Starting phenix.real_space_refine on Thu May 15 04:21:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ut9_42534/05_2025/8ut9_42534.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ut9_42534/05_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_42534/05_2025/8ut9_42534.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ut9_42534/05_2025/8ut9_42534.map" model { file = "/net/cci-nas-00/data/ceres_data/8ut9_42534/05_2025/8ut9_42534.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ut9_42534/05_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-5687/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: 8.36, per 1000 atoms: 0.66 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: 2.79 Conformation dependent library (CDL) restraints added in 1.4 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: 1.68 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: 3.74 Time building geometry restraints manager: 3.30 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: 6.920 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: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 29.550 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.380 ------------------------------------------------------------------------------- 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 : 1.273 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: 0.2751 time to fit residues: 62.3165 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 : 1.220 ------------------------------------------------------------------------------- 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: 0.3736 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.3736 ------------------------------------------------------------------------------- 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 : 1.261 Fit side-chains revert: symmetry clash REVERT: A 232 ASP cc_start: 0.7549 (t0) cc_final: 0.7132 (t0) REVERT: A 247 ARG cc_start: 0.7769 (mtt180) cc_final: 0.7509 (mtt180) REVERT: B 25 ARG cc_start: 0.7891 (ttm170) cc_final: 0.7400 (tpp80) REVERT: B 39 LYS cc_start: 0.7355 (ttmt) cc_final: 0.6635 (ttpt) REVERT: E 232 ASP cc_start: 0.7003 (m-30) cc_final: 0.6769 (m-30) outliers start: 15 outliers final: 11 residues processed: 202 average time/residue: 0.2611 time to fit residues: 74.9602 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 : 1.360 ------------------------------------------------------------------------------- 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: 0.9990 chunk 113 optimal weight: 0.1980 chunk 108 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 124 optimal weight: 0.0770 overall best weight: 0.7942 ------------------------------------------------------------------------------- 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 F 106 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.180469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.159900 restraints weight = 16385.954| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 2.33 r_work: 0.3735 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12939 Z= 0.147 Angle : 0.589 9.427 17555 Z= 0.308 Chirality : 0.043 0.282 1985 Planarity : 0.003 0.060 2315 Dihedral : 5.087 40.028 2117 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.20 % Allowed : 13.52 % 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: 0.10 (0.21), residues: 1438 helix: 1.44 (0.26), residues: 339 sheet: 0.46 (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 B 14 HIS 0.005 0.001 HIS D 159 PHE 0.016 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 0.00364 ( 12) link_NAG-ASN : angle 2.39468 ( 36) link_BETA1-4 : bond 0.00285 ( 2) link_BETA1-4 : angle 1.61643 ( 6) hydrogen bonds : bond 0.04406 ( 520) hydrogen bonds : angle 5.42979 ( 1455) SS BOND : bond 0.00388 ( 15) SS BOND : angle 1.57636 ( 30) link_BETA1-3 : bond 0.00779 ( 1) link_BETA1-3 : angle 6.15156 ( 3) covalent geometry : bond 0.00329 (12909) covalent geometry : angle 0.56963 (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 205 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 178 time to evaluate : 1.236 Fit side-chains revert: symmetry clash REVERT: A 121 ARG cc_start: 0.7721 (ptt180) cc_final: 0.7489 (ptt90) REVERT: A 232 ASP cc_start: 0.7604 (t0) cc_final: 0.7255 (t0) REVERT: A 238 PHE cc_start: 0.7530 (OUTLIER) cc_final: 0.7128 (m-10) REVERT: A 247 ARG cc_start: 0.7953 (mtt180) cc_final: 0.7700 (mtt180) REVERT: B 25 ARG cc_start: 0.7905 (ttm170) cc_final: 0.7485 (tpp80) REVERT: B 39 LYS cc_start: 0.7463 (ttmt) cc_final: 0.6737 (ttpt) REVERT: B 168 GLN cc_start: 0.7335 (mm110) cc_final: 0.6874 (pp30) REVERT: D 115 MET cc_start: 0.8705 (tpt) cc_final: 0.7745 (tpt) REVERT: E 217 GLN cc_start: 0.6891 (tp40) cc_final: 0.6635 (mt0) outliers start: 27 outliers final: 15 residues processed: 196 average time/residue: 0.2672 time to fit residues: 73.0167 Evaluate side-chains 184 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 168 time to evaluate : 1.274 ------------------------------------------------------------------------------- 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: 1.9990 chunk 132 optimal weight: 0.5980 chunk 123 optimal weight: 0.0970 chunk 145 optimal weight: 9.9990 chunk 140 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 96 optimal weight: 0.4980 chunk 154 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN B 159 HIS ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 GLN E 263 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 = 0.4073 r_free = 0.4073 target = 0.179772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.159147 restraints weight = 16370.704| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 2.35 r_work: 0.3741 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3603 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12939 Z= 0.128 Angle : 0.546 9.101 17555 Z= 0.286 Chirality : 0.041 0.283 1985 Planarity : 0.003 0.051 2315 Dihedral : 4.863 39.469 2117 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.12 % Allowed : 13.44 % Favored : 84.45 % 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: 0.09 (0.21), residues: 1438 helix: 1.61 (0.26), residues: 339 sheet: 0.38 (0.30), residues: 277 loop : -0.73 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 142 HIS 0.003 0.001 HIS D 142 PHE 0.013 0.002 PHE C 136 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 0.00360 ( 12) link_NAG-ASN : angle 2.28927 ( 36) link_BETA1-4 : bond 0.00167 ( 2) link_BETA1-4 : angle 1.47876 ( 6) hydrogen bonds : bond 0.04116 ( 520) hydrogen bonds : angle 5.22350 ( 1455) SS BOND : bond 0.00432 ( 15) SS BOND : angle 1.65789 ( 30) link_BETA1-3 : bond 0.00870 ( 1) link_BETA1-3 : angle 5.88099 ( 3) covalent geometry : bond 0.00284 (12909) covalent geometry : angle 0.52678 (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 202 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 176 time to evaluate : 1.415 Fit side-chains revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7723 (OUTLIER) cc_final: 0.6993 (m-80) REVERT: A 247 ARG cc_start: 0.8144 (mtt180) cc_final: 0.7842 (mtt180) REVERT: B 25 ARG cc_start: 0.8118 (ttm170) cc_final: 0.7856 (tpp80) REVERT: B 39 LYS cc_start: 0.7559 (ttmt) cc_final: 0.6811 (ttpt) REVERT: B 168 GLN cc_start: 0.7389 (mm110) cc_final: 0.6809 (pp30) REVERT: C 256 MET cc_start: 0.7407 (ttp) cc_final: 0.6984 (tmm) REVERT: E 217 GLN cc_start: 0.7080 (tp40) cc_final: 0.6672 (mt0) outliers start: 26 outliers final: 17 residues processed: 195 average time/residue: 0.2648 time to fit residues: 72.8110 Evaluate side-chains 179 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 1.245 ------------------------------------------------------------------------------- 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 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 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: 4.9990 chunk 116 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 124 optimal weight: 0.6980 chunk 136 optimal weight: 0.8980 chunk 84 optimal weight: 0.0050 chunk 137 optimal weight: 0.0000 chunk 100 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN C 37 ASN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.180113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.159433 restraints weight = 16371.217| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 2.35 r_work: 0.3755 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3619 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12939 Z= 0.109 Angle : 0.519 8.965 17555 Z= 0.270 Chirality : 0.041 0.275 1985 Planarity : 0.003 0.048 2315 Dihedral : 4.619 37.820 2117 