8626 (tpt) cc_final: 0.8394 (mmm) REVERT: D 163 ARG cc_start: 0.6237 (mmt90) cc_final: 0.6015 (mtm180) REVERT: E 217 GLN cc_start: 0.7160 (tp40) cc_final: 0.6725 (mt0) outliers start: 30 outliers final: 24 residues processed: 202 average time/residue: 0.2722 time to fit residues: 76.7334 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 : 1.214 ------------------------------------------------------------------------------- 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 36 THR Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 160 LYS 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 E residue 3 ILE Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 66 CYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 27 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 148 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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** B 26 HIS C 37 ASN ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 ASN ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.169753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.150047 restraints weight = 16506.860| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.17 r_work: 0.3632 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3205 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= 0.233 Angle : 0.653 9.486 17555 Z= 0.338 Chirality : 0.045 0.333 1985 Planarity : 0.004 0.051 2315 Dihedral : 5.168 42.457 2117 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.93 % Allowed : 16.53 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.21), residues: 1438 helix: 1.31 (0.27), residues: 333 sheet: -0.28 (0.32), residues: 264 loop : -1.20 (0.19), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 142 HIS 0.004 0.001 HIS A 175 PHE 0.028 0.002 PHE C 238 TYR 0.012 0.002 TYR C 200 ARG 0.008 0.001 ARG A 121 Details of bonding type rmsd link_NAG-ASN : bond 0.00259 ( 12) link_NAG-ASN : angle 2.56922 ( 36) link_BETA1-4 : bond 0.00132 ( 2) link_BETA1-4 : angle 1.70698 ( 6) hydrogen bonds : bond 0.04383 ( 520) hydrogen bonds : angle 5.49996 ( 1455) SS BOND : bond 0.00583 ( 15) SS BOND : angle 1.67779 ( 30) link_BETA1-3 : bond 0.00519 ( 1) link_BETA1-3 : angle 6.11995 ( 3) covalent geometry : bond 0.00537 (12909) covalent geometry : angle 0.63434 (17480) *********************** 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 206 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 170 time to evaluate : 1.378 Fit side-chains revert: symmetry clash REVERT: A 238 PHE cc_start: 0.8210 (OUTLIER) cc_final: 0.7692 (m-80) REVERT: A 247 ARG cc_start: 0.8494 (mtt180) cc_final: 0.8125 (mtt180) REVERT: B 25 ARG cc_start: 0.8120 (ttm170) cc_final: 0.7863 (tpp80) REVERT: B 39 LYS cc_start: 0.7733 (ttmt) cc_final: 0.7029 (ttpt) REVERT: C 256 MET cc_start: 0.7588 (ttp) cc_final: 0.7169 (tmm) REVERT: D 19 ASP cc_start: 0.8008 (p0) cc_final: 0.7689 (p0) REVERT: D 61 GLN cc_start: 0.8465 (tp40) cc_final: 0.8231 (tp40) REVERT: D 120 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7673 (mp0) REVERT: D 149 MET cc_start: 0.5949 (OUTLIER) cc_final: 0.5345 (ttm) REVERT: E 217 GLN cc_start: 0.7342 (tp40) cc_final: 0.6938 (mt0) REVERT: E 271 ASP cc_start: 0.8017 (p0) cc_final: 0.7375 (t0) outliers start: 36 outliers final: 26 residues processed: 197 average time/residue: 0.2935 time to fit residues: 81.4946 Evaluate side-chains 198 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 169 time to evaluate : 1.356 ------------------------------------------------------------------------------- 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 238 PHE Chi-restraints excluded: chain A residue 260 SER 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 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 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 61 THR Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 128 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 84 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 109 optimal weight: 0.4980 chunk 129 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 131 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 ASN ** 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 = 0.3990 r_free = 0.3990 target = 0.171893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.151119 restraints weight = 16589.047| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.37 r_work: 0.3655 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3517 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12939 Z= 0.147 Angle : 0.578 13.864 17555 Z= 0.299 Chirality : 0.042 0.309 1985 Planarity : 0.003 0.050 2315 Dihedral : 4.962 42.439 2117 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.69 % Allowed : 17.