Starting phenix.real_space_refine on Fri Aug 7 15:43:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z0l_39707/08_2026/8z0l_39707_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z0l_39707/08_2026/8z0l_39707.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z0l_39707/08_2026/8z0l_39707.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z0l_39707/08_2026/8z0l_39707.map" model { file = "/net/cci-nas-00/data/ceres_data/8z0l_39707/08_2026/8z0l_39707_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z0l_39707/08_2026/8z0l_39707_neut.cif" } resolution = 2.57 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.039 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 97 5.49 5 S 110 5.16 5 C 14214 2.51 5 N 3812 2.21 5 O 4625 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22858 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2632 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 15, 'TRANS': 309} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2604 Classifications: {'peptide': 323} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 307} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 24 Chain: "C" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2576 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 15, 'TRANS': 304} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Chain: "D" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2581 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 15, 'TRANS': 305} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 1968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1968 Classifications: {'peptide': 255} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 246} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2422 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 16, 'TRANS': 305} Chain breaks: 3 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 2, 'HIS:plan': 3, 'GLU:plan': 10, 'ARG:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 103 Chain: "G" Number of atoms: 2430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2430 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 11, 'TRANS': 290} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 2339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2339 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 11, 'TRANS': 280} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "I" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 648 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "J" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 148 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Chain: "L" Number of atoms: 1249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1249 Classifications: {'RNA': 58} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 12, 'rna3p_pur': 21, 'rna3p_pyr': 12} Link IDs: {'rna2p': 25, 'rna3p': 32} Chain breaks: 1 Chain: "M" Number of atoms: 1261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1261 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 6, 'TRANS': 166} Chain breaks: 1 Unresolved non-hydrogen bonds: 150 Unresolved non-hydrogen angles: 176 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 2, 'HIS:plan': 5, 'TYR:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 57 Time building chain proxies: 4.58, per 1000 atoms: 0.20 Number of scatterers: 22858 At special positions: 0 Unit cell: (108.75, 149.25, 161.25, 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 110 16.00 P 97 15.00 O 4625 8.00 N 3812 7.00 C 14214 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: 1.73 Conformation dependent library (CDL) restraints added in 988.9 milliseconds 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5018 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 43 sheets defined 30.0% alpha, 24.3% beta 20 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 2.49 Creating SS restraints... Processing helix chain 'A' and resid 36 through 40 removed outlier: 3.636A pdb=" N ARG A 40 " --> pdb=" O PHE A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 68 removed outlier: 3.615A pdb=" N GLU A 68 " --> pdb=" O PRO A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 128 removed outlier: 3.777A pdb=" N ARG A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 144 removed outlier: 3.748A pdb=" N ALA A 135 " --> pdb=" O PHE A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 186 through 201 removed outlier: 3.702A pdb=" N GLN A 195 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 259 removed outlier: 3.751A pdb=" N ILE A 254 " --> pdb=" O HIS A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 305 removed outlier: 3.505A pdb=" N LEU A 300 " --> pdb=" O SER A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 326 Processing helix chain 'B' and resid 63 through 71 removed outlier: 3.706A pdb=" N GLU B 68 " --> pdb=" O PRO B 64 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS B 69 " --> pdb=" O ASP B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 129 removed outlier: 3.721A pdb=" N ARG B 115 " --> pdb=" O ASP B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 145 removed outlier: 3.579A pdb=" N ALA B 135 " --> pdb=" O PHE B 131 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA B 145 " --> pdb=" O ASN B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 202 removed outlier: 3.752A pdb=" N GLN B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 259 removed outlier: 3.509A pdb=" N ILE B 254 " --> pdb=" O HIS B 250 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA B 257 " --> pdb=" O LYS B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 302 removed outlier: 3.545A pdb=" N ASP B 302 " --> pdb=" O TYR B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 326 Processing helix chain 'C' and resid 36 through 40 removed outlier: 3.517A pdb=" N LYS C 39 " --> pdb=" O ASP C 36 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG C 40 " --> pdb=" O PHE C 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 36 through 40' Processing helix chain 'C' and resid 63 through 71 removed outlier: 3.731A pdb=" N LYS C 69 " --> pdb=" O ASP C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 129 removed outlier: 3.558A pdb=" N ARG C 115 " --> pdb=" O ASP C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 144 removed outlier: 3.729A pdb=" N ALA C 135 " --> pdb=" O PHE C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 202 removed outlier: 4.132A pdb=" N GLN C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 255 removed outlier: 3.649A pdb=" N ILE C 254 " --> pdb=" O HIS C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 305 Processing helix chain 'C' and resid 312 through 326 removed outlier: 3.646A pdb=" N TYR C 318 " --> pdb=" O GLU C 314 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA C 321 " --> pdb=" O HIS C 317 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG C 325 " --> pdb=" O ALA C 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 40 removed outlier: 4.032A pdb=" N ARG D 40 " --> pdb=" O PHE D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 70 removed outlier: 3.620A 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: 3.735A 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: 3.722A pdb=" N GLN D 195 " --> pdb=" O GLU D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 259 removed outlier: 3.701A pdb=" N ILE D 254 " --> pdb=" O HIS D 250 " (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: 3.864A pdb=" N PHE E 31 " --> pdb=" O ALA E 27 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA E 35 " --> pdb=" O PHE E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 126 removed outlier: 3.546A 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 'E' and resid 230 through 232 No H-bonds generated for 'chain 'E' and resid 230 through 232' Processing helix chain 'F' and resid 19 through 29 removed outlier: 3.540A pdb=" N PHE F 28 " --> pdb=" O ILE F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 93 Processing helix chain 'F' and resid 103 through 107 Processing helix chain 'F' and resid 112 through 123 removed outlier: 3.861A pdb=" N GLU F 117 " --> pdb=" O GLU F 113 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU F 120 " --> pdb=" O HIS F 116 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU F 121 " --> pdb=" O GLU F 117 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR F 122 " --> pdb=" O MET F 118 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP F 123 " --> pdb=" O GLU F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 129 Processing helix chain 'F' and