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.52 % Allowed : 14.25 % Favored : 83.22 % 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: 0.15 (0.21), residues: 1438 helix: 1.82 (0.27), residues: 333 sheet: 0.54 (0.31), residues: 270 loop : -0.79 (0.20), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 142 HIS 0.004 0.001 HIS A 7 PHE 0.011 0.001 PHE C 136 TYR 0.010 0.001 TYR D 119 ARG 0.010 0.000 ARG C 291 Details of bonding type rmsd link_NAG-ASN : bond 0.00325 ( 12) link_NAG-ASN : angle 2.14041 ( 36) link_BETA1-4 : bond 0.00198 ( 2) link_BETA1-4 : angle 1.36768 ( 6) hydrogen bonds : bond 0.03892 ( 520) hydrogen bonds : angle 5.06191 ( 1455) SS BOND : bond 0.00307 ( 15) SS BOND : angle 1.54805 ( 30) link_BETA1-3 : bond 0.00726 ( 1) link_BETA1-3 : angle 5.74033 ( 3) covalent geometry : bond 0.00238 (12909) covalent geometry : angle 0.50046 (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 209 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 178 time to evaluate : 1.308 Fit side-chains revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7692 (OUTLIER) cc_final: 0.6962 (m-80) REVERT: A 247 ARG cc_start: 0.8151 (mtt180) cc_final: 0.7857 (mtt180) REVERT: B 25 ARG cc_start: 0.8060 (ttm170) cc_final: 0.7831 (tpp80) REVERT: B 39 LYS cc_start: 0.7619 (ttmt) cc_final: 0.6888 (ttpt) REVERT: B 69 GLU cc_start: 0.7635 (tt0) cc_final: 0.7353 (tp30) REVERT: B 168 GLN cc_start: 0.7270 (mm110) cc_final: 0.6697 (pp30) REVERT: C 37 ASN cc_start: 0.8353 (OUTLIER) cc_final: 0.8043 (p0) REVERT: C 201 GLN cc_start: 0.7220 (tt0) cc_final: 0.6981 (tt0) REVERT: D 115 MET cc_start: 0.8700 (tpt) cc_final: 0.8408 (mmm) REVERT: E 217 GLN cc_start: 0.7101 (tp40) cc_final: 0.6738 (mt0) REVERT: E 232 ASP cc_start: 0.7311 (m-30) cc_final: 0.7049 (m-30) REVERT: F 102 MET cc_start: 0.8155 (ptp) cc_final: 0.7953 (ptm) outliers start: 31 outliers final: 22 residues processed: 199 average time/residue: 0.2556 time to fit residues: 72.6624 Evaluate side-chains 190 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 1.336 ------------------------------------------------------------------------------- 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 36 THR Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 225 TRP Chi-restraints excluded: chain C residue 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 E residue 14 THR Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 110 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 115 optimal weight: 0.3980 chunk 86 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 157 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 142 optimal weight: 9.9990 chunk 83 optimal weight: 0.3980 chunk 135 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN C 239 ASN ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 47 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.179530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.158737 restraints weight = 16549.719| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 2.39 r_work: 0.3735 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3599 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2484 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= 0.126 Angle : 0.523 9.068 17555 Z= 0.274 Chirality : 0.041 0.280 1985 Planarity : 0.003 0.046 2315 Dihedral : 4.564 37.445 2117 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.61 % Allowed : 14.74 % Favored : 82.65 % 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: 0.11 (0.21), residues: 1438 helix: 1.78 (0.27), residues: 339 sheet: 0.52 (0.31), residues: 267 loop : -0.83 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 142 HIS 0.003 0.001 HIS D 159 PHE 0.012 0.001 PHE C 238 TYR 0.011 0.001 TYR D 119 ARG 0.005 0.000 ARG E 47 Details of bonding type rmsd link_NAG-ASN : bond 0.00308 ( 12) link_NAG-ASN : angle 2.12393 ( 36) link_BETA1-4 : bond 0.00185 ( 2) link_BETA1-4 : angle 1.38252 ( 6) hydrogen bonds : bond 0.03878 ( 520) hydrogen bonds : angle 5.06550 ( 1455) SS BOND : bond 0.00325 ( 15) SS BOND : angle 1.36402 ( 30) link_BETA1-3 : bond 0.00593 ( 1) link_BETA1-3 : angle 5.79718 ( 3) covalent geometry : bond 0.00281 (12909) covalent geometry : angle 0.50572 (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 201 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 169 time to