Starting phenix.real_space_refine on Sun Aug 24 20:01:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z0l_39707/08_2025/8z0l_39707_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z0l_39707/08_2025/8z0l_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_2025/8z0l_39707.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z0l_39707/08_2025/8z0l_39707.map" model { file = "/net/cci-nas-00/data/ceres_data/8z0l_39707/08_2025/8z0l_39707_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z0l_39707/08_2025/8z0l_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.36, per 1000 atoms: 0.23 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: 1.75 Conformation dependent library (CDL) restraints added in 937.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 2.68 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: 3.78 Time building geometry restraints manager: 2.19 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: 30864 2.46 - 4.93: 1228 4.93 - 7.39: 190 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: 3530 0.150 - 0.300: 114 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: 3.180 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: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.850 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: 0.000 Load rotamer database and sin/cos tables:6.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 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= 0.439 Angle : 1.135 12.323 32338 Z= 0.680 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 aren 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 covalent geometry : bond 0.00726 (23544) covalent geometry : angle 1.13524 (32338) hydrogen bonds : bond 0.23195 ( 796) hydrogen bonds : angle 7.63507 ( 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 : 0.813 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: 0.7045 (t0) REVERT: F 85 LYS cc_start: 0.7534 (mtmt) cc_final: 0.7199 (mtmt) 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: 0.6832 (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: 0.6164 time to fit residues: 486.6023 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 : 0.901 ------------------------------------------------------------------------------- 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: 3.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 3.9990 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... Flipped N/Q/H residues before XYZ refinement: A 252 GLN 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 149 GLN 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: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.115254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.100861 restraints weight = 33552.593| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.60 r_work: 0.3336 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 23544 Z= 0.226 Angle : 0.687 9.508 32338 Z= 0.375 Chirality : 0.047 0.256 3648 Planarity : 0.006 0.068 3820 Dihedral : 19.873 177.674 4200 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.24 % Favored : 94.57 % Rotamer: Outliers : 4.05 % Allowed : 16.19 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.92 (0.15), residues: 2595 helix: -0.34 (0.18), residues: 738 sheet: 1.16 (0.27), residues: 423 loop : -2.72 (0.12), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 162 TYR 0.019 0.002 TYR H 271 PHE 0.016 0.002 PHE F 151 TRP 0.023 0.002 TRP H 149 HIS 0.006 0.001 HIS E 94 Details of bonding type rmsd covalent geometry : bond 0.00529 (23544) covalent geometry : angle 0.68698 (32338) hydrogen bonds : bond 0.05965 ( 796) hydrogen bonds : angle 5.00908 ( 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 722 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 632 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.8020 (mt-10) REVERT: A 267 ASP cc_start: 0.7497 (t0) cc_final: 0.7285 (t0) REVERT: B 267 ASP cc_start: 0.7572 (t0) cc_final: 0.7221 (t0) REVERT: C 12 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8605 (mt) REVERT: C 156 GLU cc_start: 0.7465 (mp0) cc_final: 0.7254 (mp0) REVERT: C 228 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7838 (mt-10) REVERT: C 244 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7836 (mt-10) REVERT: D 60 HIS cc_start: 0.8695 (OUTLIER) cc_final: 0.8460 (p-80) REVERT: D 206 TYR cc_start: 0.8352 (p90) cc_final: 0.7856 (p90) REVERT: D 228 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7247 (mt-10) REVERT: D 242 LYS cc_start: 0.8709 (mtpp) cc_final: 0.8501 (mtmm) REVERT: F 57 ILE cc_start: 0.8632 (pt) cc_final: 0.8357 (pp) REVERT: F 171 TYR cc_start: 0.8437 (t80) cc_final: 0.8140 (t80) REVERT: F 247 ASN cc_start: 0.8317 (m-40) cc_final: 0.8103 (t0) REVERT: F 291 LYS cc_start: 0.8284 (tttp) cc_final: 0.8078 (tttp) REVERT: F 315 ASP cc_start: 0.8026 (t0) cc_final: 0.7791 (t0) REVERT: H 37 PHE cc_start: 0.7785 (t80) cc_final: 0.7479 (t80) REVERT: H 186 ASN cc_start: 0.8164 (t0) cc_final: 0.7824 (t160) REVERT: H 258 LEU cc_start: 0.8919 (mt) cc_final: 0.8693 (mp) REVERT: M 1 MET cc_start: 0.6622 (OUTLIER) cc_final: 0.6353 (pmm) REVERT: M 59 GLU cc_start: 0.7305 (mt-10) cc_final: 0.7066 (mt-10) REVERT: M 74 GLU cc_start: 0.7637 (tt0) cc_final: 0.7332 (tt0) REVERT: M 98 LEU cc_start: 0.7233 (mm) cc_final: 0.6960 (mm) REVERT: M 105 GLU cc_start: 0.7440 (tp30) cc_final: 0.7222 (tp30) REVERT: M 109 GLU cc_start: 0.7396 (pt0) cc_final: 0.7191 (pt0) REVERT: M 175 LEU cc_start: 0.8157 (tp) cc_final: 0.7879 (mp) outliers start: 90 outliers final: 31 residues processed: 667 average time/residue: 0.6704 time to fit residues: 507.7420 Evaluate side-chains 637 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 601 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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 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 157 ILE Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain D residue 38 LEU 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 181 THR Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 87 GLU 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 81 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 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: 3.9990 chunk 9 optimal weight: 1.9990 chunk 219 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 258 optimal weight: 3.9990 chunk 242 optimal weight: 0.2980 chunk 175 optimal weight: 0.7980 chunk 253 optimal weight: 2.9990 chunk 164 optimal weight: 8.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN A 252 GLN B 18 ASN B 308 ASN C 18 ASN C 308 ASN D 140 ASN D 144 ASN E 167 ASN F 82 ASN F 149 GLN 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.114919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.100332 restraints weight = 33621.397| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.61 r_work: 0.3327 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: 0.8212 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 23544 Z= 0.194 Angle : 0.616 9.229 32338 Z= 0.334 Chirality : 0.045 0.247 3648 Planarity : 0.005 0.058 3820 Dihedral : 19.586 177.469 4192 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.37 % Allowed : 18.22 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.40 (0.15), residues: 2595 helix: 0.44 (0.19), residues: 739 sheet: 1.15 (0.26), residues: 438 loop : -2.54 (0.13), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 162 TYR 0.020 0.001 TYR H 125 PHE 0.027 0.002 PHE H 273 TRP 0.017 0.002 TRP H 149 HIS 0.005 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00457 (23544) covalent geometry : angle 0.61571 (32338) hydrogen bonds : bond 0.05452 ( 796) hydrogen bonds : angle 4.64471 ( 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 710 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 635 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 ASP cc_start: 0.7497 (t0) cc_final: 0.7292 (t0) REVERT: B 229 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.7710 (ttp) REVERT: B 267 ASP cc_start: 0.7607 (t0) cc_final: 0.7284 (t0) REVERT: C 12 LEU cc_start: 0.8845 (mp) cc_final: 0.8628 (mt) REVERT: C 57 SER cc_start: 0.8417 (t) cc_final: 0.8177 (p) REVERT: C 156 GLU cc_start: 0.7404 (mp0) cc_final: 0.7147 (mp0) REVERT: C 228 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7848 (mt-10) REVERT: C 244 GLU cc_start: 0.8359 (mt-10) cc_final: 0.7966 (mt-10) REVERT: D 103 LYS cc_start: 0.8798 (mtpp) cc_final: 0.8595 (mtpt) REVERT: D 206 TYR cc_start: 0.8567 (p90) cc_final: 0.7976 (p90) REVERT: D 228 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7279 (mt-10) REVERT: F 57 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8403 (pp) REVERT: F 171 TYR cc_start: 0.8512 (t80) cc_final: 0.8263 (t80) REVERT: F 247 ASN cc_start: 0.8426 (m-40) cc_final: 0.8208 (t0) REVERT: F 277 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7269 (mtp85) REVERT: F 291 LYS cc_start: 0.8308 (tttp) cc_final: 0.7976 (tttp) REVERT: F 315 ASP cc_start: 0.7983 (t0) cc_final: 0.7743 (t0) REVERT: H 37 PHE cc_start: 0.7734 (t80) cc_final: 0.7407 (t80) REVERT: H 221 MET cc_start: 0.8012 (mmm) cc_final: 0.7773 (mmt) REVERT: M 1 MET cc_start: 0.6810 (mtm) cc_final: 0.6580 (pmm) REVERT: M 59 GLU cc_start: 0.7293 (mt-10) cc_final: 0.7054 (mt-10) REVERT: M 74 GLU cc_start: 0.7566 (tt0) cc_final: 0.7246 (tt0) REVERT: M 105 GLU cc_start: 0.7537 (tp30) cc_final: 0.7210 (tp30) REVERT: M 106 ASN cc_start: 0.8421 (t0) cc_final: 0.7950 (m-40) REVERT: M 109 GLU cc_start: 0.7482 (pt0) cc_final: 0.7276 (pt0) outliers start: 75 outliers final: 36 residues processed: 