Starting phenix.real_space_refine on Fri Jan 24 18:51:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8znr_60279/01_2025/8znr_60279_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8znr_60279/01_2025/8znr_60279.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8znr_60279/01_2025/8znr_60279.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8znr_60279/01_2025/8znr_60279.map" model { file = "/net/cci-nas-00/data/ceres_data/8znr_60279/01_2025/8znr_60279_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8znr_60279/01_2025/8znr_60279_neut.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.033 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: 5 Type Number sf(0) Gaussians P 91 5.49 5 S 111 5.16 5 C 14086 2.51 5 N 3777 2.21 5 O 4540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 22605 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2628 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 15, 'TRANS': 309} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2592 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 2621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2621 Classifications: {'peptide': 324} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 15, 'TRANS': 308} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2592 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1972 Classifications: {'peptide': 255} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 8, 'TRANS': 246} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 2235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2235 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 16, 'TRANS': 281} Chain breaks: 3 Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 74 Chain: "G" Number of atoms: 2593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2593 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 304} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "H" Number of atoms: 2368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2368 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 11, 'TRANS': 280} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 710 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain: "L" Number of atoms: 1203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1203 Classifications: {'RNA': 56} Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 11, 'rna3p_pur': 17, 'rna3p_pyr': 13} Link IDs: {'rna2p': 25, 'rna3p': 30} Chain breaks: 1 Chain: "M" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1091 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 5, 'TRANS': 149} Chain breaks: 3 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 160 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 4, 'GLU:plan': 1, 'TYR:plan': 3, 'GLN:plan1': 4, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 85 Time building chain proxies: 13.90, per 1000 atoms: 0.61 Number of scatterers: 22605 At special positions: 0 Unit cell: (108.272, 144.632, 154.328, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 111 16.00 P 91 15.00 O 4540 8.00 N 3777 7.00 C 14086 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 5.72 Conformation dependent library (CDL) restraints added in 2.8 seconds 5134 Ramachandran restraints generated. 2567 Oldfield, 0 Emsley, 2567 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4968 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 36 sheets defined 27.8% alpha, 9.2% beta 19 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 8.05 Creating SS restraints... Processing helix chain 'A' and resid 63 through 71 removed outlier: 3.897A pdb=" N GLU A 68 " --> pdb=" O PRO A 64 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS A 69 " --> pdb=" O ASP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 106 removed outlier: 3.927A pdb=" N MET A 106 " --> pdb=" O LYS A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 128 removed outlier: 3.502A pdb=" N ARG A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 144 removed outlier: 3.580A pdb=" N ALA A 135 " --> pdb=" O PHE A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 201 removed outlier: 3.739A pdb=" N GLN A 195 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 259 removed outlier: 3.581A pdb=" N ILE A 254 " --> pdb=" O HIS A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 312 through 326 Processing helix chain 'B' and resid 36 through 40 removed outlier: 3.580A pdb=" N ARG B 40 " --> pdb=" O PHE B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 68 removed outlier: 3.960A pdb=" N GLU B 68 " --> pdb=" O PRO B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 104 No H-bonds generated for 'chain 'B' and resid 102 through 104' Processing helix chain 'B' and resid 111 through 129 removed outlier: 3.570A pdb=" N ARG B 115 " --> pdb=" O ASP B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 144 removed outlier: 3.588A pdb=" N ALA B 135 " --> pdb=" O PHE B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 186 through 202 removed outlier: 3.580A pdb=" N GLN B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 259 Processing helix chain 'B' and resid 296 through 302 Processing helix chain 'B' and resid 312 through 326 Processing helix chain 'C' and resid 63 through 71 removed outlier: 3.879A pdb=" N GLU C 68 " --> pdb=" O PRO C 64 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS C 69 " --> pdb=" O ASP C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 106 removed outlier: 3.736A pdb=" N SER C 105 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N MET C 106 " --> pdb=" O LYS C 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 102 through 106' Processing helix chain 'C' and resid 111 through 129 Processing helix chain 'C' and resid 131 through 144 Processing helix chain 'C' and resid 186 through 202 removed outlier: 3.710A pdb=" N GLN C 194 " --> pdb=" O ASN C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 259 Processing helix chain 'C' and resid 296 through 302 Processing helix chain 'C' and resid 312 through 326 Processing helix chain 'D' and resid 63 through 70 removed outlier: 3.854A pdb=" N LYS D 69 " --> pdb=" O ASP D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 129 Processing helix chain 'D' and resid 131 through 144 removed outlier: 3.655A pdb=" N ALA D 135 " --> pdb=" O PHE D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 186 through 202 removed outlier: 3.829A pdb=" N GLN D 194 " --> pdb=" O ASN D 190 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN D 195 " --> pdb=" O GLU D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 260 removed outlier: 3.523A pdb=" N THR D 260 " --> pdb=" O ASN D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 302 Processing helix chain 'D' and resid 312 through 326 Processing helix chain 'E' and resid 27 through 43 removed outlier: 3.713A pdb=" N PHE E 31 " --> pdb=" O ALA E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 126 removed outlier: 3.603A pdb=" N CYS E 121 " --> pdb=" O ASP E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 168 Processing helix chain 'E' and resid 173 through 185 Processing helix chain 'F' and resid 102 through 106 Processing helix chain 'F' and resid 166 through 179 removed outlier: 3.671A pdb=" N ASN F 170 " --> pdb=" O SER F 166 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG F 179 " --> pdb=" O ASP F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 199 removed outlier: 3.932A pdb=" N GLY F 199 " --> pdb=" O ALA F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 217 through 221 Processing helix chain 'F' and resid 238 through 242 removed outlier: 3.637A pdb=" N LEU F 242 " --> pdb=" O ILE F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 266 removed outlier: 4.015A pdb=" N LEU F 258 " --> pdb=" O ALA F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 277 Processing helix chain 'F' and resid 282 through 291 Processing helix chain 'F' and resid 325 through 335 Processing helix chain 'G' and resid 39 through 43 removed outlier: 3.794A pdb=" N PHE G 43 " --> pdb=" O ARG G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 70 removed outlier: 3.697A pdb=" N LYS G 69 " --> pdb=" O LYS G 66 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU G 70 " --> pdb=" O LEU G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 129 Processing helix chain 'G' and resid 131 through 144 removed outlier: 3.516A pdb=" N ALA G 135 " --> pdb=" O PHE G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 186 through 201 Processing helix chain 'G' and resid 250 through 259 Processing helix chain 'G' and resid 296 through 305 Processing helix chain 'G' and resid 312 through 326 Processing helix chain 'H' and resid 36 through 43 removed outlier: 3.774A pdb=" N ARG H 40 " --> pdb=" O PHE H 37 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N HIS H 41 " --> pdb=" O LEU H 38 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE H 43 " --> pdb=" O ARG H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 129 Processing helix chain 'H' and resid 131 through 144 Processing helix chain 'H' and resid 186 through 202 Processing helix chain 'H' and resid 250 through 259 removed outlier: 3.549A pdb=" N ILE H 254 " --> pdb=" O HIS H 250 " (cutoff:3.500A) Processing helix chain 'H' and resid 300 through 305 Processing helix chain 'H' and resid 312 through 326 removed outlier: 4.004A pdb=" N TYR H 318 " --> pdb=" O GLU H 314 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ILE H 324 " --> pdb=" O MET H 320 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG H 325 " --> pdb=" O ALA H 321 " (cutoff:3.500A) Processing helix chain 'M' and resid 15 through 23 Processing helix chain 'M' and resid 23 through 33 removed outlier: 3.551A pdb=" N VAL M 27 " --> pdb=" O ASP M 23 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL M 33 " --> pdb=" O HIS M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 71 Processing helix chain 'M' and resid 130 through 139 removed outlier: 3.763A pdb=" N LYS M 134 " --> pdb=" O HIS M 130 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N GLN M 137 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ILE M 138 " --> pdb=" O LYS M 134 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE M 139 " --> pdb=" O ASN M 135 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 removed outlier: 4.009A pdb=" N SER A 108 " --> pdb=" O SER A 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 25 through 27 current: chain 'A' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 45 through 46 current: chain 'A' and resid 167 through 168 No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 57 removed outlier: 4.109A pdb=" N CYS A 82 " --> pdb=" O VAL A 223 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 242 through 243 Processing sheet with id=AA5, first strand: chain 'A' and resid 260 through 262 Processing sheet with id=AA6, first strand: chain 'B' and resid 106 through 109 Processing sheet with id=AA7, first strand: chain 'B' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 25 through 27 current: chain 