resid 131 through 133 No H-bonds generated for 'chain 'F' and resid 131 through 133' Processing helix chain 'F' and resid 167 through 177 Processing helix chain 'F' and resid 191 through 199 removed outlier: 3.891A pdb=" N GLY F 199 " --> pdb=" O ALA F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 206 Processing helix chain 'F' and resid 223 through 228 Processing helix chain 'F' and resid 229 through 231 No H-bonds generated for 'chain 'F' and resid 229 through 231' Processing helix chain 'F' and resid 255 through 266 Processing helix chain 'F' and resid 273 through 277 removed outlier: 3.682A pdb=" N ARG F 277 " --> pdb=" O ARG F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 293 removed outlier: 3.530A pdb=" N LEU F 289 " --> pdb=" O VAL F 285 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TYR F 292 " --> pdb=" O PHE F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 320 removed outlier: 3.554A pdb=" N ASN F 319 " --> pdb=" O SER F 316 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET F 320 " --> pdb=" O ILE F 317 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 316 through 320' Processing helix chain 'F' and resid 326 through 339 removed outlier: 3.503A pdb=" N VAL F 331 " --> pdb=" O HIS F 327 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU F 333 " --> pdb=" O GLU F 329 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ALA F 336 " --> pdb=" O THR F 332 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 40 removed outlier: 3.847A pdb=" N ARG G 40 " --> pdb=" O PHE G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 104 No H-bonds generated for 'chain 'G' and resid 102 through 104' Processing helix chain 'G' and resid 111 through 129 Processing helix chain 'G' and resid 131 through 144 removed outlier: 3.843A pdb=" N ALA G 135 " --> pdb=" O PHE G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 186 through 202 removed outlier: 3.729A pdb=" N GLN G 195 " --> pdb=" O GLU G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 259 removed outlier: 3.571A pdb=" N ILE G 254 " --> pdb=" O HIS G 250 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA G 257 " --> pdb=" O LYS G 253 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU G 258 " --> pdb=" O ILE G 254 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 303 Processing helix chain 'G' and resid 312 through 324 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 201 removed outlier: 3.719A pdb=" N ASN H 190 " --> pdb=" O ASN H 186 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN H 195 " --> pdb=" O GLU H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 250 through 259 removed outlier: 3.603A pdb=" N ILE H 254 " --> pdb=" O HIS H 250 " (cutoff:3.500A) Processing helix chain 'H' and resid 296 through 306 removed outlier: 3.526A pdb=" N MET H 304 " --> pdb=" O LEU H 300 " (cutoff:3.500A) Processing helix chain 'H' and resid 312 through 326 removed outlier: 3.904A pdb=" N ALA H 321 " --> pdb=" O HIS H 317 " (cutoff:3.500A) Processing helix chain 'M' and resid 15 through 23 removed outlier: 3.582A pdb=" N ILE M 19 " --> pdb=" O SER M 15 " (cutoff:3.500A) Processing helix chain 'M' and resid 23 through 35 removed outlier: 3.664A pdb=" N VAL M 27 " --> pdb=" O ASP M 23 " (cutoff:3.500A) Processing helix chain 'M' and resid 68 through 71 Processing helix chain 'M' and resid 72 through 77 removed outlier: 3.605A pdb=" N LEU M 77 " --> pdb=" O LEU M 73 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 118 removed outlier: 3.785A pdb=" N ARG M 114 " --> pdb=" O THR M 110 " (cutoff:3.500A) Processing helix chain 'M' and resid 126 through 139 removed outlier: 3.534A pdb=" N HIS M 130 " --> pdb=" O PRO M 126 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 106 through 109 removed outlier: 6.687A pdb=" N SER A 20 " --> pdb=" O TYR A 107 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 27 Processing sheet with id=AA3, first strand: chain 'A' and resid 45 through 46 removed outlier: 3.544A pdb=" N LYS A 31 " --> pdb=" O ASP A 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 50 through 57 Processing sheet with id=AA5, first strand: chain 'A' and resid 242 through 243 Processing sheet with id=AA6, first strand: chain 'B' and resid 106 through 109 removed outlier: 3.505A pdb=" N SER B 108 " --> pdb=" O SER B 20 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 25 through 27 Processing sheet with id=AA8, first strand: chain 'B' and resid 45 through 46 Processing sheet with id=AA9, first strand: chain 'B' and resid 50 through 57 Processing sheet with id=AB1, first strand: chain 'B' and resid 242 through 243 Processing sheet with id=AB2, first strand: chain 'B' and resid 260 through 262 Processing sheet with id=AB3, first strand: chain 'C' and resid 106 through 108 removed outlier: 3.744A pdb=" N SER C 108 " --> pdb=" O SER C 20 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 25 through 27 Processing sheet with id=AB5, first strand: chain 'C' and resid 45 through 46 Processing sheet with id=AB6, first strand: chain 'C' and resid 50 through 57 Processing sheet with id=AB7, first strand: chain 'C' and resid 242 through 243 Processing sheet with id=AB8, first strand: chain 'D' and resid 19 through 21 Processing sheet with id=AB9, first strand: chain 'D' and resid 25 through 27 Processing sheet with id=AC1, first strand: chain 'D' and resid 45 through 46 Processing sheet with id=AC2, first strand: chain 'D' and resid 50 through 56 Processing sheet with id=AC3, first strand: chain 'D' and resid 242 through 243 Processing sheet with id=AC4, first strand: chain 'D' and resid 260 through 262 Processing sheet with id=AC5, first strand: chain 'D' and resid 282 through 283 removed outlier: 3.846A pdb=" N ALA D 283 " --> pdb=" O ILE D 288 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ILE D 288 " --> pdb=" O ALA D 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'E' and resid 137 through 138 removed outlier: 5.136A pdb=" N TYR E 4 " --> pdb=" O VAL E 111 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL E 111 " --> pdb=" O TYR E 4 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LEU E 6 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU E 109 " --> pdb=" O LEU E 6 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N GLU E 8 " --> pdb=" O PHE E 107 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N PHE E 107 " --> pdb=" O GLU E 8 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN E 14 " --> pdb=" O ILE E 101 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ILE E 101 " --> pdb=" O ASN E 14 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU E 60 " --> pdb=" O ASN E 104 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N SER E 106 " --> pdb=" O PHE E 58 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N PHE E 58 " --> pdb=" O SER E 106 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N LEU E 108 " --> pdb=" O LEU E 56 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N LEU E 56 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N GLU E 110 " --> pdb=" O VAL E 54 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL E 54 " --> pdb=" O GLU E 110 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N GLU E 112 " --> pdb=" O ASN E 52 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ASN E 52 " --> pdb=" O GLU E 112 " (cutoff:3.500A) removed outlier: 14.492A pdb=" N VAL E 54 " --> pdb=" O LEU E 161 " (cutoff:3.500A) removed outlier: 9.893A pdb=" N LEU E 161 " --> pdb=" O VAL E 54 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N LEU E 56 " --> pdb=" O LEU E 159 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N PHE E 216 " --> pdb=" O ALA E 197 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ALA E 197 " --> pdb=" O PHE E 216 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLU E 218 " --> pdb=" O PHE E 195 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N PHE E 195 " --> pdb=" O GLU E 218 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE E 220 " --> pdb=" O VAL E 193 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL E 193 " --> pdb=" O CYS E 251 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 143 through 146 removed outlier: 3.973A pdb=" N LYS E 143 " --> pdb=" O GLU E 8 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N TYR E 4 " --> pdb=" O VAL E 111 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL E 111 " --> pdb=" O TYR E 4 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LEU E 6 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU E 109 " --> pdb=" O LEU E 6 