663 average time/residue: 0.6179 time to fit residues: 465.2956 Evaluate side-chains 652 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 612 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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 118 ILE Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain C residue 159 GLU 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 78 LYS 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 228 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 F residue 57 ILE 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 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 H residue 20 SER Chi-restraints excluded: chain H residue 83 THR 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 290 PHE 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 116 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 118 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 240 optimal weight: 4.9990 chunk 120 optimal weight: 0.7980 chunk 241 optimal weight: 1.9990 chunk 189 optimal weight: 10.0000 chunk 224 optimal weight: 0.6980 chunk 237 optimal weight: 0.7980 chunk 222 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN A 252 GLN B 18 ASN C 18 ASN C 308 ASN D 18 ASN D 144 ASN E 52 ASN E 167 ASN E 183 GLN F 34 ASN F 82 ASN F 149 GLN F 159 HIS G 178 ASN G 252 GLN G 256 ASN H 18 ASN H 80 GLN H 186 ASN H 190 ASN H 195 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.115467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.100854 restraints weight = 33634.155| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.61 r_work: 0.3335 rms_B_bonded: 1.99 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: 0.8202 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 23544 Z= 0.158 Angle : 0.578 9.236 32338 Z= 0.314 Chirality : 0.043 0.230 3648 Planarity : 0.005 0.052 3820 Dihedral : 19.469 177.369 4190 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.51 % Allowed : 18.89 % 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 aren not related in a simple way. whole: -1.08 (0.16), residues: 2595 helix: 0.87 (0.20), residues: 737 sheet: 1.13 (0.25), residues: 463 loop : -2.42 (0.13), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 162 TYR 0.015 0.001 TYR H 271 PHE 0.028 0.001 PHE H 43 TRP 0.017 0.001 TRP H 149 HIS 0.005 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00368 (23544) covalent geometry : angle 0.57816 (32338) hydrogen bonds : bond 0.04723 ( 796) hydrogen bonds : angle 4.43048 ( 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 696 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 618 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 259 ARG cc_start: 0.8292 (mtp180) cc_final: 0.7877 (ttm170) REVERT: B 229 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.7622 (ttp) REVERT: C 12 LEU cc_start: 0.8844 (mp) cc_final: 0.8632 (mt) REVERT: C 156 GLU cc_start: 0.7382 (mp0) cc_final: 0.7096 (mp0) REVERT: C 228 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7841 (mt-10) REVERT: C 244 GLU cc_start: 0.8411 (mt-10) cc_final: 0.7994 (mt-10) REVERT: D 206 TYR cc_start: 0.8600 (p90) cc_final: 0.8040 (p90) REVERT: F 57 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8412 (pp) REVERT: F 63 ASN cc_start: 0.8511 (m110) cc_final: 0.8269 (m-40) REVERT: F 171 TYR cc_start: 0.8515 (t80) cc_final: 0.8313 (t80) REVERT: F 247 ASN cc_start: 0.8440 (m-40) cc_final: 0.8236 (t0) REVERT: F 272 ARG cc_start: 0.8230 (mtt180) cc_final: 0.7904 (mtt180) REVERT: F 277 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7325 (mtp85) REVERT: F 291 LYS cc_start: 0.8330 (tttp) cc_final: 0.7976 (tttp) REVERT: F 315 ASP cc_start: 0.7990 (t0) cc_final: 0.7711 (t0) REVERT: H 37 PHE cc_start: 0.7692 (t80) cc_final: 0.7410 (t80) REVERT: H 290 PHE cc_start: 0.7683 (OUTLIER) cc_final: 0.7370 (m-10) REVERT: M 59 GLU cc_start: 0.7315 (mt-10) cc_final: 0.7086 (mt-10) REVERT: M 74 GLU cc_start: 0.7543 (tt0) cc_final: 0.7221 (tt0) REVERT: M 105 GLU cc_start: 0.7564 (tp30) cc_final: 0.7156 (tp30) REVERT: M 106 ASN cc_start: 0.8467 (t0) cc_final: 0.8257 (m-40) REVERT: M 109 GLU cc_start: 0.7532 (pt0) cc_final: 0.7308 (pt0) outliers start: 78 outliers final: 39 residues processed: 645 average time/residue: 0.6900 time to fit residues: 503.7863 Evaluate side-chains 643 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 600 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain B residue 81 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 229 MET Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 81 SER 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 60 GLU Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain F residue 57 ILE 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 F residue 283 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 