'B' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 45 through 46 current: chain 'B' and resid 167 through 168 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 167 through 168 current: chain 'B' and resid 246 through 249 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 50 through 51 Processing sheet with id=AA9, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AB1, first strand: chain 'B' and resid 260 through 262 Processing sheet with id=AB2, first strand: chain 'C' and resid 108 through 109 removed outlier: 3.804A pdb=" N SER C 108 " --> pdb=" O SER C 20 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 25 through 27 current: chain 'C' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 45 through 46 current: chain 'C' and resid 167 through 168 No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 50 through 57 removed outlier: 4.089A pdb=" N CYS C 82 " --> pdb=" O VAL C 223 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 242 through 243 Processing sheet with id=AB6, first strand: chain 'C' and resid 282 through 283 removed outlier: 3.846A pdb=" N ALA C 283 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE C 288 " --> pdb=" O ALA C 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 20 through 21 Processing sheet with id=AB8, first strand: chain 'D' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 25 through 27 current: chain 'D' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 45 through 46 current: chain 'D' and resid 172 through 173 No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 49 through 57 removed outlier: 3.554A pdb=" N ASN D 75 " --> pdb=" O ALA D 56 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N CYS D 82 " --> pdb=" O VAL D 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 242 through 243 Processing sheet with id=AC2, first strand: chain 'E' and resid 1 through 16 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 1 through 16 current: chain 'E' and resid 100 through 113 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 100 through 113 current: chain 'E' and resid 214 through 228 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 214 through 228 current: chain 'E' and resid 248 through 252 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 248 through 252 current: chain 'F' and resid 157 through 163 No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'E' and resid 22 through 24 Processing sheet with id=AC4, first strand: chain 'E' and resid 65 through 67 Processing sheet with id=AC5, first strand: chain 'F' and resid 35 through 37 Processing sheet with id=AC6, first strand: chain 'F' and resid 39 through 40 Processing sheet with id=AC7, first strand: chain 'F' and resid 245 through 246 removed outlier: 3.751A pdb=" N CYS F 249 " --> pdb=" O ASP F 246 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 301 through 304 removed outlier: 3.560A pdb=" N LEU F 323 " --> pdb=" O GLU F 302 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 106 through 108 removed outlier: 3.548A pdb=" N SER G 108 " --> pdb=" O SER G 20 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 25 through 27 current: chain 'G' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 45 through 46 current: chain 'G' and resid 167 through 168 No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'G' and resid 50 through 54 removed outlier: 4.151A pdb=" N CYS G 82 " --> pdb=" O VAL G 223 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 242 through 243 Processing sheet with id=AD4, first strand: chain 'G' and resid 282 through 283 removed outlier: 3.940A pdb=" N ALA G 283 " --> pdb=" O ILE G 288 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ILE G 288 " --> pdb=" O ALA G 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'H' and resid 106 through 109 removed outlier: 3.608A pdb=" N GLY H 327 " --> pdb=" O PHE H 21 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 25 through 27 current: chain 'H' and resid 90 through 99 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 90 through 99 current: chain 'H' and resid 167 through 168 No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'M' and resid 2 through 8 removed outlier: 3.626A pdb=" N VAL M 60 " --> pdb=" O GLN M 4 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'M' and resid 98 through 99 Processing sheet with id=AD9, first strand: chain 'M' and resid 143 through 144 518 hydrogen bonds defined for protein. 1446 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 50 hydrogen bonds 100 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 6.53 Time building geometry restraints manager: 6.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5232 1.33 - 1.45: 5582 1.45 - 1.58: 12102 1.58 - 1.70: 180 1.70 - 1.82: 176 Bond restraints: 23272 Sorted by residual: bond pdb=" C MET G 328 " pdb=" N PHE G 329 " ideal model delta sigma weight residual 1.332 1.208 0.125 1.40e-02 5.10e+03 7.94e+01 bond pdb=" C ILE M 20 " pdb=" N SER M 21 " ideal model delta sigma weight residual 1.334 1.435 -0.101 1.38e-02 5.25e+03 5.36e+01 bond pdb=" C GLY G 327 " pdb=" N MET G 328 " ideal model delta sigma weight residual 1.331 1.216 0.115 1.65e-02 3.67e+03 4.83e+01 bond pdb=" C SER D 251 " pdb=" N GLN D 252 " ideal model delta sigma weight residual 1.335 1.425 -0.090 1.38e-02 5.25e+03 4.22e+01 bond pdb=" C THR G 270 " pdb=" N TYR G 271 " ideal model delta sigma weight residual 1.331 1.435 -0.104 1.65e-02 3.67e+03 3.98e+01 ... (remaining 23267 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 30106 2.35 - 4.71: 1511 4.71 - 7.06: 231 7.06 - 9.42: 49 9.42 - 11.77: 9 Bond angle restraints: 31906 Sorted by residual: angle pdb=" N ILE F 132 " pdb=" CA ILE F 132 " pdb=" C ILE F 132 " ideal model delta sigma weight residual 112.17 104.66 7.51 9.50e-01 1.11e+00 6.26e+01 angle pdb=" C3' C L 50 " pdb=" O3' C L 50 " pdb=" P G L 51 " ideal model delta sigma weight residual 120.20 109.52 10.68 1.50e+00 4.44e-01 5.07e+01 angle pdb=" N ASP B 36 " pdb=" CA ASP B 36 " pdb=" C ASP B 36 " ideal model delta sigma weight residual 109.40 98.89 10.51 1.63e+00 3.76e-01 4.16e+01 angle pdb=" C3' G L 51 " pdb=" O3' G L 51 " pdb=" P G L 52 " ideal model delta sigma weight residual 120.20 110.96 9.24 1.50e+00 4.44e-01 3.80e+01 angle pdb=" N ILE G 261 " pdb=" CA ILE G 261 " pdb=" C ILE G 261 " ideal model delta sigma weight residual 113.10 107.27 5.83 9.70e-01 1.06e+00 3.61e+01 ... (remaining 31901 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.07: 13420 34.07 - 68.15: 572 68.15 - 102.22: 41 102.22 - 136.29: 0 136.29 - 170.36: 10 Dihedral angle restraints: 14043 sinusoidal: 6364 harmonic: 7679 Sorted by residual: dihedral pdb=" C5' G L 51 " pdb=" C4' G L 51 " pdb=" C3' G L 51 " pdb=" O3' G L 51 " ideal model delta sinusoidal sigma weight residual 82.00 138.25 -56.25 1 8.00e+00 1.56e-02 6.67e+01 dihedral pdb=" O4' C L 6 " pdb=" C1' C L 6 " pdb=" N1 C L 6 " pdb=" C2 C L 6 " ideal model delta sinusoidal sigma weight residual -128.00 42.36 -170.36 1 1.70e+01 3.46e-03 6.60e+01 dihedral pdb=" O4' C L 24 " pdb=" C1' C L 24 " pdb=" N1 C L 24 " pdb=" C2 C L 24 " ideal model delta sinusoidal sigma weight residual -128.00 37.26 -165.26 1 1.70e+01 3.46e-03 6.53e+01 ... (remaining 14040 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 3291 0.116 - 0.231: 263 0.231 - 0.347: 12 0.347 - 0.463: 15 0.463 - 0.578: 4 Chirality restraints: 3585 Sorted by residual: chirality pdb=" P U L 46 " pdb=" OP1 U L 46 " pdb=" OP2 U L 46 " pdb=" O5' U L 46 " both_signs ideal model delta sigma weight residual True 2.41 -2.99 -0.58 2.00e-01 2.50e+01 8.36e+00 chirality pdb=" P DT I -2 " pdb=" OP1 DT I -2 " pdb=" OP2 DT I -2 " pdb=" O5' DT I -2 " both_signs ideal model delta sigma weight residual True 2.35 -2.85 -0.50 2.00e-01 2.50e+01 6.32e+00 chirality pdb=" P DC I 5 " pdb=" OP1 DC I 5 " pdb=" OP2 DC I 5 " pdb=" O5' DC I 5 " both_signs ideal model delta sigma weight residual True 2.35 -2.81 -0.47 2.00e-01 2.50e+01 5.49e+00 ... (remaining 3582 not shown) Planarity restraints: 3777 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE F 31 " -0.021 2.00e-02 2.50e+03 4.18e-02 1.74e+01 pdb=" C ILE F 31 " 0.072 2.00e-02 2.50e+03 pdb=" O ILE F 31 " -0.027 2.00e-02 2.50e+03 pdb=" N ASP F 32 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE M 20 " -0.017 2.00e-02 2.50e+03 3.50e-02 1.22e+01 pdb=" C ILE M 20 " 0.060 2.00e-02 2.50e+03 pdb=" O ILE M 20 " -0.024 2.00e-02 2.50e+03 pdb=" N SER M 21 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 288 " 0.017 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" C ILE A 288 " -0.059 2.00e-02 2.50e+03 pdb=" O ILE A 288 " 0.022 2.00e-02 2.50e+03 pdb=" N PRO A 289 " 0.020 2.00e-02 2.50e+03 ... (remaining 3774 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2039 2.74 - 3.28: 20464 3.28 - 3.82: 37854 3.82 - 4.36: 48921 4.36 - 4.90: 79353 Nonbonded interactions: 188631 Sorted by model distance: nonbonded pdb=" O ILE E 235 " pdb=" N SER E 237 " model vdw 2.197 3.120 nonbonded pdb=" O LEU G 55 " pdb=" O2' A L 29 " model vdw 2.199 3.040 nonbonded pdb=" OH TYR D 265 " pdb=" O PHE D 273 " model vdw 2.229 3.040 nonbonded pdb=" OG1 THR G 35 " pdb=" OG1 THR G 90 " model vdw 2.239 3.040 nonbonded pdb=" O PHE D 21 " pdb=" O2' A L 15 " model vdw 2.265 3.040 ... (remaining 188626 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 12 through 37 or (resid 38 and (name N or name CA or name \ C or name O or name CB )) or resid 39 through 51 or resid 79 through 231 or resi \ d 237 or (resid 238 and (name N or name CA or name C or name O or name CB )) or \ resid 239 through 287 or (resid 288 and (name N or name CA or name C or name O o \ r name CB )) or resid 289 through 305 or (resid 306 through 307 and (name N or n \ ame CA or name C or name O or name CB )) or resid 308 through 332)) selection = (chain 'B' and (resid 12 through 37 or (resid 38 and (name N or name CA or name \ C or name O or name CB )) or resid 39 through 51 or resid 79 through 231 or resi \ d 237 or (resid 238 and (name N or name CA or name C or name O or name CB )) or \ resid 239 through 287 or (resid 288 and (name N or name CA or name C or name O o \ r name CB )) or resid 289 through 305 or (resid 306 through 307 and (name N or n \ ame CA or name C or name O or name CB )) or resid 308 through 332)) selection = (chain 'C' and (resid 12 through 37 or (resid 38 and (name N or name CA or name \ C or name O or name CB )) or resid 39 through 51 or resid 79 through 231 or resi \ d 237 or (resid 238 and (name N or name CA or name C or name O or name CB )) or \ resid 239 through 287 or (resid 288 and (name N or name CA or name C or name O o \ r name CB )) or resid 289 through 305 or (resid 306 through 307 and (name N or n \ ame CA or name C or name O or name CB )) or resid 308 through 332)) selection = (chain 'D' and (resid 12 through 37 or (resid 38 and (name N or name CA or name \ C or name O or name CB )) or resid 39 through 51 or resid 79 through 231 or resi \ d 237 or (resid 238 and (name N or name CA or name C or name O or name CB )) or \ resid 239 through 287 or (resid 288 and (name N or name CA or name C or name O o \ r name CB )) or resid 289 through 305 or (resid 306 through 307 and (name N or n \ ame CA or name C or name O or name CB )) or resid 308 through 332)) selection = (chain 'G' and (resid 12 or (resid 13 and (name N or name CA or name C or name O \ or name CB )) or resid 14 through 37 or (resid 38 and (name N or name CA or nam \ e C or name O or name CB )) or resid 39 through 51 or resid 79 through 231 or re \ sid 237 or (resid 238 and (name N or name CA or name C or name O or name CB )) o \ r resid 239 through 287 or (resid 288 and (name N or name CA or name C or name O \ or name CB )) or resid 289 through 305 or (resid 306 through 307 and (name N or \ name CA or name C or name O or name CB )) or resid 308 through 332)) selection = (chain 'H' and (resid 12 through 231 or resid 237 through 306 or (resid 307 and \ (name N or name CA or name C or name O or name CB )) or resid 308 through 332)) } 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: 2.600 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: 0.020 Extract box with map and model: 0.920 Check model and map are aligned: 0.180 Set scattering table: 0.210 Process input model: 55.140 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.110 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:12.