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N GLU E 8 " --> pdb=" O PHE E 107 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N PHE E 107 " --> pdb=" O GLU E 8 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN E 14 " --> pdb=" O ILE E 101 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ILE E 101 " --> pdb=" O ASN E 14 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU E 60 " --> pdb=" O ASN E 104 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N SER E 106 " --> pdb=" O PHE E 58 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N PHE E 58 " --> pdb=" O SER E 106 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N LEU E 108 " --> pdb=" O LEU E 56 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N LEU E 56 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N GLU E 110 " --> pdb=" O VAL E 54 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL E 54 " --> pdb=" O GLU E 110 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N GLU E 112 " --> pdb=" O ASN E 52 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ASN E 52 " --> pdb=" O GLU E 112 " (cutoff:3.500A) removed outlier: 14.492A pdb=" N VAL E 54 " --> pdb=" O LEU E 161 " (cutoff:3.500A) removed outlier: 9.893A pdb=" N LEU E 161 " --> pdb=" O VAL E 54 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N LEU E 56 " --> pdb=" O LEU E 159 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ASP E 213 " --> pdb=" O LEU F 160 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N SER F 162 " --> pdb=" O ASP E 213 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N CYS E 215 " --> pdb=" O SER F 162 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LYS F 148 " --> pdb=" O ILE F 163 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 22 through 24 removed outlier: 6.276A pdb=" N VAL E 23 " --> pdb=" O ALA F 214 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 65 through 67 Processing sheet with id=AD1, first strand: chain 'F' and resid 35 through 37 Processing sheet with id=AD2, first strand: chain 'F' and resid 39 through 40 Processing sheet with id=AD3, first strand: chain 'F' and resid 301 through 304 Processing sheet with id=AD4, first strand: chain 'G' and resid 106 through 109 removed outlier: 3.668A pdb=" N SER G 108 " --> pdb=" O SER G 20 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 25 through 27 Processing sheet with id=AD6, first strand: chain 'G' and resid 45 through 46 Processing sheet with id=AD7, first strand: chain 'G' and resid 50 through 53 Processing sheet with id=AD8, first strand: chain 'G' and resid 242 through 243 Processing sheet with id=AD9, first strand: chain 'G' and resid 260 through 262 Processing sheet with id=AE1, first strand: chain 'H' and resid 19 through 21 removed outlier: 6.391A pdb=" N SER H 20 " --> pdb=" O TYR H 107 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 25 through 27 removed outlier: 3.616A pdb=" N ASP H 94 " --> pdb=" O LYS H 31 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 25 through 27 removed outlier: 3.565A pdb=" N ILE H 93 " --> pdb=" O CYS H 213 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 242 through 243 Processing sheet with id=AE5, first strand: chain 'M' and resid 40 through 42 removed outlier: 3.603A pdb=" N ILE M 58 " --> pdb=" O LEU M 6 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL M 60 " --> pdb=" O GLN M 4 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS M 85 " --> pdb=" O ILE M 7 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 40 through 42 removed outlier: 3.603A pdb=" N ILE M 58 " --> pdb=" O LEU M 6 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL M 60 " --> pdb=" O GLN M 4 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 99 through 100 removed outlier: 3.583A pdb=" N ALA M 160 " --> pdb=" O LYS M 100 " (cutoff:3.500A) 853 hydrogen bonds defined for protein. 2328 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 47 hydrogen bonds 94 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 3.85 Time building geometry restraints manager: 2.39 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: 5297 1.33 - 1.45: 5517 1.45 - 1.57: 12365 1.57 - 1.69: 192 1.69 - 1.81: 173 Bond restraints: 23544 Sorted by residual: bond pdb=" C TYR E 249 " pdb=" N LEU E 250 " ideal model delta sigma weight residual 1.330 1.431 -0.101 1.41e-02 5.03e+03 5.09e+01 bond pdb=" C LYS D 203 " pdb=" N ARG D 204 " ideal model delta sigma weight residual 1.331 1.242 0.089 1.25e-02 6.40e+03 5.06e+01 bond pdb=" C LYS H 307 " pdb=" N ASN H 308 " ideal model delta sigma weight residual 1.330 1.253 0.077 1.37e-02 5.33e+03 3.15e+01 bond pdb=" C GLU H 272 " pdb=" N PHE H 273 " ideal model delta sigma weight residual 1.335 1.255 0.079 1.42e-02 4.96e+03 3.13e+01 bond pdb=" C ARG D 204 " pdb=" N GLU D 205 " ideal model delta sigma weight residual 1.333 1.256 0.077 1.47e-02 4.63e+03 2.74e+01 ... (remaining 23539 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 30838 2.46 - 4.93: 1247 4.93 - 7.39: 197 7.39 - 9.86: 52 9.86 - 12.32: 4 Bond angle restraints: 32338 Sorted by residual: angle pdb=" N GLY H 202 " pdb=" CA GLY H 202 " pdb=" C GLY H 202 " ideal model delta sigma weight residual 113.58 123.03 -9.45 1.07e+00 8.73e-01 7.79e+01 angle pdb=" N GLU M 22 " pdb=" CA GLU M 22 " pdb=" C GLU M 22 " ideal model delta sigma weight residual 110.97 119.56 -8.59 1.09e+00 8.42e-01 6.21e+01 angle pdb=" N ILE E 231 " pdb=" CA ILE E 231 " pdb=" C ILE E 231 " ideal model delta sigma weight residual 112.43 105.72 6.71 9.20e-01 1.18e+00 5.33e+01 angle pdb=" N THR G 270 " pdb=" CA THR G 270 " pdb=" C THR G 270 " ideal model delta sigma weight residual 110.50 100.24 10.26 1.41e+00 5.03e-01 5.30e+01 angle pdb=" N GLU M 79 " pdb=" CA GLU M 79 " pdb=" C GLU M 79 " ideal model delta sigma weight residual 111.34 101.20 10.14 1.49e+00 4.50e-01 4.63e+01 ... (remaining 32333 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.66: 13550 35.66 - 71.33: 548 71.33 - 106.99: 36 106.99 - 142.66: 6 142.66 - 178.32: 11 Dihedral angle restraints: 14151 sinusoidal: 6392 harmonic: 7759 Sorted by residual: dihedral pdb=" O4' U L 21 " pdb=" C1' U L 21 " pdb=" N1 U L 21 " pdb=" C2 U L 21 " ideal model delta sinusoidal sigma weight residual -160.00 -28.08 -131.92 1 1.50e+01 4.44e-03 7.12e+01 dihedral pdb=" O4' C L 34 " pdb=" C1' C L 34 " pdb=" N1 C L 34 " pdb=" C2 C L 34 " ideal model delta sinusoidal sigma weight residual -128.00 50.12 -178.12 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C L 52 " pdb=" C1' C L 52 " pdb=" N1 C L 52 " pdb=" C2 C L 52 " ideal model delta sinusoidal sigma weight residual -128.00 50.10 -178.10 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 14148 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.150: 3531 0.150 - 0.300: 113 0.300 - 0.450: 2 0.450 - 0.600: 0 0.600 - 0.750: 2 Chirality restraints: 3648 Sorted by residual: chirality pdb=" CB ILE M 57 " pdb=" CA ILE M 57 " pdb=" CG1 ILE M 57 " pdb=" CG2 ILE M 57 " both_signs ideal model delta sigma weight residual False 2.64 1.90 0.75 2.00e-01 2.50e+01 1.40e+01 chirality pdb=" CB VAL F 93 " pdb=" CA VAL F 93 " pdb=" CG1 VAL F 93 " pdb=" CG2 VAL F 93 " both_signs ideal model delta sigma weight residual False -2.63 -1.96 -0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" CG LEU F 202 " pdb=" CB LEU F 202 " pdb=" CD1 LEU F 202 " pdb=" CD2 LEU F 202 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.09e+00 ... (remaining 3645 not shown) Planarity restraints: 3820 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE E 231 " -0.023 2.00e-02 2.50e+03 4.52e-02 2.04e+01 pdb=" C ILE E 231 " 0.078 2.00e-02 2.50e+03 pdb=" O ILE E 231 " -0.030 2.00e-02 2.50e+03 pdb=" N LEU E 232 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG H 291 " 0.069 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO H 292 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO H 292 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO H 292 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 75 " -0.065 5.00e-02 4.00e+02 9.82e-02 1.54e+01 pdb=" N PRO C 76 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO C 76 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO C 76 " -0.053 5.00e-02 4.00e+02 ... (remaining 3817 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 5838 2.80 - 3.32: 18135 3.32 - 3.85: 35988 3.85 - 4.37: 43373 4.37 - 4.90: 74172 Nonbonded interactions: 177506 Sorted by model distance: nonbonded pdb=" OD1 ASN E 11 " pdb=" ND2 ASN E 104 " model vdw 2.273 3.120 nonbonded pdb=" OG1 THR D 35 " pdb=" OG1 THR D 90 " model vdw 2.300 3.040 