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.21), residues: 1438 helix: 1.48 (0.27), residues: 333 sheet: -0.13 (0.32), residues: 252 loop : -1.17 (0.19), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 142 HIS 0.003 0.001 HIS D 142 PHE 0.024 0.002 PHE C 238 TYR 0.026 0.001 TYR A 186 ARG 0.006 0.000 ARG E 47 Details of bonding type rmsd link_NAG-ASN : bond 0.00241 ( 12) link_NAG-ASN : angle 2.34128 ( 36) link_BETA1-4 : bond 0.00127 ( 2) link_BETA1-4 : angle 1.44817 ( 6) hydrogen bonds : bond 0.04066 ( 520) hydrogen bonds : angle 5.28490 ( 1455) SS BOND : bond 0.00401 ( 15) SS BOND : angle 1.41430 ( 30) link_BETA1-3 : bond 0.00612 ( 1) link_BETA1-3 : angle 5.82478 ( 3) covalent geometry : bond 0.00334 (12909) covalent geometry : angle 0.56106 (17480) *********************** 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 208 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 175 time to evaluate : 1.273 Fit side-chains revert: symmetry clash REVERT: A 238 PHE cc_start: 0.8083 (OUTLIER) cc_final: 0.7720 (m-80) REVERT: A 247 ARG cc_start: 0.8441 (mtt180) cc_final: 0.8130 (mtt180) REVERT: B 25 ARG cc_start: 0.8123 (ttm170) cc_final: 0.7906 (tpp80) REVERT: B 39 LYS cc_start: 0.7698 (ttmt) cc_final: 0.6992 (ttpt) REVERT: B 168 GLN cc_start: 0.7518 (mm-40) cc_final: 0.6895 (pp30) REVERT: C 256 MET cc_start: 0.7509 (ttp) cc_final: 0.7164 (tmm) REVERT: D 61 GLN cc_start: 0.8456 (tp40) cc_final: 0.8212 (tp40) REVERT: D 120 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7658 (mp0) REVERT: D 149 MET cc_start: 0.5939 (OUTLIER) cc_final: 0.5361 (ttm) REVERT: D 163 ARG cc_start: 0.6482 (mmt90) cc_final: 0.6255 (mtm180) REVERT: E 217 GLN cc_start: 0.7297 (tp40) cc_final: 0.6890 (mt0) REVERT: F 157 TYR cc_start: 0.6630 (t80) cc_final: 0.6163 (t80) outliers start: 33 outliers final: 21 residues processed: 198 average time/residue: 0.2668 time to fit residues: 74.4954 Evaluate side-chains 197 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 1.281 ------------------------------------------------------------------------------- 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 79 GLU 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 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 61 THR Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 128 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 78 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 159 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 68 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 313 ASN ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 ASN ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.167477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.146246 restraints weight = 16661.994| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.38 r_work: 0.3588 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3451 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12939 Z= 0.237 Angle : 0.674 13.932 17555 Z= 0.343 Chirality : 0.046 0.339 1985 Planarity : 0.004 0.051 2315 Dihedral : 5.186 34.509 2117 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.52 % Allowed : 17.02 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.21), residues: 1438 helix: 1.24 (0.27), residues: 333 sheet: -0.72 (0.31), residues: 276 loop : -1.32 (0.19), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 142 HIS 0.004 0.001 HIS C 7 PHE 0.030 0.002 PHE C 238 TYR 0.019 0.002 TYR A 186 ARG 0.006 0.001 ARG F 25 Details of bonding type rmsd link_NAG-ASN : bond 0.00529 ( 12) link_NAG-ASN : angle 3.24657 ( 36) link_BETA1-4 : bond 0.00101 ( 2) link_BETA1-4 : angle 1.67990 ( 6) hydrogen bonds : bond 0.04357 ( 520) hydrogen bonds : angle 5.52238 ( 1455) SS BOND : bond 0.00577 ( 15) SS BOND : angle 1.59489 ( 30) link_BETA1-3 : bond 0.00133 ( 1) link_BETA1-3 : angle 6.07712 ( 3) covalent geometry : bond 0.00550 (12909) covalent geometry : angle 0.65059 (17480) *********************** 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 210 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 179 time to evaluate : 1.264 Fit side-chains revert: symmetry clash REVERT: A 222 ASP cc_start: 0.8488 (m-30) cc_final: 0.8220 (m-30) REVERT: A 238 PHE cc_start: 0.8217 (OUTLIER) cc_final: 0.7699 (m-80) REVERT: A 247 ARG cc_start: 0.8540 (mtt180) cc_final: 0.8338 (mtt180) REVERT: B 25 ARG cc_start: 0.8128 (ttm170) cc_final: 0.7858 (tpp80) REVERT: B 39 LYS cc_start: 0.7685 (ttmt) cc_final: 0.7161 (mtpt) REVERT: C 256 MET cc_start: 0.7647 (ttp) cc_final: 0.7166 (tmm) REVERT: D 61 GLN cc_start: 0.8442 (tp40) cc_final: 0.8175 (tp40) REVERT: D 120 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7636 (mp0) REVERT: D 149 MET cc_start: 0.5903 (OUTLIER) cc_final: 0.5345 (ttm) REVERT: E 217 GLN cc_start: 0.7400 (tp40) cc_final: 0.6939 (mt0) REVERT: F 157 TYR cc_start: 0.6684 (t80) cc_final: 0.6210 (t80) outliers start: 31 outliers final: 25 residues processed: 203 average time/residue: 0.2523 time to fit residues: 73.3553 Evaluate side-chains 199 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 1.251 ------------------------------------------------------------------------------- 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 79 GLU 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 162 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 14 