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 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 0.125 23272 Z= 0.427 Angle : 1.172 11.770 31906 Z= 0.691 Chirality : 0.070 0.578 3585 Planarity : 0.010 0.096 3777 Dihedral : 18.216 170.363 9075 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.58 % Favored : 92.99 % Rotamer: Outliers : 1.40 % Allowed : 18.99 % Favored : 79.61 % 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: -3.03 (0.14), residues: 2567 helix: -2.02 (0.16), residues: 692 sheet: -0.21 (0.25), residues: 412 loop : -2.66 (0.13), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP G 149 HIS 0.019 0.003 HIS E 203 PHE 0.048 0.004 PHE H 37 TYR 0.039 0.003 TYR M 46 ARG 0.020 0.001 ARG E 162 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5134 Ramachandran restraints generated. 2567 Oldfield, 0 Emsley, 2567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5134 Ramachandran restraints generated. 2567 Oldfield, 0 Emsley, 2567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 770 time to evaluate : 2.615 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.7438 (m-30) cc_final: 0.7237 (m-30) REVERT: A 216 LYS cc_start: 0.8156 (tttt) cc_final: 0.7827 (tttp) REVERT: A 278 GLU cc_start: 0.7317 (mm-30) cc_final: 0.7094 (mm-30) REVERT: A 303 ARG cc_start: 0.8424 (mtp180) cc_final: 0.8223 (mtp180) REVERT: A 334 GLU cc_start: 0.7412 (mp0) cc_final: 0.7155 (mp0) REVERT: B 39 LYS cc_start: 0.8209 (mttt) cc_final: 0.7974 (mtpp) REVERT: B 72 MET cc_start: 0.7709 (mmm) cc_final: 0.7450 (mmm) REVERT: B 239 LYS cc_start: 0.8398 (mttt) cc_final: 0.8177 (mtmm) REVERT: B 262 ASP cc_start: 0.8428 (t0) cc_final: 0.8157 (t0) REVERT: B 278 GLU cc_start: 0.7157 (mt-10) cc_final: 0.6829 (mt-10) REVERT: B 303 ARG cc_start: 0.8172 (ttp80) cc_final: 0.7888 (ttp80) REVERT: B 331 LYS cc_start: 0.8401 (tptm) cc_final: 0.8197 (tptp) REVERT: C 52 LYS cc_start: 0.8359 (ttmt) cc_final: 0.8051 (ttpp) REVERT: C 166 ASP cc_start: 0.6931 (t0) cc_final: 0.6710 (t0) REVERT: C 183 VAL cc_start: 0.8854 (m) cc_final: 0.8599 (p) REVERT: C 184 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7359 (mm-30) REVERT: C 200 PHE cc_start: 0.8648 (m-10) cc_final: 0.8444 (m-10) REVERT: C 216 LYS cc_start: 0.7935 (tttt) cc_final: 0.7690 (ttpp) REVERT: C 224 TYR cc_start: 0.8445 (m-80) cc_final: 0.8091 (m-80) REVERT: C 262 ASP cc_start: 0.8424 (t0) cc_final: 0.7794 (t0) REVERT: C 303 ARG cc_start: 0.8282 (ttp80) cc_final: 0.7747 (ttt90) REVERT: D 66 LYS cc_start: 0.8505 (ttpt) cc_final: 0.8120 (ttmm) REVERT: D 69 LYS cc_start: 0.8609 (mtmt) cc_final: 0.8373 (mtmm) REVERT: D 172 PHE cc_start: 0.8419 (m-10) cc_final: 0.8080 (m-80) REVERT: D 204 ARG cc_start: 0.8243 (mtp85) cc_final: 0.7999 (mtp85) REVERT: D 222 GLU cc_start: 0.7611 (tt0) cc_final: 0.7371 (tt0) REVERT: D 228 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7300 (mt-10) REVERT: E 102 ASP cc_start: 0.7319 (t0) cc_final: 0.7102 (t0) REVERT: E 104 ASN cc_start: 0.7963 (t0) cc_final: 0.7737 (t160) REVERT: E 112 GLU cc_start: 0.6815 (mt-10) cc_final: 0.6575 (mt-10) REVERT: E 209 ASP cc_start: 0.7917 (t0) cc_final: 0.7705 (t0) REVERT: F 27 LEU cc_start: 0.7818 (mp) cc_final: 0.7389 (tm) REVERT: F 45 GLU cc_start: 0.7315 (tp30) cc_final: 0.6653 (tp30) REVERT: F 68 ASP cc_start: 0.7047 (t0) cc_final: 0.6704 (t70) REVERT: F 172 GLU cc_start: 0.7607 (tp30) cc_final: 0.7402 (tp30) REVERT: F 176 ARG cc_start: 0.7724 (mtt180) cc_final: 0.7489 (mtt180) REVERT: F 177 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8079 (mp) REVERT: F 230 LYS cc_start: 0.8429 (mttt) cc_final: 0.7613 (mttt) REVERT: F 266 LYS cc_start: 0.7496 (mmmm) cc_final: 0.6664 (mmmm) REVERT: F 309 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8419 (mt) REVERT: F 322 MET cc_start: 0.5412 (tpp) cc_final: 0.5074 (tpp) REVERT: G 94 ASP cc_start: 0.8250 (m-30) cc_final: 0.7943 (m-30) REVERT: G 125 TYR cc_start: 0.8192 (t80) cc_final: 0.7877 (t80) REVERT: G 166 ASP cc_start: 0.6894 (t0) cc_final: 0.6619 (t0) REVERT: G 174 SER cc_start: 0.8690 (m) cc_final: 0.8382 (t) REVERT: G 271 TYR cc_start: 0.7819 (OUTLIER) cc_final: 0.7106 (m-80) REVERT: G 288 ILE cc_start: 0.8052 (mm) cc_final: 0.7695 (mm) REVERT: G 307 LYS cc_start: 0.8390 (mtpp) cc_final: 0.8135 (mttp) REVERT: H 47 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8357 (tt) REVERT: H 105 SER cc_start: 0.8605 (t) cc_final: 0.8353 (t) REVERT: H 156 GLU cc_start: 0.6590 (OUTLIER) cc_final: 0.6200 (pt0) REVERT: H 161 ILE cc_start: 0.8174 (mt) cc_final: 0.7862 (tp) REVERT: H 181 THR cc_start: 0.8466 (p) cc_final: 0.8145 (t) REVERT: H 217 ILE cc_start: 0.8825 (pt) cc_final: 0.8440 (pp) REVERT: H 228 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7391 (mt-10) REVERT: M 34 GLU cc_start: 0.7618 (tm-30) cc_final: 0.7357 (tm-30) REVERT: M 39 PHE cc_start: 0.6515 (m-10) cc_final: 0.6248 (m-10) REVERT: M 58 ILE cc_start: 0.7055 (tt) cc_final: 0.6790 (pt) REVERT: M 101 ARG cc_start: 0.8042 (tpt-90) cc_final: 0.7092 (tmt170) outliers start: 31 outliers final: 8 residues processed: 782 average time/residue: 1.3753 time to fit residues: 1225.0874 Evaluate side-chains 720 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 707 time to evaluate : 2.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain D residue 252 GLN Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 320 MET Chi-restraints excluded: chain G residue 271 TYR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 156 GLU Chi-restraints excluded: chain M residue 19 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 0.5980 chunk 200 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 68 optimal weight: 0.0040 chunk 134 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 206 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 125 optimal weight: 0.9980 chunk 154 optimal weight: 7.9990 chunk 239 optimal weight: 0.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 HIS B 77 GLN B 80 GLN B 195 GLN B 208 ASN B 250 HIS B 256 ASN D 252 GLN E 11 ASN E 16 ASN E 20 ASN E 43 ASN E 52 ASN ** E 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 ASN E 167 ASN E 203 HIS F 34 ASN ** F 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 144 ASN F 149 GLN F 206 ASN F 270 ASN G 26 ASN G 34 GLN G 75 ASN G 186 ASN ** H 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN H 256 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.122670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.108760 restraints weight = 32979.964| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.75 r_work: 0.3340 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.130 23272 Z= 0.225 Angle : 0.634 11.362 31906 Z= 0.342 Chirality : 0.044 0.280 3585 Planarity : 0.006 0.057 3777 Dihedral : 18.466 176.319 4108 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.61 % Favored : 94.16 % Rotamer: Outliers : 3.78 % Allowed : 19.40 % Favored : 76.82 % 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: -2.12 (0.15), residues: 2567 helix: -0.78 (0.18), residues: 713 sheet: 0.27 (0.25), residues: 453 loop : -2.44 (0.14), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 149 HIS 0.006 0.001 HIS B 317 PHE 0.016 0.002 PHE H 37 TYR 0.013 0.001 TYR G 271 ARG 0.008 0.001 ARG E 162 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5134 Ramachandran restraints generated. 2567 Oldfield, 0 Emsley, 2567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5134 Ramachandran restraints generated. 2567 Oldfield, 0 Emsley, 2567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 775 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 691 time to evaluate : 2.698 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 ARG cc_start: 0.8423 (ttm110) cc_final: 0.8203 (mtm-85) REVERT: A 77 GLN cc_start: 0.7819 (mm-40) cc_final: 0.7459 (mm-40) REVERT: A 216 LYS cc_start: 0.8343 (tttt) cc_final: 0.8045 (tttp) REVERT: A 334 GLU cc_start: 0.7599 (mp0) cc_final: 0.7343 (mp0) REVERT: B 20 SER cc_start: 0.8136 (OUTLIER) cc_final: 0.7923 (p) REVERT: B 39 LYS cc_start: 0.8249 (mttt) cc_final: 0.7954 (mtpp) REVERT: B 72 MET cc_start: 0.7958 (mmm) cc_final: 0.7651 (mmm) REVERT: B 83 THR cc_start: 0.8711 (p) cc_final: 0.8494 (m) REVERT: B 156 GLU cc_start: 0.7367 (mp0) cc_final: 0.7076 (mp0) REVERT: B 278 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7202 (mt-10) REVERT: B 331 LYS cc_start: 0.8525 (tptm) cc_final: 0.8309 (tptp) REVERT: C 52 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.8020 (ptmt) REVERT: C 66 LYS cc_start: 0.8136 (mtpt) cc_final: 0.7863 (mtpp) REVERT: C 166 ASP cc_start: 0.7241 (t0) cc_final: 0.6972 (t0) REVERT: C 200 PHE cc_start: 0.8655 (m-10) cc_final: 0.8440 (m-10) REVERT: C 224 TYR cc_start: 0.8556 (m-80) cc_final: 0.8291 (m-80) REVERT: C 239 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8267 (mtmm) REVERT: D 18 ASN cc_start: 0.8273 (m-40) cc_final: 0.8055 (m-40) REVERT: D 228 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7507 (mt-10) REVERT: D 278 GLU cc_start: 0.7667 (mp0) cc_final: 0.7380 (mp0) REVERT: D 307 LYS cc_start: 0.8782 (mtpp) cc_final: 0.8551 (mttp) REVERT: D 309 GLU cc_start: 0.7830 (tt0) cc_final: 0.7595 (tt0) REVERT: E 209 ASP cc_start: 0.8090 (t0) cc_final: 0.7832 (t0) REVERT: F 45 GLU cc_start: 0.7685 (tp30) cc_final: 0.7212 (tp30) REVERT: F 61 ASP cc_start: 0.7097 (t0) cc_final: 0.6745 (t0) REVERT: F 176 ARG cc_start: 0.7881 (mtt180) cc_final: 0.7652 (mtt180) REVERT: F 210 LEU cc_start: 0.8290 (mt) cc_final: 0.8046 (mp) REVERT: F 230 LYS cc_start: 0.8516 (mttt) cc_final: 0.8211 (mttt) REVERT: F 237 ILE cc_start: 0.7892 (pt) cc_final: 0.7445 (pp) REVERT: F 247 ASN cc_start: 0.8232 (m-40) cc_final: 0.7946 (t0) REVERT: F 266 LYS cc_start: 0.7509 (mmmm) cc_final: 0.6987 (mmmm) REVERT: F 272 ARG cc_start: 0.7433 (mmt90) cc_final: 0.6921 (mmt90) REVERT: F 277 ARG cc_start: 0.8175 (mtt90) cc_final: 0.7223 (mtt90) REVERT: F 322 MET cc_start: 0.5390 (tpp) cc_final: 0.5034 (tpp) REVERT: G 174 SER cc_start: 0.8586 (m) cc_final: 0.8333 (t) REVERT: G 307 LYS cc_start: 0.8664 (mtpp) cc_final: 0.8385 (mttp) REVERT: H 105 SER cc_start: 0.8668 (t) cc_final: 0.8373 (t) REVERT: H 140 ASN cc_start: 0.8081 (m-40) cc_final: 0.7688 (m-40) REVERT: H 141 ASN cc_start: 0.7746 (m-40) cc_final: 0.7299 (m-40) REVERT: H 146 ARG cc_start: 0.8136 (ttp-170) cc_final: 0.7863 (ttp-170) REVERT: H 161 ILE cc_start: 0.8225 (mt) cc_final: 0.7961 (tp) REVERT: H 216 LYS cc_start: 0.8264 (ttpp) cc_final: 0.7782 (ttpp) REVERT: H 217 ILE cc_start: 0.8787 (pt) cc_final: 0.8564 (pp) REVERT: H 320 MET cc_start: 0.8272 (mpp) cc_final: 0.8024 (mpp) REVERT: M 58 ILE cc_start: 0.7067 (OUTLIER) cc_final: 0.6717 (pt) REVERT: M 158 PHE cc_start: 0.7407 (m-80) cc_final: 0.7127 (m-80) outliers start: 84 outliers final: 35 residues processed: 732 average time/residue: 1.4206 time to fit residues: 1179.7141 Evaluate side-chains 701 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 662 time to evaluate : 2.