evaluate : 1.312 Fit side-chains revert: symmetry clash REVERT: A 123 ASN cc_start: 0.8273 (OUTLIER) cc_final: 0.8069 (t0) REVERT: A 139 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7637 (mm-30) REVERT: A 238 PHE cc_start: 0.7750 (OUTLIER) cc_final: 0.7044 (m-80) REVERT: A 247 ARG cc_start: 0.8192 (mtt180) cc_final: 0.7951 (mtt180) REVERT: B 25 ARG cc_start: 0.8087 (ttm170) cc_final: 0.7861 (tpp80) REVERT: B 39 LYS cc_start: 0.7659 (ttmt) cc_final: 0.6907 (ttpt) REVERT: B 69 GLU cc_start: 0.7680 (tt0) cc_final: 0.7373 (tp30) REVERT: C 34 GLU cc_start: 0.7938 (tp30) cc_final: 0.7503 (tp30) REVERT: C 185 LEU cc_start: 0.7288 (OUTLIER) cc_final: 0.7044 (mp) REVERT: C 256 MET cc_start: 0.7430 (ttp) cc_final: 0.7082 (tmm) REVERT: D 115 MET cc_start: 0.8675 (tpt) cc_final: 0.8374 (mmm) REVERT: E 217 GLN cc_start: 0.7142 (tp40) cc_final: 0.6749 (mt0) REVERT: E 232 ASP cc_start: 0.7365 (m-30) cc_final: 0.7092 (m-30) REVERT: F 115 MET cc_start: 0.7641 (tpt) cc_final: 0.7326 (tpt) REVERT: F 157 TYR cc_start: 0.6218 (t80) cc_final: 0.5780 (t80) outliers start: 32 outliers final: 22 residues processed: 189 average time/residue: 0.2589 time to fit residues: 69.3106 Evaluate side-chains 188 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 163 time to evaluate : 1.177 ------------------------------------------------------------------------------- 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 123 ASN 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 C residue 130 ARG Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 225 TRP Chi-restraints excluded: chain C residue 239 ASN 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 102 MET Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 113 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 27 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 26 optimal weight: 0.4980 chunk 148 optimal weight: 6.9990 chunk 89 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 126 optimal weight: 0.0970 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN A 217 GLN C 239 ASN ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 GLN E 201 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.176064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.155204 restraints weight = 16451.219| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 2.37 r_work: 0.3697 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3559 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12939 Z= 0.165 Angle : 0.558 9.222 17555 Z= 0.290 Chirality : 0.042 0.294 1985 Planarity : 0.003 0.046 2315 Dihedral : 4.618 34.123 2117 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.69 % Allowed : 15.31 % Favored : 82.00 % 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: -0.04 (0.21), residues: 1438 helix: 1.74 (0.27), residues: 339 sheet: 0.36 (0.31), residues: 269 loop : -0.95 (0.19), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 142 HIS 0.003 0.001 HIS F 159 PHE 0.012 0.002 PHE C 92 TYR 0.012 0.001 TYR D 119 ARG 0.005 0.000 ARG F 25 Details of bonding type rmsd link_NAG-ASN : bond 0.00250 ( 12) link_NAG-ASN : angle 2.42741 ( 36) link_BETA1-4 : bond 0.00119 ( 2) link_BETA1-4 : angle 1.46997 ( 6) hydrogen bonds : bond 0.03986 ( 520) hydrogen bonds : angle 5.11716 ( 1455) SS BOND : bond 0.00413 ( 15) SS BOND : angle 1.41665 ( 30) link_BETA1-3 : bond 0.00549 ( 1) link_BETA1-3 : angle 5.91589 ( 3) covalent geometry : bond 0.00376 (12909) covalent geometry : angle 0.53870 (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 213 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 180 time to evaluate : 1.320 Fit side-chains revert: symmetry clash REVERT: A 139 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7719 (mm-30) REVERT: A 238 PHE cc_start: 0.7947 (OUTLIER) cc_final: 0.7264 (m-80) REVERT: A 247 ARG cc_start: 0.8288 (mtt180) cc_final: 0.8010 (mtt180) REVERT: A 256 MET cc_start: 0.8033 (ptm) cc_final: 0.7685 (ttp) REVERT: B 25 ARG cc_start: 0.8119 (ttm170) cc_final: 0.7870 (tpp80) REVERT: B 39 LYS cc_start: 0.7676 (ttmt) cc_final: 0.6961 (ttpt) REVERT: B 168 GLN cc_start: 0.7426 (mm110) cc_final: 0.6832 (pp30) REVERT: C 190 ASN cc_start: 0.7318 (t0) cc_final: 0.7071 (t0) REVERT: C 256 MET cc_start: 0.7476 (ttp) cc_final: 0.7065 (tmm) REVERT: D 61 GLN cc_start: 0.8422 (tp40) cc_final: 