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 128 SER 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 133 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 79 optimal weight: 0.0270 chunk 41 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 159 optimal weight: 9.9990 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 ASN ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 47 GLN ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.171876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.151018 restraints weight = 16577.144| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.37 r_work: 0.3642 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3504 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12939 Z= 0.138 Angle : 0.583 13.318 17555 Z= 0.301 Chirality : 0.042 0.310 1985 Planarity : 0.003 0.049 2315 Dihedral : 4.911 33.351 2117 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.52 % Allowed : 18.00 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.21), residues: 1438 helix: 1.55 (0.27), residues: 329 sheet: -0.56 (0.31), residues: 266 loop : -1.25 (0.19), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 142 HIS 0.004 0.001 HIS D 142 PHE 0.022 0.002 PHE C 238 TYR 0.021 0.001 TYR A 186 ARG 0.006 0.000 ARG E 47 Details of bonding type rmsd link_NAG-ASN : bond 0.00309 ( 12) link_NAG-ASN : angle 2.82150 ( 36) link_BETA1-4 : bond 0.00250 ( 2) link_BETA1-4 : angle 1.42023 ( 6) hydrogen bonds : bond 0.04072 ( 520) hydrogen bonds : angle 5.26317 ( 1455) SS BOND : bond 0.00417 ( 15) SS BOND : angle 1.35851 ( 30) link_BETA1-3 : bond 0.00588 ( 1) link_BETA1-3 : angle 5.65428 ( 3) covalent geometry : bond 0.00312 (12909) covalent geometry : angle 0.56180 (17480) ********************** 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 205 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 174 time to evaluate : 2.343 Fit side-chains revert: symmetry clash REVERT: A 238 PHE cc_start: 0.8014 (OUTLIER) cc_final: 0.7638 (m-80) REVERT: A 247 ARG cc_start: 0.8452 (mtt180) cc_final: 0.8128 (mtt180) REVERT: B 39 LYS cc_start: 0.7673 (ttmt) cc_final: 0.6965 (ttpt) REVERT: C 256 MET cc_start: 0.7538 (ttp) cc_final: 0.7161 (tmm) REVERT: D 61 GLN cc_start: 0.8467 (tp40) cc_final: 0.8209 (tp40) REVERT: D 120 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7628 (mp0) REVERT: D 149 MET cc_start: 0.5979 (OUTLIER) cc_final: 0.5438 (ttm) REVERT: E 217 GLN cc_start: 0.7336 (tp40) cc_final: 0.6871 (mt0) REVERT: F 157 TYR cc_start: 0.6646 (t80) cc_final: 0.6192 (t80) outliers start: 31 outliers final: 25 residues processed: 199 average time/residue: 0.3345 time to fit residues: 94.2553 Evaluate side-chains 195 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 167 time to evaluate : 1.273 ------------------------------------------------------------------------------- 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 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 162 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 14 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 128 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 143 optimal weight: 7.9990 chunk 67 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 159 optimal weight: 9.9990 chunk 103 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 130 optimal weight: 0.0870 chunk 151 optimal weight: 4.9990 chunk 84 optimal weight: 0.0050 overall best weight: 0.5376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN A 174 HIS ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 ASN ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.173928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.153178 restraints weight = 16515.026| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.37 r_work: 0.3665 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3528 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.3458 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= 0.124 Angle : 0.554 12.525 17555 Z= 0.287 Chirality : 0.042 0.306 1985 Planarity : 0.003 0.049 2315 Dihedral : 4.686 30.829 2117 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.28 % Allowed : 18.40 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.21), residues: 1438 helix: 1.79 (0.27), residues: 329 sheet: -0.32 (0.32), residues: 254 loop : -1.24 (0.19), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 171 HIS 0.003 0.001 HIS D 142 PHE 0.015 0.001 PHE C 242 TYR 0.021 0.001 TYR A 186 ARG 0.006 0.000 ARG E 47 Details of bonding type rmsd link_NAG-ASN : bond 0.00232 ( 12) link_NAG-ASN : angle 2.54145 ( 36) link_BETA1-4 : bond 0.00175 ( 2) link_BETA1-4 : angle 1.38820 ( 6) hydrogen bonds : bond 0.03928 ( 520) hydrogen bonds : angle 5.13192 ( 1455) SS BOND : bond 0.00343 ( 15) SS BOND : angle 1.30568 ( 30) link_BETA1-3 : bond 0.00521 ( 1) link_BETA1-3 : angle 5.40928 ( 3) covalent geometry : bond 0.00278 (12909) covalent geometry : angle 0.53480 (17480) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6118.40 seconds wall clock time: 109 minutes 7.57 seconds (6547.57 seconds total)