nonbonded pdb=" OG1 THR C 35 " pdb=" OG1 THR C 90 " model vdw 2.322 3.040 nonbonded pdb=" O GLU D 278 " pdb=" OH TYR D 318 " model vdw 2.323 3.040 nonbonded pdb=" O GLU A 278 " pdb=" OH TYR A 318 " model vdw 2.325 3.040 ... (remaining 177501 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 11 through 38 or (resid 39 and (name N or name CA or name \ C or name O or name CB )) or resid 40 through 51 or resid 79 through 174 or (res \ id 175 and (name N or name CA or name C or name O or name CB )) or resid 176 thr \ ough 202 or (resid 203 and (name N or name CA or name C or name O or name CB )) \ or resid 204 through 231 or resid 236 through 238 or (resid 239 and (name N or n \ ame CA or name C or name O or name CB )) or resid 240 through 283 or (resid 284 \ and (name N or name CA or name C or name O or name CB )) or resid 285 through 28 \ 7 or (resid 288 and (name N or name CA or name C or name O or name CB )) or resi \ d 289 through 302 or (resid 303 and (name N or name CA or name C or name O or na \ me CB )) or resid 304 through 306 or (resid 307 and (name N or name CA or name C \ or name O or name CB )) or resid 308 through 330 or (resid 331 through 332 and \ (name N or name CA or name C or name O or name CB )) or resid 333)) selection = (chain 'B' and ((resid 11 and (name N or name CA or name C or name O or name CB \ )) or resid 12 through 38 or (resid 39 and (name N or name CA or name C or name \ O or name CB )) or resid 40 through 51 or resid 79 through 174 or (resid 175 and \ (name N or name CA or name C or name O or name CB )) or resid 176 through 202 o \ r (resid 203 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 04 through 231 or resid 236 through 283 or (resid 284 and (name N or name CA or \ name C or name O or name CB )) or resid 285 through 287 or (resid 288 and (name \ N or name CA or name C or name O or name CB )) or resid 289 through 302 or (resi \ d 303 and (name N or name CA or name C or name O or name CB )) or resid 304 thro \ ugh 306 or (resid 307 and (name N or name CA or name C or name O or name CB )) o \ r resid 308 through 330 or (resid 331 through 332 and (name N or name CA or name \ C or name O or name CB )) or resid 333)) selection = (chain 'C' and ((resid 11 and (name N or name CA or name C or name O or name CB \ )) or resid 12 through 51 or resid 79 through 174 or (resid 175 and (name N or n \ ame CA or name C or name O or name CB )) or resid 176 through 202 or (resid 203 \ and (name N or name CA or name C or name O or name CB )) or resid 204 through 23 \ 1 or resid 236 through 283 or (resid 284 and (name N or name CA or name C or nam \ e O or name CB )) or resid 285 through 287 or (resid 288 and (name N or name CA \ or name C or name O or name CB )) or resid 289 through 302 or (resid 303 and (na \ me N or name CA or name C or name O or name CB )) or resid 304 through 306 or (r \ esid 307 and (name N or name CA or name C or name O or name CB )) or resid 308 t \ hrough 330 or (resid 331 through 332 and (name N or name CA or name C or name O \ or name CB )) or resid 333)) selection = (chain 'D' and ((resid 11 and (name N or name CA or name C or name O or name CB \ )) or resid 12 through 51 or resid 79 through 174 or (resid 175 and (name N or n \ ame CA or name C or name O or name CB )) or resid 176 through 202 or (resid 203 \ and (name N or name CA or name C or name O or name CB )) or resid 204 through 23 \ 1 or resid 236 through 238 or (resid 239 and (name N or name CA or name C or nam \ e O or name CB )) or resid 240 through 283 or (resid 284 and (name N or name CA \ or name C or name O or name CB )) or resid 285 through 287 or (resid 288 and (na \ me N or name CA or name C or name O or name CB )) or resid 289 through 302 or (r \ esid 303 and (name N or name CA or name C or name O or name CB )) or resid 304 t \ hrough 330 or (resid 331 through 332 and (name N or name CA or name C or name O \ or name CB )) or resid 333)) selection = (chain 'G' and ((resid 11 and (name N or name CA or name C or name O or name CB \ )) or resid 12 through 38 or (resid 39 and (name N or name CA or name C or name \ O or name CB )) or resid 40 through 51 or resid 79 through 174 or (resid 175 and \ (name N or name CA or name C or name O or name CB )) or resid 176 through 202 o \ r (resid 203 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 04 through 231 or resid 236 through 287 or (resid 288 and (name N or name CA or \ name C or name O or name CB )) or resid 289 through 302 or (resid 303 and (name \ N or name CA or name C or name O or name CB )) or resid 304 through 306 or (resi \ d 307 and (name N or name CA or name C or name O or name CB )) or resid 308 thro \ ugh 331 or (resid 332 and (name N or name CA or name C or name O or name CB )) o \ r resid 333)) selection = (chain 'H' and ((resid 11 and (name N or name CA or name C or name O or name CB \ )) or resid 12 through 306 or (resid 307 and (name N or name CA or name C or nam \ e O or name CB )) or resid 308 through 333)) } 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: 2.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 21.310 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 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 0.101 23544 Z= 0.475 Angle : 1.142 12.323 32338 Z= 0.714 Chirality : 0.066 0.750 3648 Planarity : 0.009 0.103 3820 Dihedral : 18.583 178.321 9133 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.17 % Favored : 93.53 % Rotamer: Outliers : 1.08 % Allowed : 15.70 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.14), residues: 2595 helix: -1.97 (0.15), residues: 721 sheet: 0.91 (0.26), residues: 398 loop : -2.94 (0.12), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG H 40 TYR 0.038 0.003 TYR B 138 PHE 0.047 0.003 PHE D 43 TRP 0.026 0.002 TRP A 149 HIS 0.010 0.002 HIS H 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00736 / 0.47 (23544) covalent geometry : angle 1.14239 / 0.71 (32338) hydrogen bonds : bond 0.23195 / 15.26 ( 796) hydrogen bonds : angle 7.63507 / 5.25 ( 2422) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 686 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8343 (mtmm) cc_final: 0.8120 (mtpp) REVERT: A 70 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7949 (mt-10) REVERT: A 123 ASP cc_start: 0.7956 (m-30) cc_final: 0.7726 (m-30) REVERT: A 267 ASP cc_start: 0.7785 (t0) cc_final: 0.7427 (t0) REVERT: B 242 LYS cc_start: 0.8593 (mtpm) cc_final: 0.8373 (mtpm) REVERT: B 267 ASP cc_start: 0.7656 (t0) cc_final: 0.7072 (t0) REVERT: C 89 ASP cc_start: 0.8156 (p0) cc_final: 0.7930 (p0) REVERT: C 244 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7692 (mt-10) REVERT: C 314 GLU cc_start: 0.7870 (mp0) cc_final: 0.7444 (mp0) REVERT: D 61 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7506 (mt-10) REVERT: D 206 TYR cc_start: 0.8172 (p90) cc_final: 0.7731 (p90) REVERT: F 57 ILE cc_start: 0.8672 (pt) cc_final: 0.8350 (pp) REVERT: F 83 ASP cc_start: 0.7326 (t70) cc_final: 0.7034 (t0) REVERT: F 85 LYS cc_start: 0.7534 (mtmt) cc_final: 0.7171 (mtmm) REVERT: F 171 TYR cc_start: 0.8349 (t80) cc_final: 0.7898 (t80) REVERT: F 260 ILE cc_start: 0.8419 (mt) cc_final: 0.8195 (mp) REVERT: F 315 ASP cc_start: 0.7923 (t0) cc_final: 0.7690 (t0) REVERT: H 37 PHE cc_start: 0.7823 (t80) cc_final: 0.7537 (t80) REVERT: H 43 PHE cc_start: 0.8754 (t80) cc_final: 0.8539 (t80) REVERT: H 186 ASN cc_start: 0.8361 (t0) cc_final: 0.7909 (t160) REVERT: H 273 PHE cc_start: 0.7982 (p90) cc_final: 0.7736 (p90) REVERT: M 1 MET cc_start: 0.6352 (mtm) cc_final: 0.5929 (pmm) REVERT: M 59 GLU cc_start: 0.7354 (mt-10) cc_final: 0.7020 (mt-10) REVERT: M 74 GLU cc_start: 0.7460 (tt0) cc_final: 0.7149 (tt0) REVERT: M 98 LEU cc_start: 0.7147 (mm) cc_final: 0.6831 (mm) REVERT: M 105 GLU cc_start: 0.7587 (tp30) cc_final: 0.7347 (tp30) REVERT: M 109 GLU cc_start: 0.7148 (pt0) cc_final: 0.6907 (pt0) outliers start: 24 outliers final: 6 residues processed: 695 average time/residue: 0.5839 time to fit residues: 463.2531 Evaluate side-chains 633 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 626 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain H residue 290 PHE Chi-restraints excluded: chain M residue 143 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.0770 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 0.0570 overall best weight: 1.