0.8176 (tp40) REVERT: D 115 MET cc_start: 0.8689 (tpt) cc_final: 0.8411 (mmm) REVERT: D 120 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7715 (mp0) REVERT: D 149 MET cc_start: 0.5956 (OUTLIER) cc_final: 0.5201 (ttm) REVERT: E 217 GLN cc_start: 0.7244 (tp40) cc_final: 0.6850 (mt0) REVERT: E 232 ASP cc_start: 0.7464 (m-30) cc_final: 0.7222 (m-30) REVERT: F 115 MET cc_start: 0.7651 (tpt) cc_final: 0.7333 (tpt) REVERT: F 157 TYR cc_start: 0.6404 (t80) cc_final: 0.5937 (t80) outliers start: 33 outliers final: 22 residues processed: 202 average time/residue: 0.2547 time to fit residues: 73.4953 Evaluate side-chains 195 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 170 time to evaluate : 1.219 ------------------------------------------------------------------------------- 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 217 GLN 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 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 120 GLU Chi-restraints excluded: chain D residue 149 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 256 MET Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 110 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 84 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 63 optimal weight: 6.9990 chunk 138 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 129 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN A 217 GLN C 37 ASN ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.176235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.155314 restraints weight = 16499.598| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 2.38 r_work: 0.3699 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3562 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12939 Z= 0.144 Angle : 0.541 9.111 17555 Z= 0.282 Chirality : 0.042 0.293 1985 Planarity : 0.003 0.045 2315 Dihedral : 4.660 40.824 2117 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.69 % Allowed : 15.96 % Favored : 81.35 % 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: -0.09 (0.21), residues: 1438 helix: 1.88 (0.27), residues: 333 sheet: 0.30 (0.32), residues: 255 loop : -1.01 (0.19), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 142 HIS 0.003 0.001 HIS E 7 PHE 0.030 0.002 PHE C 238 TYR 0.011 0.001 TYR D 119 ARG 0.005 0.000 ARG C 291 Details of bonding type rmsd link_NAG-ASN : bond 0.00250 ( 12) link_NAG-ASN : angle 2.22417 ( 36) link_BETA1-4 : bond 0.00164 ( 2) link_BETA1-4 : angle 1.42229 ( 6) hydrogen bonds : bond 0.03943 ( 520) hydrogen bonds : angle 5.08963 ( 1455) SS BOND : bond 0.00380 ( 15) SS BOND : angle 1.34362 ( 30) link_BETA1-3 : bond 0.00657 ( 1) link_BETA1-3 : angle 5.81027 ( 3) covalent geometry : bond 0.00329 (12909) covalent geometry : angle 0.52402 (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 213 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 180 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7655 (mm-30) REVERT: A 238 PHE cc_start: 0.7938 (OUTLIER) cc_final: 0.7654 (m-10) REVERT: A 247 ARG cc_start: 0.8271 (mtt180) cc_final: 0.7979 (mtt180) REVERT: B 25 ARG cc_start: 0.8133 (ttm170) cc_final: 0.7884 (tpp80) REVERT: B 39 LYS cc_start: 0.7706 (ttmt) cc_final: 0.6996 (ttpt) REVERT: C 190 ASN cc_start: 0.7346 (t0) cc_final: 0.7122 (t0) REVERT: C 256 MET cc_start: 0.7465 (ttp) cc_final: 0.7076 (tmm) REVERT: D 61 GLN cc_start: 0.8431 (tp40) cc_final: 0.8210 (tp40) REVERT: D 115 MET cc_start: 0.8675 (tpt) cc_final: 0.8425 (mmm) REVERT: D 120 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7710 (mp0) REVERT: D 149 MET cc_start: 0.6003 (OUTLIER) cc_final: 0.5262 (ttm) REVERT: E 217 GLN cc_start: 0.7241 (tp40) cc_final: 0.6843 (mt0) REVERT: E 232 ASP cc_start: 0.7466 (m-30) cc_final: 0.7216 (m-30) REVERT: F 115 MET cc_start: 0.7663 (tpt) cc_final: 0.7351 (tpt) REVERT: F 157 TYR cc_start: 0.6431 (t80) cc_final: 0.5987 (t80) outliers start: 33 outliers final: 22 residues processed: 203 average time/residue: 0.2536 time to fit residues: 73.2605 Evaluate side-chains 196 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 1.277 ------------------------------------------------------------------------------- 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 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 311 MET Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 