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 239 LYS Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 331 LYS Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain F residue 137 SER Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain G residue 62 MET Chi-restraints excluded: chain G residue 161 ILE Chi-restraints excluded: chain G residue 286 ILE Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 307 LYS Chi-restraints excluded: chain M residue 19 ILE Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 102 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 0.2980 chunk 247 optimal weight: 3.9990 chunk 227 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 chunk 135 optimal weight: 0.7980 chunk 217 optimal weight: 0.0980 chunk 35 optimal weight: 0.5980 chunk 95 optimal weight: 4.9990 chunk 171 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 178 ASN ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 GLN B 18 ASN B 77 GLN B 80 GLN B 208 ASN ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 ASN D 252 GLN E 43 ASN ** E 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN E 203 HIS ** F 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 206 ASN G 26 ASN G 77 GLN G 186 ASN ** H 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN H 256 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.121722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.107663 restraints weight = 32596.613| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.76 r_work: 0.3323 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 23272 Z= 0.222 Angle : 0.586 9.949 31906 Z= 0.313 Chirality : 0.043 0.261 3585 Planarity : 0.005 0.054 3777 Dihedral : 18.138 175.707 4085 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.22 % Favored : 94.66 % Rotamer: Outliers : 4.14 % Allowed : 19.80 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.15), residues: 2567 helix: -0.04 (0.19), residues: 708 sheet: 0.69 (0.26), residues: 418 loop : -2.20 (0.14), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 33 HIS 0.008 0.001 HIS B 317 PHE 0.016 0.002 PHE M 43 TYR 0.014 0.001 TYR G 271 ARG 0.008 0.001 ARG E 162 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5134 Ramachandran restraints generated. 2567 Oldfield, 0 Emsley, 2567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5134 Ramachandran restraints generated. 2567 Oldfield, 0 Emsley, 2567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 681 time to evaluate : 2.791 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 ARG cc_start: 0.8431 (ttm110) cc_final: 0.8114 (mtm-85) REVERT: A 29 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7039 (mm-30) REVERT: A 39 LYS cc_start: 0.8786 (ptpp) cc_final: 0.8519 (ptpp) REVERT: A 77 GLN cc_start: 0.7871 (mm-40) cc_final: 0.7660 (mm110) REVERT: A 89 ASP cc_start: 0.8301 (p0) cc_final: 0.7991 (p0) REVERT: A 334 GLU cc_start: 0.7585 (mp0) cc_final: 0.7329 (mp0) REVERT: B 72 MET cc_start: 0.8030 (mmm) cc_final: 0.7739 (mmm) REVERT: B 83 THR cc_start: 0.8660 (p) cc_final: 0.8444 (m) REVERT: B 156 GLU cc_start: 0.7251 (mp0) cc_final: 0.6960 (mp0) REVERT: B 163 THR cc_start: 0.8825 (OUTLIER) cc_final: 0.8481 (p) REVERT: B 222 GLU cc_start: 0.7974 (tt0) cc_final: 0.7707 (tt0) REVERT: B 278 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7282 (mt-10) REVERT: B 331 LYS cc_start: 0.8558 (tptm) cc_final: 0.8316 (tptp) REVERT: C 17 GLU cc_start: 0.7719 (tt0) cc_final: 0.7480 (tt0) REVERT: C 52 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.8014 (ptmt) REVERT: C 66 LYS cc_start: 0.8075 (mtpt) cc_final: 0.7814 (mtpp) REVERT: C 166 ASP cc_start: 0.7303 (t0) cc_final: 0.6923 (t0) REVERT: C 181 THR cc_start: 0.8715 (m) cc_final: 0.8468 (p) REVERT: C 239 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8239 (mtmm) REVERT: D 15 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.7362 (mtp-110) REVERT: D 70 GLU cc_start: 0.7483 (mt-10) cc_final: 0.7149 (mt-10) REVERT: D 204 ARG cc_start: 0.8323 (mtp85) cc_final: 0.8038 (mtp180) REVERT: D 307 LYS cc_start: 0.8734 (mtpp) cc_final: 0.8514 (mttp) REVERT: D 309 GLU cc_start: 0.7813 (tt0) cc_final: 0.7589 (tt0) REVERT: E 102 ASP cc_start: 0.7421 (t0) cc_final: 0.7207 (t0) REVERT: E 209 ASP cc_start: 0.8051 (t0) cc_final: 0.7749 (t0) REVERT: F 45 GLU cc_start: 0.7736 (tp30) cc_final: 0.7219 (tp30) REVERT: F 61 ASP cc_start: 0.7060 (t0) cc_final: 0.6722 (t0) REVERT: F 63 ASN cc_start: 0.8399 (m-40) cc_final: 0.8136 (m110) REVERT: F 68 ASP cc_start: 0.7341 (t0) cc_final: 0.7033 (t0) REVERT: F 172 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7096 (mp0) REVERT: F 230 LYS cc_start: 0.8606 (mttt) cc_final: 0.8261 (mttt) REVERT: F 237 ILE cc_start: 0.7877 (pt) cc_final: 0.7411 (pp) REVERT: F 247 ASN cc_start: 0.8259 (m-40) cc_final: 0.7840 (t0) REVERT: F 266 LYS cc_start: 0.7554 (mmmm) cc_final: 0.6991 (mmmm) REVERT: F 322 MET cc_start: 0.5604 (tpp) cc_final: 0.5288 (tpp) REVERT: G 94 ASP cc_start: 0.8126 (m-30) cc_final: 0.7899 (m-30) REVERT: G 174 SER cc_start: 0.8596 (m) cc_final: 0.8378 (t) REVERT: G 267 ASP cc_start: 0.8243 (m-30) cc_final: 0.8038 (m-30) REVERT: G 273 PHE cc_start: 0.8262 (p90) cc_final: 0.7954 (p90) REVERT: G 288 ILE cc_start: 0.7892 (mm) cc_final: 0.7482 (mm) REVERT: G 307 LYS cc_start: 0.8653 (mtpp) cc_final: 0.8402 (mttp) REVERT: H 105 SER cc_start: 0.8661 (t) cc_final: 0.8319 (t) REVERT: H 151 ASN cc_start: 0.8460 (m-40) cc_final: 0.8187 (m110) REVERT: H 161 ILE cc_start: 0.8238 (mt) cc_final: 0.7960 (tp) REVERT: H 216 LYS cc_start: 0.8284 (ttpp) cc_final: 0.7844 (ttpp) REVERT: H 217 ILE cc_start: 0.8819 (pt) cc_final: 0.8582 (pp) REVERT: H 226 SER cc_start: 0.8466 (p) cc_final: 0.8167 (m) outliers start: 92 outliers final: 47 residues processed: 720 average time/residue: 1.4301 time to fit residues: 1166.8460 Evaluate side-chains 716 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 664 time to evaluate : 2.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 239 LYS Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain D residue 15 ARG Chi-restraints excluded: chain D residue 129 ASP Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain E residue 89 LYS Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain F residue 229 ASP Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 320 MET Chi-restraints excluded: chain G residue 18 ASN Chi-restraints excluded: chain G residue 34 GLN Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 62 MET Chi-restraints excluded: chain G residue 68 GLU Chi-restraints excluded: chain G residue 184 GLU Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 286 ILE Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 167 LYS Chi-restraints excluded: chain H residue 222 GLU Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain H residue 256 ASN Chi-restraints excluded: chain H residue 300 LEU Chi-restraints excluded: chain M residue 58 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 126 optimal weight: 3.9990 chunk 146 optimal weight: 0.1980 chunk 247 optimal weight: 3.9990 chunk 184 optimal weight: 0.6980 chunk 166 optimal weight: 4.9990 chunk 221 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 198 optimal weight: 2.9990 chunk 260 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 ASN B 77 GLN B 80 GLN ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 ASN D 252 GLN E 43 ASN ** E 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 HIS F 51 ASN F 82 ASN G 186 ASN H 178 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.119068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.104887 restraints weight = 33118.233| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.78 r_work: 0.3277 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.127 23272 Z= 0.383 Angle : 0.628 10.518 31906 Z= 0.331 Chirality : 0.046 0.263 3585 Planarity : 0.005 0.050 3777 Dihedral : 17.975 175.553 4081 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.84 % Favored : 94.08 % Rotamer: Outliers : 4.68 % Allowed : 20.61 % Favored : 74.71 % 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: -1.40 (0.16), residues: 2567 helix: 0.20 (0.20), residues: 708 sheet: 0.54 (0.26), residues: 425 loop : -2.09 (0.14), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 33 HIS 0.008 0.002 HIS B 317 PHE 0.028 0.002 PHE H 37 TYR 0.022 0.002 TYR A 271 ARG 0.009 0.001 ARG E 162 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5134 Ramachandran restraints generated. 2567 Oldfield, 0 Emsley, 2567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5134 Ramachandran restraints generated. 