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 HIS B 18 ASN ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN C 18 ASN C 317 HIS D 18 ASN D 140 ASN D 250 HIS ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 HIS ** F 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 159 HIS F 238 ASN F 270 ASN F 319 ASN G 18 ASN G 140 ASN H 80 GLN H 140 ASN H 190 ASN H 195 GLN M 53 HIS M 141 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.115678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.101294 restraints weight = 33489.841| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.60 r_work: 0.3343 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 23544 Z= 0.220 Angle : 0.701 7.798 32338 Z= 0.394 Chirality : 0.049 0.415 3648 Planarity : 0.006 0.066 3820 Dihedral : 19.938 178.317 4200 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.39 % Favored : 94.45 % Rotamer: Outliers : 4.00 % Allowed : 16.19 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.15), residues: 2595 helix: -0.40 (0.18), residues: 738 sheet: 1.25 (0.27), residues: 413 loop : -2.74 (0.12), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 162 TYR 0.024 0.002 TYR H 271 PHE 0.016 0.002 PHE F 151 TRP 0.026 0.002 TRP H 149 HIS 0.006 0.001 HIS E 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.22 (23544) covalent geometry : angle 0.70073 / 0.39 (32338) hydrogen bonds : bond 0.06690 / 4.51 ( 796) hydrogen bonds : angle 5.22950 / 3.61 ( 2422) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 629 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7901 (mt-10) REVERT: A 267 ASP cc_start: 0.7498 (t0) cc_final: 0.7292 (t0) REVERT: B 181 THR cc_start: 0.8788 (t) cc_final: 0.8553 (p) REVERT: B 267 ASP cc_start: 0.7568 (t0) cc_final: 0.7279 (t0) REVERT: C 12 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8620 (mt) REVERT: C 228 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7832 (mt-10) REVERT: C 244 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7991 (mt-10) REVERT: D 206 TYR cc_start: 0.8265 (p90) cc_final: 0.8055 (p90) REVERT: D 228 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7211 (mt-10) REVERT: F 57 ILE cc_start: 0.8638 (pt) cc_final: 0.8331 (pp) REVERT: F 171 TYR cc_start: 0.8410 (t80) cc_final: 0.8084 (t80) REVERT: F 247 ASN cc_start: 0.8377 (m-40) cc_final: 0.8151 (t0) REVERT: F 277 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7434 (mtp85) REVERT: F 315 ASP cc_start: 0.8063 (t0) cc_final: 0.7840 (t0) REVERT: H 37 PHE cc_start: 0.7813 (t80) cc_final: 0.7482 (t80) REVERT: H 186 ASN cc_start: 0.8160 (t0) cc_final: 0.7838 (t160) REVERT: H 258 LEU cc_start: 0.8923 (mt) cc_final: 0.8700 (mp) REVERT: M 1 MET cc_start: 0.6598 (OUTLIER) cc_final: 0.6386 (pmm) REVERT: M 59 GLU cc_start: 0.7265 (mt-10) cc_final: 0.7025 (mt-10) REVERT: M 74 GLU cc_start: 0.7659 (tt0) cc_final: 0.7363 (tt0) REVERT: M 98 LEU cc_start: 0.7246 (mm) cc_final: 0.6973 (mm) REVERT: M 105 GLU cc_start: 0.7442 (tp30) cc_final: 0.7237 (tp30) REVERT: M 175 LEU cc_start: 0.8137 (tp) cc_final: 0.7858 (mp) outliers start: 89 outliers final: 38 residues processed: 662 average time/residue: 0.5985 time to fit residues: 451.4981 Evaluate side-chains 641 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 598 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain C residue 307 LYS Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 277 ARG Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 272 GLU Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 267 ASP Chi-restraints excluded: chain H residue 290 PHE Chi-restraints excluded: chain H residue 294 THR Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 14 ILE Chi-restraints excluded: chain M residue 143 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 131 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 9 optimal weight: 0.0970 chunk 219 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 258 optimal weight: 6.9990 chunk 242 optimal weight: 0.5980 chunk 175 optimal weight: 0.5980 chunk 253 optimal weight: 5.9990 chunk 164 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 208 ASN B 26 ASN B 250 HIS B 308 ASN C 18 ASN D 140 ASN E 59 HIS F 82 ASN F 159 HIS F 270 ASN G 178 ASN G 252 GLN H 190 ASN H 195 GLN H 256 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.116802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.102320 restraints weight = 33729.087| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.61 r_work: 0.3359 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 23544 Z= 0.146 Angle : 0.598 7.613 32338 Z= 0.333 Chirality : 0.045 0.329 3648 Planarity : 0.005 0.052 3820 Dihedral : 19.712 177.669 4194 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.64 % Allowed : 18.08 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.15), residues: 2595 helix: 0.43 (0.19), residues: 738 sheet: 1.17 (0.26), residues: 458 loop : -2.52 (0.13), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 162 TYR 0.016 0.001 TYR F 292 PHE 0.022 0.001 PHE H 273 TRP 0.014 0.001 TRP H 149 HIS 0.005 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 (23544) covalent geometry : angle 0.59787 / 0.33 (32338) hydrogen bonds : bond 0.04959 / 3.31 ( 796) hydrogen bonds : angle 4.63681 / 3.22 ( 2422) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 634 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 ASP cc_start: 0.7493 (t0) cc_final: 0.7292 (t0) REVERT: B 267 ASP cc_start: 0.7569 (t0) cc_final: 0.7289 (t0) REVERT: C 12 LEU cc_start: 0.8802 (mp) cc_final: 0.8595 (mt) REVERT: C 57 SER cc_start: 0.8383 (t) cc_final: 0.8154 (p) REVERT: C 228 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7888 (mt-10) REVERT: C 244 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7979 (mt-10) REVERT: F 57 ILE cc_start: 0.8622 (OUTLIER) cc_final: 0.8351 (pp) REVERT: F 61 ASP cc_start: 0.6992 (t0) cc_final: 0.6783 (t0) REVERT: F 171 TYR cc_start: 0.8382 (t80) cc_final: 0.8098 (t80) REVERT: F 315 ASP cc_start: 0.8025 (t0) cc_final: 0.7743 (t0) REVERT: G 320 MET cc_start: 0.8664 (mmt) cc_final: 0.8218 (mmt) REVERT: H 37 PHE cc_start: 0.7698 (t80) cc_final: 0.7452 (t80) REVERT: M 59 GLU cc_start: 0.7265 (mt-10) cc_final: 0.7033 (mt-10) REVERT: M 74 GLU cc_start: 0.7602 (tt0) cc_final: 0.7273 (tt0) REVERT: M 98 LEU cc_start: 0.7265 (mm) cc_final: 0.7052 (mm) REVERT: M 105 GLU cc_start: 0.7554 (tp30) cc_final: 0.7184 (tp30) REVERT: M 106 ASN cc_start: 0.8474 (m-40) cc_final: 0.7737 (m-40) REVERT: M 109 GLU cc_start: 0.7404 (pt0) cc_final: 0.7200 (pt0) outliers start: 81 outliers final: 36 residues processed: 661 average time/residue: 0.6469 time to fit residues: 486.6186 Evaluate side-chains 644 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 607 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 140 ASN Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 135 MET Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 149 TRP Chi-restraints excluded: chain H residue 185 ASP Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 252 GLN Chi-restraints excluded: chain H residue 290 PHE Chi-restraints excluded: chain H residue 294 THR Chi-restraints excluded: chain M residue 14 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 118 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 240 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 241 optimal weight: 0.6980 chunk 189 optimal weight: 10.0000 chunk 224 optimal weight: 2.9990 chunk 237 optimal weight: 4.9990 chunk 222 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 60 HIS A 208 ASN A 252 GLN B 18 ASN B 140 ASN B 308 ASN ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN D 140 ASN D 144 ASN E 52 ASN E 183 GLN F 82 ASN F 159 HIS ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 140 ASN G 178 ASN G 256 ASN H 18 ASN H 80 GLN ** H 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN H 195 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.111902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.097392 restraints weight = 33600.314| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.60 r_work: 0.3282 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 23544 Z= 0.347 Angle : 0.713 10.264 32338 Z= 0.393 Chirality : 0.052 0.420 3648 Planarity : 0.006 0.065 3820 Dihedral : 19.579 179.852 4188 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 4.14 % Allowed : 18.26 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.15), residues: 2595 helix: 0.50 (0.19), residues: 739 sheet: 1.05 (0.26), residues: 431 loop : -2.56 (0.13), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 150 TYR 0.028 0.002 TYR A 271 PHE 0.024 0.002 PHE H 273 TRP 0.017 0.002 TRP H 149 HIS 0.010 0.002 HIS E 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00843 / 0.35 (23544) covalent geometry : angle 0.71278 / 0.39 (32338) hydrogen bonds : bond 0.07277 / 4.91 ( 796) hydrogen bonds : angle 4.92692 / 3.39 ( 2422) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 616 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8095 (pt0) REVERT: A 267 ASP cc_start: 0.7541 (t0) cc_final: 0.7296 (t0) REVERT: B 229 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.7769 (ttp) REVERT: B 241 PHE cc_start: 0.8778 (t80) cc_final: 0.8441 (t80) REVERT: B 271 TYR cc_start: 0.8508 (OUTLIER) cc_final: 0.8281 (m-80) REVERT: C 57 SER cc_start: 0.8344 (t) cc_final: 0.8126 (p) REVERT: C 156 GLU cc_start: 0.7559 (mp0) cc_final: 0.7343 (mp0) REVERT: C 244 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8130 (mt-10) REVERT: D 103 LYS cc_start: 0.8832 (mtpp) cc_final: 0.8621 (mtpt) REVERT: F 17 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7742 (mm-30) REVERT: F 57 ILE cc_start: 0.8659 (pt) cc_final: 0.8367 (pp) REVERT: F 247 ASN cc_start: 0.8341 (m-40) cc_final: 0.8084 (t0) REVERT: F 277 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7347 (mtp85) REVERT: F 315 ASP cc_start: 0.7969 (t0) cc_final: 0.7730 (t0) REVERT: H 37 PHE cc_start: 0.7899 (t80) cc_final: 0.7584 (t80) REVERT: H 42 THR cc_start: 0.8594 (p) cc_final: 0.8297 (t) REVERT: H 221 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7823 (mmt) REVERT: M 74 GLU cc_start: 0.7616 (tt0) cc_final: 0.7304 (tt0) REVERT: M 105 GLU cc_start: 0.7636 (tp30) cc_final: 0.7353 (tp30) REVERT: M 106 ASN cc_start: 0.8606 (m-40) cc_final: 0.7976 (m-40) REVERT: M 109 GLU cc_start: 0.7554 (pt0) cc_final: 0.7335 (pt0) outliers start: 92 outliers final: 49 residues processed: 645 average time/residue: 0.5695 time to fit residues: 417.3308 Evaluate side-chains 659 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 605 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 52 ASN Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 277 ARG Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain G residue 29 GLU Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 140 ASN Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 185 ASP Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 221 MET Chi-restraints excluded: chain H residue 252 GLN Chi-restraints excluded: chain H residue 267 ASP Chi-restraints excluded: chain H residue 278 GLU Chi-restraints excluded: chain H residue 294 THR Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 14 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 85 optimal weight: 0.6980 chunk 242 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 189 optimal weight: 6.9990 chunk 95 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 167 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 195 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 208 ASN A 252 GLN B 18 ASN C 308 ASN D 144 ASN E 52 ASN E 183 GLN F 34 ASN F 51 ASN F 71 ASN F 149 GLN F 159 HIS G 140 ASN H 18 ASN H 80 GLN H 186 ASN H 190 ASN H 195 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.114845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.100289 restraints weight = 33359.395| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.60 r_work: 0.3326 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23544 Z= 0.140 Angle : 0.584 7.839 32338 Z= 0.327 Chirality : 0.045 0.339 3648 Planarity : 0.005 0.052 3820 Dihedral : 19.462 178.048 4186 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.37 % Allowed : 19.66 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.16), residues: 2595 helix: 0.95 (0.20), residues: 736 sheet: 1.02 (0.25), residues: 452 loop : -2.42 (0.13), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 162 TYR 0.021 0.001 TYR H 271 PHE 0.028 0.001 PHE H 43 TRP 0.012 0.001 TRP H 149 HIS 0.006 0.001 HIS E 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (23544) covalent geometry : angle 0.58394 / 0.33 (32338) hydrogen bonds : bond 0.04935 / 3.33 ( 796) hydrogen bonds : angle 4.52763 / 3.14 ( 2422) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 618 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 GLU cc_start: 0.7938 (tt0) cc_final: 0.7719 (tt0) REVERT: B 241 PHE cc_start: 0.8779 (t80) cc_final: 0.8515 (t80) REVERT: C 57 SER cc_start: 0.8311 (t) cc_final: 0.8110 (p) REVERT: C 156 GLU cc_start: 0.7552 (mp0) cc_final: 0.7333 (mp0) REVERT: C 244 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8115 (mt-10) REVERT: F 57 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8412 (pp) REVERT: F 61 ASP cc_start: 0.7030 (t0) cc_final: 0.6820 (t0) REVERT: F 83 ASP cc_start: 0.7641 (t0) cc_final: 0.7372 (t0) REVERT: F 247 ASN cc_start: 0.8336 (m-40) cc_final: 0.8083 (t0) REVERT: F 277 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7356 (mtp85) REVERT: F 315 ASP cc_start: 0.7938 (t0) cc_final: 0.7659 (t0) REVERT: H 37 PHE cc_start: 0.7745 (t80) cc_final: 0.7433 (t80) REVERT: H 265 TYR cc_start: 0.7450 (p90) cc_final: 0.7245 (p90) REVERT: H 315 ASP cc_start: 0.6891 (m-30) cc_final: 0.6672 (m-30) REVERT: M 74 GLU cc_start: 0.7571 (tt0) cc_final: 0.7245 (tt0) REVERT: M 105 GLU cc_start: 0.7617 (tp30) cc_final: 0.7293 (tp30) REVERT: M 106 ASN cc_start: 0.8588 (m-40) cc_final: 0.7926 (m-40) REVERT: M 109 GLU cc_start: 0.7511 (pt0) cc_final: 0.7282 (pt0) outliers start: 75 outliers final: 44 residues processed: 641 average time/residue: 0.6373 time to fit residues: 462.9229 Evaluate side-chains 654 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 608 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 242 LYS Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 135 MET Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 277 ARG Chi-restraints excluded: chain G residue 18 ASN Chi-restraints excluded: chain G residue 29 GLU Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 104 GLU Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 253 LYS Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 156 GLU Chi-restraints excluded: chain H residue 252 GLN Chi-restraints excluded: chain H residue 278 GLU Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 14 ILE Chi-restraints excluded: chain M residue 138 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 70 optimal weight: 2.9990 chunk 226 optimal weight: 0.0020 chunk 211 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 202 optimal weight: 0.0770 chunk 137 optimal weight: 5.9990 chunk 243 optimal weight: 1.9990 chunk 255 optimal weight: 0.2980 chunk 212 optimal weight: 4.9990 chunk 173 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 overall best weight: 0.8750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 208 ASN A 252 GLN B 18 ASN B 80 GLN B 140 ASN D 18 ASN D 144 ASN F 51 ASN F 71 ASN F 149 GLN F 159 HIS G 140 ASN G 178 ASN H 18 ASN H 186 ASN H 195 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.115307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.100729 restraints weight = 33765.743| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.61 r_work: 0.3334 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23544 Z= 0.143 Angle : 0.562 7.515 32338 Z= 0.314 Chirality : 0.044 0.304 3648 Planarity : 0.005 0.050 3820 Dihedral : 19.366 178.116 4186 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.97 % Allowed : 20.42 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.16), residues: 2595 helix: 1.16 (0.20), residues: 740 sheet: 1.07 (0.25), residues: 466 loop : -2.33 (0.13), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 162 TYR 0.015 0.001 TYR A 265 PHE 0.023 0.001 PHE H 273 TRP 0.013 0.001 TRP H 149 HIS 0.006 0.001 HIS E 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (23544) covalent geometry : angle 0.56200 / 0.31 (32338) hydrogen bonds : bond 0.04608 / 3.09 ( 796) hydrogen bonds : angle 4.32352 / 3.00 ( 2422) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 620 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 12 LEU cc_start: 0.8847 (mp) cc_final: 0.8633 (mt) REVERT: C 71 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.8197 (mm) REVERT: C 244 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8109 (mt-10) REVERT: F 57 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8393 (pp) REVERT: F 83 ASP cc_start: 0.7630 (t0) cc_final: 0.7379 (t0) REVERT: F 247 ASN cc_start: 0.8346 (m-40) cc_final: 0.8093 (t0) REVERT: F 315 ASP cc_start: 0.7961 (t0) cc_final: 0.7666 (t0) REVERT: F 320 MET cc_start: 0.8633 (mtp) cc_final: 0.8414 (mtp) REVERT: G 309 GLU cc_start: 0.7895 (tt0) cc_final: 0.7612 (mt-10) REVERT: H 37 PHE cc_start: 0.7719 (t80) cc_final: 0.7452 (t80) REVERT: H 315 ASP cc_start: 0.6875 (m-30) cc_final: 