275 SER 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: 0.3980 chunk 159 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 120 optimal weight: 0.0170 chunk 104 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN C 229 ASN C 313 ASN ** D 26 HIS ** 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 = 0.4045 r_free = 0.4045 target = 0.177185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.156435 restraints weight = 16315.449| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 2.36 r_work: 0.3720 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3583 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2926 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= 0.120 Angle : 0.535 10.669 17555 Z= 0.277 Chirality : 0.041 0.286 1985 Planarity : 0.003 0.045 2315 Dihedral : 4.544 30.619 2117 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.12 % Allowed : 16.37 % Favored : 81.51 % 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: -0.04 (0.21), residues: 1438 helix: 1.97 (0.27), residues: 333 sheet: 0.35 (0.32), residues: 255 loop : -1.01 (0.19), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 142 HIS 0.003 0.001 HIS C 174 PHE 0.020 0.001 PHE C 238 TYR 0.011 0.001 TYR D 119 ARG 0.005 0.000 ARG C 291 Details of bonding type rmsd link_NAG-ASN : bond 0.00563 ( 12) link_NAG-ASN : angle 2.91575 ( 36) link_BETA1-4 : bond 0.00204 ( 2) link_BETA1-4 : angle 1.35921 ( 6) hydrogen bonds : bond 0.03873 ( 520) hydrogen bonds : angle 5.00682 ( 1455) SS BOND : bond 0.00328 ( 15) SS BOND : angle 1.24540 ( 30) link_BETA1-3 : bond 0.00609 ( 1) link_BETA1-3 : angle 5.69301 ( 3) covalent geometry : bond 0.00265 (12909) covalent geometry : angle 0.51141 (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 204 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 178 time to evaluate : 1.244 Fit side-chains revert: symmetry clash REVERT: A 139 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7562 (mm-30) REVERT: A 238 PHE cc_start: 0.7895 (OUTLIER) cc_final: 0.7664 (m-10) REVERT: A 247 ARG cc_start: 0.8258 (mtt180) cc_final: 0.7981 (mtt180) REVERT: B 25 ARG cc_start: 0.8132 (ttm170) cc_final: 0.7910 (tpp80) REVERT: B 39 LYS cc_start: 0.7711 (ttmt) cc_final: 0.6982 (ttpt) REVERT: B 69 GLU cc_start: 0.7755 (tt0) cc_final: 0.7432 (tp30) REVERT: B 127 ARG cc_start: 0.7916 (mtp180) cc_final: 0.7662 (mtp180) REVERT: B 168 GLN cc_start: 0.7448 (mm-40) cc_final: 0.6831 (pp30) REVERT: C 256 MET cc_start: 0.7371 (ttp) cc_final: 0.7007 (tmm) REVERT: D 61 GLN cc_start: 0.8378 (tp40) cc_final: 0.8135 (tp40) REVERT: D 115 MET cc_start: 0.8663 (tpt) cc_final: 0.8452 (mmm) REVERT: D 120 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7712 (mp0) REVERT: D 149 MET cc_start: 0.5996 (OUTLIER) cc_final: 0.5439 (ttm) REVERT: E 217 GLN cc_start: 0.7205 (tp40) cc_final: 0.6832 (mt0) REVERT: E 232 ASP cc_start: 0.7461 (m-30) cc_final: 0.7241 (m-30) REVERT: F 115 MET cc_start: 0.7648 (tpt) cc_final: 0.7349 (tpt) REVERT: F 157 TYR cc_start: 0.6452 (t80) cc_final: 0.6026 (t80) outliers start: 26 outliers final: 18 residues processed: 197 average time/residue: 0.2569 time to fit residues: 71.4688 Evaluate side-chains 189 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 168 time to evaluate : 1.200 ------------------------------------------------------------------------------- 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 238 PHE Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain B residue 56 ILE 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 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 120 GLU Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 275 SER 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: 0.8980 chunk 49 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 159 optimal weight: 9.