2567 Oldfield, 0 Emsley, 2567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 679 time to evaluate : 2.466 Fit side-chains revert: symmetry clash REVERT: A 23 ARG cc_start: 0.8474 (ttm110) cc_final: 0.8182 (mtm-85) REVERT: A 39 LYS cc_start: 0.8869 (ptpp) cc_final: 0.8595 (ptpp) REVERT: A 89 ASP cc_start: 0.8263 (p0) cc_final: 0.7980 (p0) REVERT: A 334 GLU cc_start: 0.7628 (mp0) cc_final: 0.7353 (mp0) REVERT: B 72 MET cc_start: 0.8057 (mmm) cc_final: 0.7767 (mmm) REVERT: B 83 THR cc_start: 0.8674 (p) cc_final: 0.8452 (m) REVERT: B 163 THR cc_start: 0.8855 (OUTLIER) cc_final: 0.8536 (p) REVERT: B 222 GLU cc_start: 0.8051 (tt0) cc_final: 0.7760 (tt0) REVERT: B 278 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7178 (mt-10) REVERT: B 280 TYR cc_start: 0.8348 (m-80) cc_final: 0.8145 (m-80) REVERT: B 331 LYS cc_start: 0.8646 (tptm) cc_final: 0.8397 (tptp) REVERT: C 17 GLU cc_start: 0.7804 (tt0) cc_final: 0.7540 (tt0) REVERT: C 52 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8084 (ptmt) REVERT: C 66 LYS cc_start: 0.8151 (mtpt) cc_final: 0.7893 (mtpp) REVERT: C 85 SER cc_start: 0.8446 (OUTLIER) cc_final: 0.8216 (p) REVERT: C 166 ASP cc_start: 0.7378 (t0) cc_final: 0.6993 (t0) REVERT: C 181 THR cc_start: 0.8767 (m) cc_final: 0.8524 (p) REVERT: C 183 VAL cc_start: 0.8891 (m) cc_final: 0.8690 (p) REVERT: C 239 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8257 (mtmm) REVERT: D 15 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.7373 (mtp-110) REVERT: D 92 ARG cc_start: 0.8247 (ttt90) cc_final: 0.8001 (ttt180) REVERT: D 148 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7694 (mt) REVERT: D 204 ARG cc_start: 0.8369 (mtp85) cc_final: 0.8066 (mtp180) REVERT: D 278 GLU cc_start: 0.7700 (mp0) cc_final: 0.7489 (mp0) REVERT: D 307 LYS cc_start: 0.8702 (mtpp) cc_final: 0.8496 (mttp) REVERT: D 309 GLU cc_start: 0.7899 (tt0) cc_final: 0.7658 (tt0) REVERT: E 173 ASP cc_start: 0.7114 (p0) cc_final: 0.6861 (p0) REVERT: E 209 ASP cc_start: 0.8150 (t0) cc_final: 0.7788 (t0) REVERT: E 231 ILE cc_start: 0.8566 (pp) cc_final: 0.8358 (mm) REVERT: F 45 GLU cc_start: 0.7790 (tp30) cc_final: 0.7239 (tp30) REVERT: F 61 ASP cc_start: 0.7163 (t0) cc_final: 0.6807 (t0) REVERT: F 63 ASN cc_start: 0.8454 (m-40) cc_final: 0.8031 (m110) REVERT: F 68 ASP cc_start: 0.7383 (t0) cc_final: 0.7073 (t0) REVERT: F 172 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7175 (mp0) REVERT: F 176 ARG cc_start: 0.7962 (mtt180) cc_final: 0.7667 (mtt180) REVERT: F 230 LYS cc_start: 0.8639 (mttt) cc_final: 0.8249 (mttt) REVERT: F 237 ILE cc_start: 0.7995 (pt) cc_final: 0.7521 (pp) REVERT: F 247 ASN cc_start: 0.8281 (m-40) cc_final: 0.7793 (t0) REVERT: F 266 LYS cc_start: 0.7553 (mmmm) cc_final: 0.6983 (mmmm) REVERT: F 322 MET cc_start: 0.5708 (tpp) cc_final: 0.5381 (tpp) REVERT: G 166 ASP cc_start: 0.7314 (t0) cc_final: 0.6979 (t0) REVERT: G 273 PHE cc_start: 0.8363 (p90) cc_final: 0.8110 (p90) REVERT: G 307 LYS cc_start: 0.8699 (mtpp) cc_final: 0.8440 (mttp) REVERT: H 105 SER cc_start: 0.8711 (t) cc_final: 0.8364 (t) REVERT: H 151 ASN cc_start: 0.8570 (m-40) cc_final: 0.8361 (m110) REVERT: H 156 GLU cc_start: 0.6748 (OUTLIER) cc_final: 0.6457 (pt0) REVERT: H 216 LYS cc_start: 0.8386 (ttpp) cc_final: 0.8090 (tttm) REVERT: H 217 ILE cc_start: 0.8840 (pt) cc_final: 0.8629 (pp) REVERT: H 226 SER cc_start: 0.8542 (p) cc_final: 0.8238 (m) outliers start: 104 outliers final: 50 residues processed: 725 average time/residue: 1.4394 time to fit residues: 1184.3726 Evaluate side-chains 715 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 657 time to evaluate : 3.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 239 LYS Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain D residue 15 ARG Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain E residue 89 LYS Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain F residue 137 SER Chi-restraints excluded: chain F residue 144 ASN Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain F residue 229 ASP Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 320 MET Chi-restraints excluded: chain G residue 18 ASN Chi-restraints excluded: chain G residue 62 MET Chi-restraints excluded: chain G residue 68 GLU Chi-restraints excluded: chain G residue 159 GLU Chi-restraints excluded: chain G residue 184 GLU Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 205 GLU Chi-restraints excluded: chain G residue 271 TYR Chi-restraints excluded: chain G residue 286 ILE Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 156 GLU Chi-restraints excluded: chain H residue 167 LYS Chi-restraints excluded: chain H residue 184 GLU Chi-restraints excluded: chain H residue 222 GLU Chi-restraints excluded: chain H residue 299 LYS Chi-restraints excluded: chain H residue 300 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 110 optimal weight: 0.6980 chunk 258 optimal weight: 0.7980 chunk 228 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 236 optimal weight: 1.9990 chunk 211 optimal weight: 0.0970 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 190 ASN A 208 ASN A 333 GLN B 77 GLN ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 ASN D 252 GLN E 43 ASN ** E 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 145 GLN G 34 GLN G 80 GLN G 186 ASN H 208 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.121546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.107267 restraints weight = 32814.234| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.77 r_work: 0.3317 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23272 Z= 0.187 Angle : 0.566 11.433 31906 Z= 0.296 Chirality : 0.042 0.270 3585 Planarity : 0.004 0.053 3777 Dihedral : 17.851 176.642 4081 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.60 % Favored : 95.33 % Rotamer: Outliers : 4.23 % Allowed : 21.83 % Favored : 73.94 % 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: -1.07 (0.16), residues: 2567 helix: 0.60 (0.20), residues: 707 sheet: 0.63 (0.26), residues: 449 loop : -1.96 (0.15), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 33 HIS 0.007 0.001 HIS B 317 PHE 0.020 0.001 PHE M 43 TYR 0.014 0.001 TYR D 271 ARG 0.009 0.000 ARG B 284 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5134 Ramachandran restraints generated. 2567 Oldfield, 0 Emsley, 2567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5134 Ramachandran restraints generated. 2567 Oldfield, 0 Emsley, 2567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 668 time to evaluate : 2.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ARG cc_start: 0.8443 (ttm110) cc_final: 0.8193 (mtm-85) REVERT: A 39 LYS cc_start: 0.8849 (ptpp) cc_final: 0.8597 (ptpp) REVERT: A 89 ASP cc_start: 0.8210 (p0) cc_final: 0.7951 (p0) REVERT: A 129 ASP cc_start: 0.7161 (t0) cc_final: 0.6924 (t0) REVERT: A 167 LYS cc_start: 0.8788 (ptmm) cc_final: 0.8579 (ptmt) REVERT: A 334 GLU cc_start: 0.7583 (mp0) cc_final: 0.7325 (mp0) REVERT: B 39 LYS cc_start: 0.8326 (mtpt) cc_final: 0.8033 (mtpp) REVERT: B 72 MET cc_start: 0.8060 (mmm) cc_final: 0.7793 (mmm) REVERT: B 83 THR cc_start: 0.8646 (p) cc_final: 0.8420 (m) REVERT: B 156 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.7006 (mp0) REVERT: B 163 THR cc_start: 0.8824 (OUTLIER) cc_final: 0.8508 (p) REVERT: B 278 GLU cc_start: 0.7460 (mt-10) cc_final: 0.7189 (mt-10) REVERT: B 331 LYS cc_start: 0.8659 (tptm) cc_final: 0.8406 (tptp) REVERT: C 17 GLU cc_start: 0.7759 (tt0) cc_final: 0.7527 (tt0) REVERT: C 39 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.8044 (mtmm) REVERT: C 52 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.8072 (ptmt) REVERT: C 66 LYS cc_start: 0.8133 (mtpt) cc_final: 0.7885 (mtpp) REVERT: C 72 MET cc_start: 0.7948 (mmm) cc_final: 0.7688 (mmm) REVERT: C 85 SER cc_start: 0.8494 (OUTLIER) cc_final: 0.8257 (p) REVERT: C 86 THR cc_start: 0.8571 (OUTLIER) cc_final: 0.8332 (p) REVERT: C 166 ASP cc_start: 0.7433 (t0) cc_final: 0.7082 (t0) REVERT: C 181 THR cc_start: 0.8729 (m) cc_final: 0.8500 (p) REVERT: C 183 VAL cc_start: 0.8884 (m) cc_final: 0.8682 (p) REVERT: C 239 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8266 (mtmm) REVERT: D 15 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.7314 (mtp-110) REVERT: D 70 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7112 (mt-10) REVERT: D 92 ARG cc_start: 0.8200 (ttt90) cc_final: 0.7983 (ttt180) REVERT: D 148 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7500 (mt) REVERT: D 204 ARG cc_start: 0.8308 (mtp85) cc_final: 0.8044 (mtp85) REVERT: D 309 GLU cc_start: 0.7878 (tt0) cc_final: 0.7614 (tt0) REVERT: E 209 ASP cc_start: 0.8121 (t0) cc_final: 0.7763 (t0) REVERT: F 45 GLU cc_start: 0.7742 (tp30) cc_final: 0.7165 (tp30) REVERT: F 61 ASP cc_start: 0.7097 (t0) cc_final: 0.6778 (t0) REVERT: F 63 ASN cc_start: 0.8413 (m-40) cc_final: 0.8065 (m110) REVERT: F 68 ASP cc_start: 0.7408 (t0) cc_final: 0.7114 (t0) REVERT: F 172 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7098 (mp0) REVERT: F 228 LEU cc_start: 0.8480 (mp) cc_final: 0.8278 (mp) REVERT: F 230 LYS cc_start: 0.8596 (mttt) cc_final: 0.8206 (mttt) REVERT: F 237 ILE cc_start: 0.7992 (pt) cc_final: 0.7508 (pp) REVERT: F 247 ASN cc_start: 0.8273 (m-40) cc_final: 0.7784 (t0) REVERT: F 266 LYS cc_start: 0.7583 (mmmm) cc_final: 0.7009 (mmmm) REVERT: F 322 MET cc_start: 0.5703 (tpp) cc_final: 0.5367 (tpp) REVERT: G 89 ASP cc_start: 0.8089 (p0) cc_final: 0.7754 (p0) REVERT: G 166 ASP cc_start: 0.7296 (t0) cc_final: 0.6962 (t0) REVERT: G 288 ILE cc_start: 0.7874 (mm) cc_final: 0.7669 (mm) REVERT: G 307 LYS cc_start: 0.8666 (mtpp) cc_final: 0.8429 (mttp) REVERT: H 105 SER cc_start: 0.8661 (t) cc_final: 0.8301 (t) REVERT: H 146 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7757 (ttp-170) REVERT: H 151 ASN cc_start: 0.8526 (m-40) cc_final: 0.8317 (m110) REVERT: H 152 ARG cc_start: 0.8344 (ttp80) cc_final: 0.8082 (mtm180) REVERT: H 217 ILE cc_start: 0.8810 (pt) cc_final: 0.8602 (pp) REVERT: H 223 VAL cc_start: 0.7074 (OUTLIER) cc_final: 0.6721 (m) REVERT: H 325 ARG cc_start: 0.8253 (tmm-80) cc_final: 0.8029 (tmm-80) REVERT: M 8 ILE cc_start: 0.7028 (OUTLIER) cc_final: 0.6411 (pp) outliers start: 94 outliers final: 49 residues processed: 703 average time/residue: 1.4697 time to fit residues: 1168.9355 Evaluate side-chains 724 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 662 time to evaluate : 2.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 239 LYS Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain D residue 15 ARG Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain E residue 89 LYS Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 137 SER Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain F residue 229 ASP Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 320 MET Chi-restraints excluded: chain G residue 18 ASN Chi-restraints excluded: chain G residue 62 MET Chi-restraints excluded: chain G residue 68 GLU Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 159 GLU Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 271 TYR Chi-restraints excluded: chain G residue 286 ILE Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain H residue 146 ARG Chi-restraints excluded: chain H residue 167 LYS Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 184 GLU Chi-restraints excluded: chain H residue 222 GLU Chi-restraints excluded: chain H residue 223 VAL Chi-restraints excluded: chain H residue 299 LYS Chi-restraints excluded: chain H residue 300 LEU Chi-restraints excluded: chain H residue 307 LYS Chi-restraints excluded: chain M residue 8 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 144 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 chunk 29 optimal weight: 0.0270 chunk 72 optimal weight: 0.6980 chunk 238 optimal weight: 1.9990 chunk 110 optimal weight: 0.0270 chunk 249 optimal weight: 7.9990 chunk 122 optimal weight: 0.9980 chunk 27 optimal weight: 0.0010 chunk 183 optimal weight: 2.9990 overall best weight: 0.3502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 208 ASN A 333 GLN B 80 GLN ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 GLN ** E 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 145 GLN G 186 ASN G 256 ASN H 208 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.123320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.109003 restraints weight = 32637.565| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.78 r_work: 0.3344 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 23272 Z= 0.157 Angle : 0.547 12.089 31906 Z= 0.285 Chirality : 0.041 0.273 3585 Planarity : 0.004 0.054 3777 Dihedral : 17.708 178.535 4081 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.60 % Favored : 95.33 % Rotamer: Outliers : 4.05 % Allowed : 22.77 % Favored : 73.18 % 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: -0.84 (0.16), residues: 2567 helix: 0.89 (0.20), residues: 702 sheet: 0.69 (0.26), residues: 450 loop : -1.84 (0.15), residues: 1415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 33 HIS 0.006 0.001 HIS B 317 PHE 0.021 0.001 PHE H 231 TYR 0.015 0.001 TYR C 114 ARG 0.009 0.000 ARG B 284 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5134 Ramachandran restraints generated. 