0.6614 (m-30) REVERT: M 74 GLU cc_start: 0.7545 (tt0) cc_final: 0.7213 (tt0) REVERT: M 105 GLU cc_start: 0.7645 (tp30) cc_final: 0.7395 (tp30) REVERT: M 106 ASN cc_start: 0.8599 (m-40) cc_final: 0.8082 (m110) REVERT: M 109 GLU cc_start: 0.7560 (pt0) cc_final: 0.7309 (pt0) outliers start: 66 outliers final: 43 residues processed: 638 average time/residue: 0.6330 time to fit residues: 457.9797 Evaluate side-chains 652 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 607 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 135 MET Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain G residue 18 ASN Chi-restraints excluded: chain G residue 29 GLU Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 253 LYS Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 156 GLU Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 252 GLN Chi-restraints excluded: chain H residue 267 ASP Chi-restraints excluded: chain H residue 278 GLU Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 90 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 144 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 188 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 211 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 208 ASN A 252 GLN B 18 ASN B 140 ASN ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN D 80 GLN D 144 ASN F 51 ASN F 71 ASN F 149 GLN F 159 HIS G 140 ASN H 18 ASN H 80 GLN H 186 ASN H 195 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.113457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.098925 restraints weight = 33595.505| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.60 r_work: 0.3303 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 23544 Z= 0.244 Angle : 0.620 7.951 32338 Z= 0.342 Chirality : 0.048 0.367 3648 Planarity : 0.005 0.053 3820 Dihedral : 19.340 178.909 4186 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.37 % Allowed : 19.97 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.16), residues: 2595 helix: 1.07 (0.20), residues: 740 sheet: 0.97 (0.25), residues: 463 loop : -2.32 (0.13), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 284 TYR 0.020 0.002 TYR H 271 PHE 0.043 0.002 PHE H 43 TRP 0.017 0.002 TRP H 149 HIS 0.006 0.002 HIS E 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00585 / 0.24 (23544) covalent geometry : angle 0.61976 / 0.34 (32338) hydrogen bonds : bond 0.05612 / 3.78 ( 796) hydrogen bonds : angle 4.47085 / 3.09 ( 2422) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 624 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7504 (mp0) REVERT: B 55 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8322 (tp) REVERT: B 229 MET cc_start: 0.8561 (OUTLIER) cc_final: 0.7695 (ttp) REVERT: C 71 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.8249 (mm) REVERT: D 284 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.7433 (ttm170) REVERT: F 57 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8430 (pp) REVERT: F 83 ASP cc_start: 0.7677 (t0) cc_final: 0.7384 (t0) REVERT: F 247 ASN cc_start: 0.8408 (m-40) cc_final: 0.8166 (t0) REVERT: F 277 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7390 (mtp85) REVERT: F 315 ASP cc_start: 0.7988 (t0) cc_final: 0.7709 (t0) REVERT: H 37 PHE cc_start: 0.7820 (t80) cc_final: 0.7524 (t80) REVERT: H 315 ASP cc_start: 0.6992 (m-30) cc_final: 0.6713 (m-30) REVERT: M 74 GLU cc_start: 0.7582 (tt0) cc_final: 0.7284 (tt0) REVERT: M 105 GLU cc_start: 0.7645 (tp30) cc_final: 0.7381 (tp30) REVERT: M 106 ASN cc_start: 0.8626 (m-40) cc_final: 0.8111 (m110) REVERT: M 109 GLU cc_start: 0.7640 (pt0) cc_final: 0.7372 (pt0) outliers start: 75 outliers final: 46 residues processed: 645 average time/residue: 0.5899 time to fit residues: 431.7909 Evaluate side-chains 671 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 618 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 271 TYR Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 284 ARG Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 277 ARG Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain G residue 29 GLU Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 140 ASN Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 253 LYS Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 286 ILE Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 156 GLU Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 252 GLN Chi-restraints excluded: chain H residue 278 GLU Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 14 ILE Chi-restraints excluded: chain M residue 61 LEU Chi-restraints excluded: chain M residue 90 ILE Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 138 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 107 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 247 optimal weight: 8.9990 chunk 126 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 224 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 215 optimal weight: 4.9990 chunk 178 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 208 ASN A 252 GLN B 18 ASN B 80 GLN ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN D 144 ASN F 51 ASN F 71 ASN F 149 GLN F 159 HIS G 140 ASN H 18 ASN H 80 GLN H 186 ASN H 195 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.114541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.100014 restraints weight = 33376.626| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.60 r_work: 0.3323 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 23544 Z= 0.160 Angle : 0.579 7.708 32338 Z= 0.322 Chirality : 0.045 0.321 3648 Planarity : 0.005 0.050 3820 Dihedral : 19.296 178.376 4186 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.37 % Allowed : 20.38 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.16), residues: 2595 helix: 1.18 (0.20), residues: 739 sheet: 0.96 (0.25), residues: 463 loop : -2.26 (0.13), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 162 TYR 0.019 0.001 TYR H 271 PHE 0.023 0.001 PHE H 273 TRP 0.017 0.001 TRP H 149 HIS 0.005 0.001 HIS E 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (23544) covalent geometry : angle 0.57854 / 0.32 (32338) hydrogen bonds : bond 0.04911 / 3.32 ( 796) hydrogen bonds : angle 4.35353 / 3.01 ( 2422) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 613 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8321 (tp) REVERT: C 71 ILE cc_start: 0.8489 (OUTLIER) cc_final: 0.8240 (mm) REVERT: D 284 ARG cc_start: 0.7655 (ttm170) cc_final: 0.7385 (ttm170) REVERT: E 184 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7879 (mt0) REVERT: F 57 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8430 (pp) REVERT: F 83 ASP cc_start: 0.7621 (t0) cc_final: 0.7355 (t0) REVERT: F 247 ASN cc_start: 0.8415 (m-40) cc_final: 0.8182 (t0) REVERT: F 277 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7431 (mtp85) REVERT: F 307 VAL cc_start: 0.9088 (OUTLIER) cc_final: 0.8815 (t) REVERT: F 315 ASP cc_start: 0.7963 (t0) cc_final: 0.7654 (t0) REVERT: G 165 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7909 (mm-30) REVERT: G 309 GLU cc_start: 0.7894 (tt0) cc_final: 0.7630 (mt-10) REVERT: H 37 PHE cc_start: 0.7765 (t80) cc_final: 0.7476 (t80) REVERT: H 265 TYR cc_start: 0.7556 (OUTLIER) cc_final: 0.6947 (p90) REVERT: H 315 ASP cc_start: 0.6906 (m-30) cc_final: 0.6644 (m-30) REVERT: M 74 GLU cc_start: 0.7541 (tt0) cc_final: 0.7245 (tt0) REVERT: M 105 GLU cc_start: 0.7652 (tp30) cc_final: 0.7425 (tp30) REVERT: M 106 ASN cc_start: 0.8611 (m-40) cc_final: 0.8139 (m110) REVERT: M 109 GLU cc_start: 0.7637 (pt0) cc_final: 0.7388 (pt0) outliers start: 75 outliers final: 45 residues processed: 633 average time/residue: 0.5857 time to fit residues: 419.9791 Evaluate side-chains 657 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 605 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 184 GLN Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 277 ARG Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain G residue 29 GLU Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 253 LYS Chi-restraints excluded: chain G residue 286 ILE Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 252 GLN Chi-restraints excluded: chain H residue 265 TYR Chi-restraints excluded: chain H residue 267 ASP Chi-restraints excluded: chain H residue 294 THR Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 14 ILE Chi-restraints excluded: chain M residue 61 LEU Chi-restraints excluded: chain M residue 90 ILE Chi-restraints excluded: chain M residue 138 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 89 optimal weight: 0.7980 chunk 127 optimal weight: 2.9990 chunk 