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN C 313 ASN ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.174413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.153581 restraints weight = 16494.900| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 2.36 r_work: 0.3682 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3544 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12939 Z= 0.169 Angle : 0.570 9.169 17555 Z= 0.295 Chirality : 0.042 0.303 1985 Planarity : 0.003 0.046 2315 Dihedral : 4.632 31.447 2117 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.12 % Allowed : 17.02 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.19 (0.21), residues: 1438 helix: 1.83 (0.27), residues: 333 sheet: 0.09 (0.32), residues: 262 loop : -1.05 (0.19), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 142 HIS 0.004 0.001 HIS A 7 PHE 0.023 0.002 PHE C 238 TYR 0.011 0.001 TYR D 119 ARG 0.011 0.001 ARG C 291 Details of bonding type rmsd link_NAG-ASN : bond 0.00231 ( 12) link_NAG-ASN : angle 2.65852 ( 36) link_BETA1-4 : bond 0.00140 ( 2) link_BETA1-4 : angle 1.46713 ( 6) hydrogen bonds : bond 0.03980 ( 520) hydrogen bonds : angle 5.11784 ( 1455) SS BOND : bond 0.00434 ( 15) SS BOND : angle 1.38194 ( 30) link_BETA1-3 : bond 0.00432 ( 1) link_BETA1-3 : angle 5.79102 ( 3) covalent geometry : bond 0.00391 (12909) covalent geometry : angle 0.54934 (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 204 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 178 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.8034 (OUTLIER) cc_final: 0.7661 (m-80) REVERT: A 247 ARG cc_start: 0.8374 (mtt180) cc_final: 0.8113 (mtt180) REVERT: A 256 MET cc_start: 0.8041 (ptm) cc_final: 0.7778 (ttp) REVERT: B 25 ARG cc_start: 0.8147 (ttm170) cc_final: 0.7898 (tpp80) REVERT: B 39 LYS cc_start: 0.7712 (ttmt) cc_final: 0.6996 (ttpt) REVERT: C 256 MET cc_start: 0.7461 (ttp) cc_final: 0.7032 (tmm) REVERT: D 61 GLN cc_start: 0.8395 (tp40) cc_final: 0.8162 (tp40) REVERT: D 102 MET cc_start: 0.7710 (mtp) cc_final: 0.7247 (mtp) REVERT: D 115 MET cc_start: 0.8675 (tpt) cc_final: 0.8433 (mmm) REVERT: D 120 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7727 (mp0) REVERT: E 217 GLN cc_start: 0.7343 (tp40) cc_final: 0.6911 (mt0) REVERT: E 232 ASP cc_start: 0.7525 (m-30) cc_final: 0.7299 (m-30) REVERT: F 115 MET cc_start: 0.7723 (tpt) cc_final: 0.7429 (tpt) REVERT: F 157 TYR cc_start: 0.6572 (t80) cc_final: 0.6122 (t80) outliers start: 26 outliers final: 22 residues processed: 198 average time/residue: 0.2563 time to fit residues: 72.6475 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 : 1.226 ------------------------------------------------------------------------------- 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 127 SER 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 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 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 120 GLU Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain F residue 12 ASN 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: 1.9990 chunk 46 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 159 optimal weight: 9.9990 chunk 103 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 151 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN C 313 ASN ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.174940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.155793 restraints weight = 16321.877| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 2.12 r_work: 0.3696 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3568 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.196 12939 Z= 0.304 Angle : 0.837 59.190 17555 Z= 0.484 Chirality : 0.044 0.512 1985 Planarity : 0.003 0.046 2315 Dihedral : 4.638 31.462 2117 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.28 % Allowed : 16.78 % Favored : 80.94 % Cbeta Deviations : 0.06 % 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: -0.22 (0.21), residues: 1438 helix: 1.80 (0.27), residues: 333 sheet: 0.08 (0.32), residues: 262 loop : -1.06 (0.19), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 142 HIS 0.003 0.001 HIS E 7 PHE 0.021 0.002 PHE C 238 TYR 0.011 0.001 TYR D 119 ARG 0.009 0.000 ARG C 291 Details of bonding type rmsd link_NAG-ASN : bond 0.00291 ( 12) link_NAG-ASN : angle 2.66371 ( 36) link_BETA1-4 : bond 0.00161 ( 2) link_BETA1-4 : angle 1.48125 ( 6) hydrogen bonds : bond 0.03963 ( 520) hydrogen bonds : angle 5.11556 ( 1455) SS BOND : bond 0.00545 ( 15) SS BOND : angle 1.40169 ( 30) link_BETA1-3 : bond 0.00060 ( 1) link_BETA1-3 : angle 5.87935 ( 3) covalent geometry : bond 0.00565 (12909) covalent geometry : angle 0.82350 (17480) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5912.64 seconds wall clock time: 104 minutes 0.18 seconds (6240.18 seconds total)