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 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 H residue 290 PHE 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: 3.9990 chunk 242 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 126 optimal weight: 0.7980 chunk 189 optimal weight: 8.9990 chunk 95 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 167 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 195 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 208 ASN A 252 GLN B 18 ASN C 18 ASN ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN D 140 ASN D 144 ASN E 52 ASN F 82 ASN F 139 GLN F 144 ASN F 149 GLN F 159 HIS F 206 ASN F 319 ASN G 140 ASN G 252 GLN H 18 ASN H 80 GLN H 186 ASN H 190 ASN H 195 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.112513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.097875 restraints weight = 33325.339| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.61 r_work: 0.3287 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 23544 Z= 0.297 Angle : 0.653 9.452 32338 Z= 0.352 Chirality : 0.048 0.252 3648 Planarity : 0.006 0.055 3820 Dihedral : 19.423 179.045 4190 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 4.00 % Allowed : 19.12 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.16), residues: 2595 helix: 0.91 (0.20), residues: 736 sheet: 1.02 (0.26), residues: 445 loop : -2.44 (0.13), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 162 TYR 0.023 0.002 TYR H 271 PHE 0.025 0.002 PHE H 273 TRP 0.023 0.002 TRP H 149 HIS 0.006 0.002 HIS E 94 Details of bonding type rmsd covalent geometry : bond 0.00716 (23544) covalent geometry : angle 0.65275 (32338) hydrogen bonds : bond 0.06213 ( 796) hydrogen bonds : angle 4.64211 ( 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 709 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 620 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 ASP cc_start: 0.7577 (t0) cc_final: 0.7369 (t0) REVERT: B 229 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.7766 (ttp) REVERT: B 241 PHE cc_start: 0.8756 (t80) cc_final: 0.8463 (t80) REVERT: C 71 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.8245 (mm) REVERT: C 156 GLU cc_start: 0.7306 (mp0) cc_final: 0.6982 (mp0) REVERT: C 244 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8124 (mt-10) REVERT: D 206 TYR cc_start: 0.8696 (p90) cc_final: 0.8088 (p90) REVERT: F 57 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8419 (pp) REVERT: F 247 ASN cc_start: 0.8526 (m-40) cc_final: 0.8170 (t0) REVERT: F 277 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7432 (mtp85) REVERT: F 291 LYS cc_start: 0.8348 (tttp) cc_final: 0.8015 (tttp) REVERT: F 315 ASP cc_start: 0.7986 (t0) cc_final: 0.7709 (t0) REVERT: H 37 PHE cc_start: 0.7826 (t80) cc_final: 0.7505 (t80) REVERT: H 265 TYR cc_start: 0.7616 (OUTLIER) cc_final: 0.7272 (p90) REVERT: H 290 PHE cc_start: 0.7779 (OUTLIER) cc_final: 0.7575 (m-10) REVERT: H 315 ASP cc_start: 0.7063 (m-30) cc_final: 0.6818 (m-30) REVERT: M 59 GLU cc_start: 0.7328 (mt-10) cc_final: 0.7127 (mt-10) REVERT: M 74 GLU cc_start: 0.7528 (tt0) cc_final: 0.7233 (tt0) REVERT: M 105 GLU cc_start: 0.7604 (tp30) cc_final: 0.7340 (tp30) REVERT: M 106 ASN cc_start: 0.8534 (t0) cc_final: 0.8087 (m-40) REVERT: M 109 GLU cc_start: 0.7685 (pt0) cc_final: 0.7438 (pt0) outliers start: 89 outliers final: 48 residues processed: 649 average time/residue: 0.6637 time to fit residues: 487.2190 Evaluate side-chains 673 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 619 time to evaluate : 0.890 ------------------------------------------------------------------------------- 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 332 LYS 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 229 MET Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain C residue 71 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 C residue 286 ILE Chi-restraints excluded: chain D residue 38 LEU 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 242 LYS Chi-restraints excluded: chain D residue 269 THR 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 F residue 57 ILE Chi-restraints excluded: chain F residue 127 GLU 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 181 THR Chi-restraints excluded: chain G residue 212 THR 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 81 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 265 TYR Chi-restraints excluded: chain H residue 267 ASP Chi-restraints excluded: chain H residue 275 ILE Chi-restraints excluded: chain H residue 278 GLU Chi-restraints excluded: chain H residue 290 PHE Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 14 ILE Chi-restraints excluded: chain M residue 66 GLU Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 