169 optimal weight: 0.9980 chunk 238 optimal weight: 0.4980 chunk 263 optimal weight: 10.0000 chunk 5 optimal weight: 0.2980 chunk 208 optimal weight: 0.9980 chunk 187 optimal weight: 0.8980 chunk 209 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 185 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 208 ASN A 252 GLN B 18 ASN D 18 ASN D 144 ASN F 51 ASN F 71 ASN F 149 GLN F 159 HIS G 140 ASN H 18 ASN H 80 GLN H 186 ASN H 195 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.116270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.101742 restraints weight = 33538.257| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.59 r_work: 0.3352 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23544 Z= 0.124 Angle : 0.554 7.701 32338 Z= 0.308 Chirality : 0.044 0.336 3648 Planarity : 0.005 0.050 3820 Dihedral : 19.278 177.827 4185 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.61 % Allowed : 21.50 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.16), residues: 2595 helix: 1.33 (0.20), residues: 738 sheet: 1.02 (0.25), residues: 473 loop : -2.20 (0.14), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 162 TYR 0.014 0.001 TYR G 265 PHE 0.033 0.001 PHE H 43 TRP 0.015 0.001 TRP H 149 HIS 0.005 0.001 HIS E 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (23544) covalent geometry : angle 0.55377 / 0.31 (32338) hydrogen bonds : bond 0.04146 / 2.79 ( 796) hydrogen bonds : angle 4.16804 / 2.89 ( 2422) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 608 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 71 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.8217 (mm) REVERT: F 57 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8434 (pp) REVERT: F 83 ASP cc_start: 0.7580 (t0) cc_final: 0.7322 (t0) REVERT: F 247 ASN cc_start: 0.8410 (m-40) cc_final: 0.8187 (t0) REVERT: F 315 ASP cc_start: 0.7960 (t0) cc_final: 0.7633 (t0) REVERT: F 320 MET cc_start: 0.8647 (mtp) cc_final: 0.8424 (mtp) REVERT: G 165 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7888 (mm-30) REVERT: G 309 GLU cc_start: 0.7878 (tt0) cc_final: 0.7625 (mt-10) REVERT: H 37 PHE cc_start: 0.7690 (t80) cc_final: 0.7429 (t80) REVERT: H 265 TYR cc_start: 0.7472 (OUTLIER) cc_final: 0.6935 (p90) REVERT: H 315 ASP cc_start: 0.6818 (m-30) cc_final: 0.6558 (m-30) REVERT: M 74 GLU cc_start: 0.7496 (tt0) cc_final: 0.7206 (tt0) REVERT: M 105 GLU cc_start: 0.7605 (tp30) cc_final: 0.7318 (tp30) REVERT: M 106 ASN cc_start: 0.8555 (m-40) cc_final: 0.8241 (m110) REVERT: M 109 GLU cc_start: 0.7623 (pt0) cc_final: 0.7422 (pt0) outliers start: 58 outliers final: 39 residues processed: 627 average time/residue: 0.5886 time to fit residues: 417.4572 Evaluate side-chains 652 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 610 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain G residue 29 GLU Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 253 LYS Chi-restraints excluded: chain G residue 286 ILE Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 252 GLN Chi-restraints excluded: chain H residue 265 TYR Chi-restraints excluded: chain H residue 290 PHE Chi-restraints excluded: chain H residue 294 THR Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 61 LEU Chi-restraints excluded: chain M residue 90 ILE Chi-restraints excluded: chain M residue 138 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 157 optimal weight: 3.9990 chunk 246 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 173 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 225 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 228 optimal weight: 4.9990 chunk 206 optimal weight: 0.2980 chunk 51 optimal weight: 1.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 208 ASN A 252 GLN B 18 ASN B 80 GLN D 18 ASN D 144 ASN F 51 ASN F 63 ASN F 71 ASN F 149 GLN F 159 HIS G 140 ASN H 18 ASN H 80 GLN ** H 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN H 195 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.115611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.100877 restraints weight = 33404.727| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.62 r_work: 0.3336 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23544 Z= 0.151 Angle : 0.571 10.023 32338 Z= 0.314 Chirality : 0.045 0.272 3648 Planarity : 0.005 0.053 3820 Dihedral : 19.243 178.072 4185 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.16 % Allowed : 22.90 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.16), residues: 2595 helix: 1.33 (0.20), residues: 738 sheet: 1.02 (0.25), residues: 457 loop : -2.14 (0.14), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 162 TYR 0.015 0.001 TYR G 265 PHE 0.038 0.001 PHE H 43 TRP 0.017 0.001 TRP H 149 HIS 0.005 0.001 HIS E 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (23544) covalent geometry : angle 0.57064 / 0.31 (32338) hydrogen bonds : bond 0.04547 / 3.08 ( 796) hydrogen bonds : angle 4.20112 / 2.92 ( 2422) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 613 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ASP cc_start: 0.7273 (t0) cc_final: 0.7028 (t0) REVERT: B 55 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8324 (tp) REVERT: C 12 LEU cc_start: 0.8839 (mp) cc_final: 0.8619 (mt) REVERT: C 71 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8221 (mm) REVERT: F 57 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8437 (pp) REVERT: F 83 ASP cc_start: 0.7608 (t0) cc_final: 0.7351 (t0) REVERT: F 247 ASN cc_start: 0.8465 (m-40) cc_final: 0.8240 (t0) REVERT: F 307 VAL cc_start: 0.9074 (OUTLIER) cc_final: 0.8789 (t) REVERT: F 315 ASP cc_start: 0.7988 (t0) cc_final: 0.7646 (t0) REVERT: F 320 MET cc_start: 0.8643 (mtp) cc_final: 0.8419 (mtp) REVERT: G 165 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7858 (mm-30) REVERT: G 309 GLU cc_start: 0.7838 (tt0) cc_final: 0.7593 (mt-10) REVERT: H 37 PHE cc_start: 0.7724 (t80) cc_final: 0.7429 (t80) REVERT: H 315 ASP cc_start: 0.6838 (m-30) cc_final: 0.6576 (m-30) REVERT: M 74 GLU cc_start: 0.7509 (tt0) cc_final: 0.7223 (tt0) REVERT: M 106 ASN cc_start: 0.8593 (m-40) cc_final: 0.8371 (m110) REVERT: M 109 GLU cc_start: 0.7706 (pt0) cc_final: 0.7475 (pt0) outliers start: 48 outliers final: 35 residues processed: 629 average time/residue: 0.6012 time to fit residues: 429.1344 Evaluate side-chains 643 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 604 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain G residue 29 GLU Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 140 ASN Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 229 MET Chi-restraints excluded: chain G residue 253 LYS Chi-restraints excluded: chain G residue 286 ILE Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 200 PHE Chi-restraints excluded: chain H residue 252 GLN Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 61 LEU Chi-restraints excluded: chain M residue 90 ILE Chi-restraints excluded: chain M residue 138 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 155 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 chunk 62 optimal weight: 0.5980 chunk 179 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 136 optimal weight: 0.6980 chunk 219 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 208 ASN A 252 GLN B 18 ASN D 18 ASN D 144 ASN F 71 ASN F 82 ASN F 149 GLN F 159 HIS H 18 ASN H 80 GLN ** H 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN H 195 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.115608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.100867 restraints weight = 33513.925| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.62 r_work: 0.3336 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.194 23544 Z= 0.203 Angle : 0.745 59.101 32338 Z= 0.436 Chirality : 0.044 0.257 3648 Planarity : 0.005 0.052 3820 Dihedral : 19.243 178.079 4185 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.25 % Allowed : 22.63 % Favored : 75.12 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.16), residues: 2595 helix: 1.30 (0.20), residues: 738 sheet: 1.02 (0.25), residues: 457 loop : -2.14 (0.14), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 162 TYR 0.055 0.001 TYR H 265 PHE 0.081 0.002 PHE H 290 TRP 0.016 0.001 TRP H 149 HIS 0.005 0.001 HIS E 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.20 (23544) covalent geometry : angle 0.74512 / 0.44 (32338) hydrogen bonds : bond 0.04557 / 3.09 ( 796) hydrogen bonds : angle 4.21289 / 2.92 ( 2422) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10058.14 seconds wall clock time: 171 minutes 3.63 seconds (10263.63 seconds total)