2567 Oldfield, 0 Emsley, 2567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5134 Ramachandran restraints generated. 2567 Oldfield, 0 Emsley, 2567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 669 time to evaluate : 2.469 Fit side-chains revert: symmetry clash REVERT: A 23 ARG cc_start: 0.8405 (ttm110) cc_final: 0.8152 (mtm-85) REVERT: A 89 ASP cc_start: 0.8217 (p0) cc_final: 0.7962 (p0) REVERT: A 129 ASP cc_start: 0.7121 (t0) cc_final: 0.6877 (t0) REVERT: A 334 GLU cc_start: 0.7601 (mp0) cc_final: 0.7333 (mp0) REVERT: B 72 MET cc_start: 0.8108 (mmm) cc_final: 0.7818 (mmm) REVERT: B 83 THR cc_start: 0.8628 (p) cc_final: 0.8397 (m) REVERT: B 156 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6829 (mp0) REVERT: B 163 THR cc_start: 0.8793 (OUTLIER) cc_final: 0.8476 (p) REVERT: B 278 GLU cc_start: 0.7467 (mt-10) cc_final: 0.7202 (mt-10) REVERT: C 17 GLU cc_start: 0.7790 (tt0) cc_final: 0.7569 (tt0) REVERT: C 39 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.8025 (mtmm) REVERT: C 52 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.8002 (ptmt) REVERT: C 66 LYS cc_start: 0.8123 (mtpt) cc_final: 0.7888 (mtpp) REVERT: C 72 MET cc_start: 0.7980 (mmm) cc_final: 0.7729 (mmm) REVERT: C 86 THR cc_start: 0.8552 (OUTLIER) cc_final: 0.8328 (p) REVERT: C 166 ASP cc_start: 0.7394 (t0) cc_final: 0.7036 (t0) REVERT: C 181 THR cc_start: 0.8725 (m) cc_final: 0.8482 (p) REVERT: C 183 VAL cc_start: 0.8876 (m) cc_final: 0.8673 (p) REVERT: C 239 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8263 (mtmm) REVERT: C 267 ASP cc_start: 0.8642 (m-30) cc_final: 0.8391 (m-30) REVERT: D 15 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.7167 (mtp-110) REVERT: D 70 GLU cc_start: 0.7342 (mt-10) cc_final: 0.7045 (mt-10) REVERT: D 204 ARG cc_start: 0.8281 (mtp85) cc_final: 0.8026 (mtp85) REVERT: D 309 GLU cc_start: 0.7875 (tt0) cc_final: 0.7530 (tt0) REVERT: E 182 LEU cc_start: 0.8665 (mt) cc_final: 0.8462 (mm) REVERT: E 209 ASP cc_start: 0.8105 (t0) cc_final: 0.7730 (t0) REVERT: F 45 GLU cc_start: 0.7736 (tp30) cc_final: 0.7135 (tp30) REVERT: F 61 ASP cc_start: 0.7099 (t0) cc_final: 0.6724 (t0) REVERT: F 63 ASN cc_start: 0.8414 (m-40) cc_final: 0.7920 (m110) REVERT: F 68 ASP cc_start: 0.7316 (t0) cc_final: 0.6999 (t0) REVERT: F 172 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7106 (mp0) REVERT: F 210 LEU cc_start: 0.8269 (mt) cc_final: 0.8058 (mp) REVERT: F 228 LEU cc_start: 0.8479 (mp) cc_final: 0.8270 (mp) REVERT: F 237 ILE cc_start: 0.7964 (pt) cc_final: 0.7497 (pp) REVERT: F 247 ASN cc_start: 0.8274 (m-40) cc_final: 0.7808 (t0) REVERT: F 266 LYS cc_start: 0.7625 (mmmm) cc_final: 0.7057 (mmmm) REVERT: G 166 ASP cc_start: 0.7299 (t0) cc_final: 0.6976 (t0) REVERT: G 239 LYS cc_start: 0.8130 (mptt) cc_final: 0.7926 (mptt) REVERT: G 307 LYS cc_start: 0.8637 (mtpp) cc_final: 0.8397 (mttp) REVERT: H 43 PHE cc_start: 0.8195 (t80) cc_final: 0.7928 (t80) REVERT: H 105 SER cc_start: 0.8629 (t) cc_final: 0.8203 (t) REVERT: H 140 ASN cc_start: 0.8035 (m-40) cc_final: 0.7761 (m-40) REVERT: H 146 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7848 (ttp-170) REVERT: H 152 ARG cc_start: 0.8300 (ttp80) cc_final: 0.8035 (mtm180) REVERT: H 216 LYS cc_start: 0.8267 (ttpp) cc_final: 0.7992 (ttpp) REVERT: H 226 SER cc_start: 0.8405 (p) cc_final: 0.8170 (m) REVERT: H 325 ARG cc_start: 0.8229 (tmm-80) cc_final: 0.8011 (tmm-80) REVERT: M 8 ILE cc_start: 0.6928 (OUTLIER) cc_final: 0.6341 (pp) outliers start: 90 outliers final: 46 residues processed: 704 average time/residue: 1.4363 time to fit residues: 1146.0558 Evaluate side-chains 715 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 659 time to evaluate : 2.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 239 LYS Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain D residue 15 ARG Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain E residue 89 LYS Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain F residue 137 SER Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain F residue 229 ASP Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 320 MET Chi-restraints excluded: chain G residue 18 ASN Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 62 MET Chi-restraints excluded: chain G residue 68 GLU Chi-restraints excluded: chain G residue 159 GLU Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 184 GLU Chi-restraints excluded: chain G residue 271 TYR Chi-restraints excluded: chain G residue 286 ILE Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain H residue 146 ARG Chi-restraints excluded: chain H residue 156 GLU Chi-restraints excluded: chain H residue 167 LYS Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 184 GLU Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain H residue 299 LYS Chi-restraints excluded: chain H residue 307 LYS Chi-restraints excluded: chain M residue 8 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 31 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 256 optimal weight: 8.9990 chunk 88 optimal weight: 2.9990 chunk 185 optimal weight: 5.9990 chunk 234 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 258 optimal weight: 5.9990 chunk 223 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 208 ASN ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 GLN D 252 GLN E 20 ASN ** E 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 159 HIS F 270 ASN G 186 ASN H 151 ASN ** H 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 208 ASN ** H 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.117205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.103053 restraints weight = 33068.721| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.76 r_work: 0.3248 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.159 23272 Z= 0.540 Angle : 0.686 15.635 31906 Z= 0.354 Chirality : 0.050 0.278 3585 Planarity : 0.005 0.046 3777 Dihedral : 17.670 175.417 4081 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.16 % Favored : 93.77 % Rotamer: Outliers : 4.50 % Allowed : 23.36 % Favored : 72.14 % 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: -1.08 (0.16), residues: 2567 helix: 0.42 (0.20), residues: 711 sheet: 0.67 (0.26), residues: 439 loop : -1.86 (0.15), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 33 HIS 0.008 0.002 HIS B 317 PHE 0.025 0.002 PHE M 43 TYR 0.030 0.002 TYR G 271 ARG 0.010 0.001 ARG E 162 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5134 Ramachandran restraints generated. 2567 Oldfield, 0 Emsley, 2567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5134 Ramachandran restraints generated. 2567 Oldfield, 0 Emsley, 2567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 670 time to evaluate : 2.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 ARG cc_start: 0.8493 (ttm110) cc_final: 0.8140 (ttp-110) REVERT: A 129 ASP cc_start: 0.7443 (t0) cc_final: 0.7202 (t0) REVERT: A 334 GLU cc_start: 0.7611 (mp0) cc_final: 0.7367 (mp0) REVERT: B 72 MET cc_start: 0.8090 (mmm) cc_final: 0.7837 (mmm) REVERT: B 83 THR cc_start: 0.8675 (p) cc_final: 0.8439 (m) REVERT: B 156 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6849 (mp0) REVERT: B 163 THR cc_start: 0.8853 (OUTLIER) cc_final: 0.8522 (p) REVERT: B 244 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7934 (mt-10) REVERT: B 278 GLU cc_start: 0.7464 (mt-10) cc_final: 0.7182 (mt-10) REVERT: C 17 GLU cc_start: 0.7795 (tt0) cc_final: 0.7529 (tt0) REVERT: C 39 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.8076 (mtmm) REVERT: C 52 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8123 (ptmt) REVERT: C 72 MET cc_start: 0.8073 (mmm) cc_final: 0.7839 (mmm) REVERT: C 86 THR cc_start: 0.8639 (OUTLIER) cc_final: 0.8325 (p) REVERT: C 156 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7269 (mp0) REVERT: C 166 ASP cc_start: 0.7505 (t0) cc_final: 0.7135 (t0) REVERT: C 171 SER cc_start: 0.8755 (p) cc_final: 0.8508 (m) REVERT: C 181 THR cc_start: 0.8801 (m) cc_final: 0.8542 (p) REVERT: C 239 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8337 (mtmm) REVERT: D 69 LYS cc_start: 0.8802 (mtmt) cc_final: 0.8561 (mtmm) REVERT: D 70 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7188 (mt-10) REVERT: D 204 ARG cc_start: 0.8405 (mtp85) cc_final: 0.8110 (mtp85) REVERT: D 309 GLU cc_start: 0.7897 (tt0) cc_final: 0.7655 (tt0) REVERT: E 209 ASP cc_start: 0.8136 (t0) cc_final: 0.7767 (t0) REVERT: F 45 GLU cc_start: 0.7820 (tp30) cc_final: 0.7257 (tp30) REVERT: F 61 ASP cc_start: 0.7202 (t0) cc_final: 0.6899 (t0) REVERT: F 63 ASN cc_start: 0.8448 (m-40) cc_final: 0.8125 (m110) REVERT: F 68 ASP cc_start: 0.7330 (t0) cc_final: 0.7030 (t0) REVERT: F 79 ILE cc_start: 0.8265 (OUTLIER) cc_final: 0.8063 (mm) REVERT: F 172 GLU cc_start: 0.8095 (tp30) cc_final: 0.7815 (mm-30) REVERT: F 237 ILE cc_start: 0.8064 (pt) cc_final: 0.7604 (pp) REVERT: F 247 ASN cc_start: 0.8334 (m-40) cc_final: 0.8086 (t0) REVERT: F 266 LYS cc_start: 0.7578 (mmmm) cc_final: 0.7010 (mmmm) REVERT: F 290 ASP cc_start: 0.7616 (m-30) cc_final: 0.7268 (m-30) REVERT: G 166 ASP cc_start: 0.7380 (t0) cc_final: 0.7035 (t0) REVERT: G 239 LYS cc_start: 0.8210 (mptt) cc_final: 0.7732 (mptt) REVERT: G 307 LYS cc_start: 0.8685 (mtpp) cc_final: 0.8459 (mttp) REVERT: H 105 SER cc_start: 0.8721 (t) cc_final: 0.8381 (t) REVERT: H 146 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7812 (ttp-170) REVERT: H 216 LYS cc_start: 0.8373 (ttpp) cc_final: 0.8020 (ttpp) REVERT: H 226 SER cc_start: 0.8544 (p) cc_final: 0.8292 (m) REVERT: M 8 ILE cc_start: 0.7088 (OUTLIER) cc_final: 0.6467 (pp) REVERT: M 14 ILE cc_start: 0.7874 (OUTLIER) cc_final: 0.7607 (mp) REVERT: M 18 ILE cc_start: 0.8113 (tp) cc_final: 0.7912 (tt) outliers start: 100 outliers final: 54 residues processed: 717 average time/residue: 1.4230 time to fit residues: 1158.1946 Evaluate side-chains 711 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 646 time to evaluate : 2.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 239 LYS Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain D residue 15 ARG Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain E residue 89 LYS Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 137 SER Chi-restraints excluded: chain F residue 144 ASN Chi-restraints excluded: chain F residue 229 ASP Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 320 MET Chi-restraints excluded: chain G residue 62 MET Chi-restraints excluded: chain G residue 68 GLU Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 159 GLU Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 184 GLU Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 205 GLU Chi-restraints excluded: chain G residue 271 TYR Chi-restraints excluded: chain G residue 286 ILE Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 146 ARG Chi-restraints excluded: chain H residue 156 GLU Chi-restraints excluded: chain H residue 167 LYS Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 184 GLU Chi-restraints excluded: chain H residue 299 LYS Chi-restraints excluded: chain H residue 300 LEU Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 14 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 147 optimal weight: 0.9980 chunk 125 optimal weight: 0.9980 chunk 176 optimal weight: 0.5980 chunk 97 optimal weight: 0.8980 chunk 134 optimal weight: 0.9990 chunk 207 optimal weight: 0.9990 chunk 35 optimal weight: 0.3980 chunk 182 optimal weight: 0.8980 chunk 115 optimal weight: 0.7980 chunk 155 optimal weight: 0.9990 chunk 177 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A 140 ASN A 208 ASN B 308 ASN D 252 GLN E 14 ASN ** E 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 206 ASN F 270 ASN G 80 GLN H 18 ASN ** H 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 208 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.120551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.106225 restraints weight = 32731.806| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.76 r_work: 0.3297 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 23272 Z= 0.220 Angle : 0.594 14.147 31906 Z= 0.307 Chirality : 0.043 0.285 3585 Planarity : 0.005 0.057 3777 Dihedral : 17.659 176.186 4081 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.75 % Favored : 95.17 % Rotamer: Outliers : 3.29 % Allowed : 25.02 % Favored : 71.69 % 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: -0.91 (0.16), residues: 2567 helix: 0.65 (0.20), residues: 709 sheet: 0.62 (0.26), residues: 452 loop : -1.77 (0.15), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 33 HIS 0.007 0.001 HIS B 317 PHE 0.025 0.001 PHE B 43 TYR 0.016 0.001 TYR D 169 ARG 0.007 0.000 ARG E 162 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5134 Ramachandran restraints generated. 2567 Oldfield, 0 Emsley, 2567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5134 Ramachandran restraints generated. 2567 Oldfield, 0 Emsley, 2567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 655 time to evaluate : 2.715 Fit side-chains revert: symmetry clash REVERT: A 23 ARG cc_start: 0.8444 (ttm110) cc_final: 0.8218 (mtm-85) REVERT: A 129 ASP cc_start: 0.7318 (t0) cc_final: 0.7070 (t0) REVERT: A 334 GLU cc_start: 0.7600 (mp0) cc_final: 0.7364 (mp0) REVERT: B 72 MET cc_start: 0.8089 (mmm) cc_final: 0.7815 (mmm) REVERT: B 83 THR cc_start: 0.8651 (p) cc_final: 0.8434 (m) REVERT: B 156 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6706 (mp0) REVERT: B 163 THR cc_start: 0.8799 (OUTLIER) cc_final: 0.8476 (p) REVERT: B 216 LYS cc_start: 0.8231 (tttp) cc_final: 0.7986 (tttt) REVERT: B 278 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7175 (mt-10) REVERT: C 17 GLU cc_start: 0.7704 (tt0) cc_final: 0.7462 (tt0) REVERT: C 52 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8115 (ptmt) REVERT: C 66 LYS cc_start: 0.8131 (mtpt) cc_final: 0.7883 (mtpp) REVERT: C 72 MET cc_start: 0.8004 (mmm) cc_final: 0.7769 (mmm) REVERT: C 81 SER cc_start: 0.8656 (t) cc_final: 0.8386 (m) REVERT: C 86 THR cc_start: 0.8571 (OUTLIER) cc_final: 0.8311 (p) REVERT: C 156 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7151 (mp0) REVERT: C 166 ASP cc_start: 0.7512 (t0) cc_final: 0.7134 (t0) REVERT: C 171 SER cc_start: 0.8741 (p) cc_final: 0.8482 (m) REVERT: C 181 THR cc_start: 0.8751 (m) cc_final: 0.8510 (p) REVERT: C 239 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8280 (mtmm) REVERT: C 267 ASP cc_start: 0.8649 (m-30) cc_final: 0.8398 (m-30) REVERT: D 69 LYS cc_start: 0.8783 (mtmt) cc_final: 0.8551 (mtmm) REVERT: D 70 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7166 (mt-10) REVERT: D 204 ARG cc_start: 0.8322 (mtp85) cc_final: 0.8014 (mtp85) REVERT: D 303 ARG cc_start: 0.8501 (mtm110) cc_final: 0.7940 (mtp-110) REVERT: D 309 GLU cc_start: 0.7907 (tt0) cc_final: 0.7581 (tt0) REVERT: E 102 ASP cc_start: 0.7595 (m-30) cc_final: 0.7311 (m-30) REVERT: E 182 LEU cc_start: 0.8690 (mt) cc_final: 0.8432 (mm) REVERT: E 209 ASP cc_start: 0.8123 (t0) cc_final: 0.7719 (t0) REVERT: F 45 GLU cc_start: 0.7726 (tp30) cc_final: 0.7160 (tp30) REVERT: F 61 ASP cc_start: 0.7178 (t0) cc_final: 0.6854 (t0) REVERT: F 63 ASN cc_start: 0.8378 (m-40) cc_final: 0.7979 (m110) REVERT: F 68 ASP cc_start: 0.7297 (t0) cc_final: 0.6992 (t0) REVERT: F 172 GLU cc_start: 0.8030 (tp30) cc_final: 0.7701 (mm-30) REVERT: F 210 LEU cc_start: 0.8430 (mt) cc_final: 0.8209 (mp) REVERT: F 237 ILE cc_start: 0.8056 (pt) cc_final: 0.7596 (pp) REVERT: F 247 ASN cc_start: 0.8308 (m-40) cc_final: 0.7772 (t0) REVERT: F 266 LYS cc_start: 0.7636 (mmmm) cc_final: 0.7050 (mmmm) REVERT: F 290 ASP cc_start: 0.7628 (m-30) cc_final: 0.7287 (m-30) REVERT: F 306 ILE cc_start: 0.7799 (mt) cc_final: 0.7537 (mp) REVERT: G 166 ASP cc_start: 0.7337 (t0) cc_final: 0.7001 (t0) REVERT: G 239 LYS cc_start: 0.8204 (mptt) cc_final: 0.7780 (mptt) REVERT: G 307 LYS cc_start: 0.8642 (mtpp) cc_final: 0.8416 (mttp) REVERT: H 102 VAL cc_start: 0.8559 (t) cc_final: 0.8342 (p) REVERT: H 105 SER cc_start: 0.8685 (t) cc_final: 0.8299 (t) REVERT: H 146 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7661 (ttp-170) REVERT: H 216 LYS cc_start: 0.8259 (ttpp) cc_final: 0.7888 (ttpp) REVERT: H 226 SER cc_start: 0.8509 (p) cc_final: 0.8248 (m) REVERT: H 260 THR cc_start: 0.8457 (m) cc_final: 0.8035 (p) REVERT: M 8 ILE cc_start: 0.6984 (OUTLIER) cc_final: 0.6391 (pp) REVERT: M 14 ILE cc_start: 0.7850 (OUTLIER) cc_final: 0.7602 (mp) REVERT: M 18 ILE cc_start: 0.7962 (tp) cc_final: 0.7747 (tt) outliers start: 73 outliers final: 48 residues processed: 689 average time/residue: 1.4795 time to fit residues: 1153.6879 Evaluate side-chains 712 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 655 time to evaluate : 2.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 239 LYS Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain D residue 15 ARG Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain F residue 137 SER Chi-restraints excluded: chain F residue 229 ASP Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 320 MET Chi-restraints excluded: chain G residue 18 ASN Chi-restraints excluded: chain G residue 62 MET Chi-restraints excluded: chain G residue 68 GLU Chi-restraints excluded: chain G residue 159 GLU Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 184 GLU Chi-restraints excluded: chain G residue 205 GLU Chi-restraints excluded: chain G residue 271 TYR Chi-restraints excluded: chain G residue 286 ILE Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain H residue 146 ARG Chi-restraints excluded: chain H residue 167 LYS Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 184 GLU Chi-restraints excluded: chain H residue 227 GLN Chi-restraints excluded: chain H residue 299 LYS Chi-restraints excluded: chain H residue 300 LEU Chi-restraints excluded: chain H residue 307 LYS Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 14 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 1.9990 chunk 259 optimal weight: 0.5980 chunk 119 optimal weight: 2.9990 chunk 159 optimal weight: 0.0670 chunk 186 optimal weight: 0.3980 chunk 257 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 131 optimal weight: 0.9980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 208 ASN B 80 GLN D 252 GLN E 14 ASN E 94 HIS ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 145 GLN G 80 GLN H 140 ASN H 208 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.121929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.107526 restraints weight = 32745.309| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.78 r_work: 0.3322 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23272 Z= 0.187 Angle : 0.582 15.873 31906 Z= 0.298 Chirality : 0.042 0.232 3585 Planarity : 0.004 0.056 3777 Dihedral : 17.624 177.338 4081 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.91 % Favored : 95.01 % Rotamer: Outliers : 3.06 % Allowed : 25.83 % Favored : 71.11 % 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: -0.77 (0.16), residues: 2567 helix: 0.78 (0.20), residues: 713 sheet: 0.65 (0.25), residues: 469 loop : -1.71 (0.15), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 33 HIS 0.006 0.001 HIS B 317 PHE 0.020 0.001 PHE M 43 TYR 0.013 0.001 TYR G 271 ARG 0.008 0.000 ARG E 162 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5134 Ramachandran restraints generated. 2567 Oldfield, 0 Emsley, 2567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5134 Ramachandran restraints generated. 2567 Oldfield, 0 Emsley, 2567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 642 time to evaluate : 2.492 Fit side-chains revert: symmetry clash REVERT: A 23 ARG cc_start: 0.8426 (ttm110) cc_final: 0.8195 (mtm-85) REVERT: A 129 ASP cc_start: 0.7250 (t0) cc_final: 0.7016 (t0) REVERT: A 334 GLU cc_start: 0.7618 (mp0) cc_final: 0.7379 (mp0) REVERT: B 72 MET cc_start: 0.8130 (mmm) cc_final: 0.7813 (mmm) REVERT: B 83 THR cc_start: 0.8660 (p) cc_final: 0.8427 (m) REVERT: B 156 GLU cc_start: 0.7069 (OUTLIER) cc_final: 0.6663 (mp0) REVERT: B 163 THR cc_start: 0.8783 (OUTLIER) cc_final: 0.8449 (p) REVERT: B 216 LYS cc_start: 0.8204 (tttp) cc_final: 0.7939 (tttt) REVERT: B 278 GLU cc_start: 0.7433 (mt-10) cc_final: 0.7154 (mt-10) REVERT: C 17 GLU cc_start: 0.7750 (tt0) cc_final: 0.7523 (tt0) REVERT: C 52 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.8047 (ptmt) REVERT: C 66 LYS cc_start: 0.8141 (mtpt) cc_final: 0.7772 (ttmm) REVERT: C 72 MET cc_start: 0.8030 (mmm) cc_final: 0.7779 (mmm) REVERT: C 81 SER cc_start: 0.8660 (t) cc_final: 0.8402 (m) REVERT: C 86 THR cc_start: 0.8612 (m) cc_final: 0.8342 (p) REVERT: C 156 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7179 (mp0) REVERT: C 166 ASP cc_start: 0.7472 (t0) cc_final: 0.7115 (t0) REVERT: C 171 SER cc_start: 0.8732 (p) cc_final: 0.8478 (m) REVERT: C 181 THR cc_start: 0.8726 (m) cc_final: 0.8481 (p) REVERT: C 229 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.7953 (ttp) REVERT: C 239 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8294 (mtmm) REVERT: C 267 ASP cc_start: 0.8639 (m-30) cc_final: 0.8379 (m-30) REVERT: D 70 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7224 (mt-10) REVERT: D 204 ARG cc_start: 0.8307 (mtp85) cc_final: 0.7992 (mtp85) REVERT: D 303 ARG cc_start: 0.8490 (mtm110) cc_final: 0.7928 (mtp-110) REVERT: D 309 GLU cc_start: 0.7910 (tt0) cc_final: 0.7589 (tt0) REVERT: E 102 ASP cc_start: 0.7527 (m-30) cc_final: 0.7271 (m-30) REVERT: E 182 LEU cc_start: 0.8677 (mt) cc_final: 0.8437 (mm) REVERT: E 209 ASP cc_start: 0.8127 (t0) cc_final: 0.7716 (t0) REVERT: F 45 GLU cc_start: 0.7659 (tp30) cc_final: 0.7102 (tp30) REVERT: F 61 ASP cc_start: 0.7195 (t0) cc_final: 0.6864 (t0) REVERT: F 68 ASP cc_start: 0.7287 (t0) cc_final: 0.6983 (t0) REVERT: F 172 GLU cc_start: 0.7960 (tp30) cc_final: 0.7657 (mm-30) REVERT: F 210 LEU cc_start: 0.8339 (mt) cc_final: 0.8128 (mp) REVERT: F 237 ILE cc_start: 0.8082 (pt) cc_final: 0.7650 (pp) REVERT: F 247 ASN cc_start: 0.8312 (m-40) cc_final: 0.8079 (t0) REVERT: F 266 LYS cc_start: 0.7700 (mmmm) cc_final: 0.7156 (mmmm) REVERT: F 290 ASP cc_start: 0.7606 (m-30) cc_final: 0.7245 (m-30) REVERT: F 306 ILE cc_start: 0.7803 (mt) cc_final: 0.7558 (mp) REVERT: F 322 MET cc_start: 0.5935 (tpp) cc_final: 0.5696 (tpp) REVERT: G 89 ASP cc_start: 0.8081 (p0) cc_final: 0.7718 (p0) REVERT: G 166 ASP cc_start: 0.7354 (t0) cc_final: 0.7026 (t0) REVERT: G 307 LYS cc_start: 0.8639 (mtpp) cc_final: 0.8417 (mttp) REVERT: H 102 VAL cc_start: 0.8534 (t) cc_final: 0.8321 (p) REVERT: H 105 SER cc_start: 0.8670 (t) cc_final: 0.8279 (t) REVERT: H 146 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7737 (ttp-170) REVERT: H 156 GLU cc_start: 0.6559 (OUTLIER) cc_final: 0.6054 (pt0) REVERT: H 216 LYS cc_start: 0.8127 (ttpp) cc_final: 0.7810 (ttpp) REVERT: H 226 SER cc_start: 0.8502 (p) cc_final: 0.8235 (m) REVERT: M 8 ILE cc_start: 0.6921 (OUTLIER) cc_final: 0.6429 (pp) REVERT: M 19 ILE cc_start: 0.7549 (mm) cc_final: 0.7325 (tt) REVERT: M 58 ILE cc_start: 0.7160 (tt) cc_final: 0.6889 (pt) outliers start: 68 outliers final: 43 residues processed: 671 average time/residue: 1.4552 time to fit residues: 1103.4865 Evaluate side-chains 696 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 644 time to evaluate : 2.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 239 LYS Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain F residue 229 ASP Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 320 MET Chi-restraints excluded: chain G residue 62 MET Chi-restraints excluded: chain G residue 68 GLU Chi-restraints excluded: chain G residue 159 GLU Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 205 GLU Chi-restraints excluded: chain G residue 271 TYR Chi-restraints excluded: chain G residue 286 ILE Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain H residue 146 ARG Chi-restraints excluded: chain H residue 156 GLU Chi-restraints excluded: chain H residue 167 LYS Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 184 GLU Chi-restraints excluded: chain H residue 227 GLN Chi-restraints excluded: chain H residue 299 LYS Chi-restraints excluded: chain H residue 300 LEU Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 14 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 161 optimal weight: 0.5980 chunk 173 optimal weight: 0.0970 chunk 47 optimal weight: 1.9990 chunk 238 optimal weight: 0.7980 chunk 54 optimal weight: 0.0980 chunk 15 optimal weight: 1.9990 chunk 149 optimal weight: 0.0970 chunk 133 optimal weight: 1.9990 chunk 247 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 206 optimal weight: 0.1980 overall best weight: 0.2176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 208 ASN B 308 ASN D 252 GLN D 256 ASN E 14 ASN E 104 ASN F 35 HIS F 47 ASN F 51 ASN F 82 ASN ** H 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 208 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.124613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.110162 restraints weight = 32807.953| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.77 r_work: 0.3357 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 23272 Z= 0.147 Angle : 0.570 15.174 31906 Z= 0.292 Chirality : 0.041 0.310 3585 Planarity : 0.005 0.057 3777 Dihedral : 17.604 179.987 4081 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.29 % Favored : 95.64 % Rotamer: Outliers : 2.61 % Allowed : 26.37 % Favored : 71.02 % 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: -0.60 (0.16), residues: 2567 helix: 0.94 (0.20), residues: 712 sheet: 0.82 (0.25), residues: 485 loop : -1.67 (0.15), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 149 HIS 0.005 0.001 HIS B 317 PHE 0.019 0.001 PHE A 273 TYR 0.012 0.001 TYR C 206 ARG 0.007 0.000 ARG E 162 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5134 Ramachandran restraints generated. 2567 Oldfield, 0 Emsley, 2567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5134 Ramachandran restraints generated. 2567 Oldfield, 0 Emsley, 2567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 723 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 665 time to evaluate : 2.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 ARG cc_start: 0.8405 (ttm110) cc_final: 0.8137 (ttm110) REVERT: A 39 LYS cc_start: 0.8739 (ptpp) cc_final: 0.8479 (ptmm) REVERT: A 129 ASP cc_start: 0.7246 (t0) cc_final: 0.6982 (t0) REVERT: A 167 LYS cc_start: 0.8814 (ptmm) cc_final: 0.8600 (ptmt) REVERT: A 301 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8302 (mm) REVERT: A 334 GLU cc_start: 0.7619 (mp0) cc_final: 0.7387 (mp0) REVERT: B 72 MET cc_start: 0.8147 (mmm) cc_final: 0.7871 (mmm) REVERT: B 83 THR cc_start: 0.8657 (p) cc_final: 0.8427 (m) REVERT: B 156 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.6556 (mp0) REVERT: B 163 THR cc_start: 0.8689 (OUTLIER) cc_final: 0.8374 (p) REVERT: B 216 LYS cc_start: 0.8189 (tttp) cc_final: 0.7916 (tttt) REVERT: B 278 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7306 (mt-10) REVERT: B 331 LYS cc_start: 0.8675 (tptp) cc_final: 0.8471 (tppt) REVERT: C 17 GLU cc_start: 0.7704 (tt0) cc_final: 0.7480 (tt0) REVERT: C 52 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.7940 (ptmm) REVERT: C 66 LYS cc_start: 0.8141 (mtpt) cc_final: 0.7878 (ttmm) REVERT: C 72 MET cc_start: 0.7964 (mmm) cc_final: 0.7741 (mmm) REVERT: C 81 SER cc_start: 0.8560 (t) cc_final: 0.8342 (m) REVERT: C 156 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7192 (mp0) REVERT: C 166 ASP cc_start: 0.7513 (t0) cc_final: 0.7152 (t0) REVERT: C 171 SER cc_start: 0.8764 (p) cc_final: 0.8520 (m) REVERT: C 181 THR cc_start: 0.8701 (m) cc_final: 0.8449 (p) REVERT: C 267 ASP cc_start: 0.8618 (m-30) cc_final: 0.8340 (m-30) REVERT: C 303 ARG cc_start: 0.8574 (ttp80) cc_final: 0.8157 (ttt90) REVERT: C 309 GLU cc_start: 0.7313 (mt-10) cc_final: 0.7090 (mt-10) REVERT: D 69 LYS cc_start: 0.8683 (mtmt) cc_final: 0.8470 (mtmm) REVERT: D 70 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7372 (mt-10) REVERT: D 73 ASP cc_start: 0.7265 (p0) cc_final: 0.6991 (p0) REVERT: D 204 ARG cc_start: 0.8197 (mtp85) cc_final: 0.7910 (mtp85) REVERT: D 278 GLU cc_start: 0.7730 (mp0) cc_final: 0.7450 (mp0) REVERT: D 309 GLU cc_start: 0.7956 (tt0) cc_final: 0.7676 (tt0) REVERT: E 102 ASP cc_start: 0.7444 (m-30) cc_final: 0.7165 (m-30) REVERT: E 182 LEU cc_start: 0.8663 (mt) cc_final: 0.8462 (mm) REVERT: E 209 ASP cc_start: 0.8056 (t0) cc_final: 0.7650 (t0) REVERT: F 45 GLU cc_start: 0.7535 (tp30) cc_final: 0.7008 (tp30) REVERT: F 61 ASP cc_start: 0.7158 (t0) cc_final: 0.6844 (t0) REVERT: F 68 ASP cc_start: 0.7245 (t0) cc_final: 0.6950 (t0) REVERT: F 172 GLU cc_start: 0.7963 (tp30) cc_final: 0.7718 (mm-30) REVERT: F 176 ARG cc_start: 0.8053 (mmm-85) cc_final: 0.7735 (mtt180) REVERT: F 228 LEU cc_start: 0.8452 (mp) cc_final: 0.8233 (mp) REVERT: F 237 ILE cc_start: 0.8117 (pt) cc_final: 0.7704 (pp) REVERT: F 247 ASN cc_start: 0.8323 (m-40) cc_final: 0.8096 (t0) REVERT: F 266 LYS cc_start: 0.7685 (mmmm) cc_final: 0.7184 (mmmm) REVERT: F 290 ASP cc_start: 0.7551 (m-30) cc_final: 0.7159 (m-30) REVERT: F 306 ILE cc_start: 0.7813 (mt) cc_final: 0.7574 (mp) REVERT: G 40 ARG cc_start: 0.8208 (ptt180) cc_final: 0.7994 (ptt180) REVERT: G 89 ASP cc_start: 0.8122 (p0) cc_final: 0.7732 (p0) REVERT: G 166 ASP cc_start: 0.7299 (t0) cc_final: 0.6969 (t0) REVERT: G 229 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.8002 (ttp) REVERT: G 307 LYS cc_start: 0.8611 (mtpp) cc_final: 0.8380 (mttp) REVERT: H 43 PHE cc_start: 0.8150 (t80) cc_final: 0.7834 (t80) REVERT: H 102 VAL cc_start: 0.8475 (t) cc_final: 0.8249 (p) REVERT: H 105 SER cc_start: 0.8586 (t) cc_final: 0.8175 (t) REVERT: H 226 SER cc_start: 0.8475 (p) cc_final: 0.8192 (m) REVERT: H 260 THR cc_start: 0.8263 (m) cc_final: 0.7979 (p) REVERT: H 273 PHE cc_start: 0.8048 (p90) cc_final: 0.7844 (p90) REVERT: M 8 ILE cc_start: 0.6814 (OUTLIER) cc_final: 0.6325 (pp) outliers start: 58 outliers final: 39 residues processed: 689 average time/residue: 1.4477 time to fit residues: 1133.6354 Evaluate side-chains 693 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 647 time to evaluate : 2.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 229 ASP Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 320 MET Chi-restraints excluded: chain G residue 18 ASN Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 68 GLU Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 184 GLU Chi-restraints excluded: chain G residue 229 MET Chi-restraints excluded: chain G residue 286 ILE Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain H residue 146 ARG Chi-restraints excluded: chain H residue 167 LYS Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 184 GLU Chi-restraints excluded: chain H residue 227 GLN Chi-restraints excluded: chain H residue 299 LYS Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 14 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 182 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 205 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 126 optimal weight: 5.9990 chunk 256 optimal weight: 5.9990 chunk 208 optimal weight: 0.5980 chunk 179 optimal weight: 7.9990 chunk 222 optimal weight: 2.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 208 ASN B 80 GLN B 308 ASN D 144 ASN E 104 ASN ** F 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.120448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.106090 restraints weight = 32518.952| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.75 r_work: 0.3289 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 23272 Z= 0.317 Angle : 0.615 14.173 31906 Z= 0.316 Chirality : 0.044 0.255 3585 Planarity : 0.005 0.052 3777 Dihedral : 17.554 175.851 4081 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.99 % Favored : 94.94 % Rotamer: Outliers : 2.75 % Allowed : 27.00 % Favored : 70.25 % 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: -0.72 (0.16), residues: 2567 helix: 0.79 (0.20), residues: 710 sheet: 0.63 (0.25), residues: 481 loop : -1.65 (0.15), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 149 HIS 0.007 0.001 HIS F 39 PHE 0.024 0.002 PHE M 43 TYR 0.021 0.001 TYR G 271 ARG 0.010 0.001 ARG E 162 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20824.60 seconds wall clock time: 368 minutes 30.35 seconds (22110.35 seconds total)