116 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 70 optimal weight: 3.9990 chunk 226 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 202 optimal weight: 0.6980 chunk 137 optimal weight: 3.9990 chunk 243 optimal weight: 0.2980 chunk 255 optimal weight: 7.9990 chunk 212 optimal weight: 2.9990 chunk 173 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN A 252 GLN B 18 ASN C 18 ASN C 308 ASN D 80 GLN D 140 ASN D 144 ASN E 52 ASN F 34 ASN F 71 ASN F 159 HIS G 140 ASN G 252 GLN H 18 ASN H 80 GLN H 186 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 = 0.3622 r_free = 0.3622 target = 0.114699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.100083 restraints weight = 33625.635| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.61 r_work: 0.3323 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 23544 Z= 0.153 Angle : 0.572 9.275 32338 Z= 0.311 Chirality : 0.043 0.229 3648 Planarity : 0.005 0.052 3820 Dihedral : 19.342 177.580 4190 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.78 % Allowed : 19.70 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.16), residues: 2595 helix: 1.13 (0.20), residues: 738 sheet: 1.09 (0.25), residues: 456 loop : -2.35 (0.13), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 162 TYR 0.022 0.001 TYR F 271 PHE 0.034 0.001 PHE H 43 TRP 0.011 0.001 TRP D 33 HIS 0.004 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00358 (23544) covalent geometry : angle 0.57241 (32338) hydrogen bonds : bond 0.04679 ( 796) hydrogen bonds : angle 4.35519 ( 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 699 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 615 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 ARG cc_start: 0.8328 (mtm-85) cc_final: 0.7858 (ttm170) REVERT: A 267 ASP cc_start: 0.7574 (t0) cc_final: 0.7353 (t0) REVERT: A 334 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7457 (mp0) REVERT: B 55 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8337 (tp) REVERT: B 229 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.7667 (ttp) REVERT: B 241 PHE cc_start: 0.8775 (t80) cc_final: 0.8456 (t80) REVERT: C 71 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.8219 (mm) REVERT: D 17 GLU cc_start: 0.8081 (tt0) cc_final: 0.7851 (tt0) REVERT: D 156 GLU cc_start: 0.7250 (mp0) cc_final: 0.7049 (mp0) REVERT: D 206 TYR cc_start: 0.8703 (p90) cc_final: 0.8154 (p90) REVERT: F 57 ILE cc_start: 0.8666 (OUTLIER) cc_final: 0.8426 (pp) REVERT: F 247 ASN cc_start: 0.8476 (m-40) cc_final: 0.8265 (t0) REVERT: F 291 LYS cc_start: 0.8350 (tttp) cc_final: 0.8004 (tttp) REVERT: F 315 ASP cc_start: 0.7955 (t0) cc_final: 0.7651 (t0) REVERT: H 37 PHE cc_start: 0.7722 (t80) cc_final: 0.7435 (t80) REVERT: H 290 PHE cc_start: 0.7756 (OUTLIER) cc_final: 0.7437 (m-10) REVERT: H 315 ASP cc_start: 0.6915 (m-30) cc_final: 0.6649 (m-30) REVERT: M 59 GLU cc_start: 0.7254 (mt-10) cc_final: 0.7048 (mt-10) REVERT: M 74 GLU cc_start: 0.7534 (tt0) cc_final: 0.7230 (tt0) REVERT: M 105 GLU cc_start: 0.7564 (tp30) cc_final: 0.7233 (tp30) REVERT: M 106 ASN cc_start: 0.8524 (t0) cc_final: 0.8243 (m-40) REVERT: M 109 GLU cc_start: 0.7614 (pt0) cc_final: 0.7405 (pt0) outliers start: 84 outliers final: 46 residues processed: 643 average time/residue: 0.6829 time to fit residues: 495.8889 Evaluate side-chains 662 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 610 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 55 LEU 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 C residue 18 ASN Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 183 VAL 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 118 ILE Chi-restraints excluded: chain D residue 140 ASN 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 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 234 LEU 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 286 ILE Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain H residue 50 THR 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 267 ASP Chi-restraints excluded: chain H residue 290 PHE Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 14 ILE Chi-restraints excluded: chain M residue 90 ILE Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 116 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 144 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 188 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 chunk 30 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 211 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN A 252 GLN B 18 ASN B 80 GLN C 18 ASN ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN D 140 ASN D 144 ASN E 236 ASN F 71 ASN F 149 GLN F 159 HIS G 140 ASN G 252 GLN H 18 ASN H 80 GLN H 186 ASN H 190 ASN H 195 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.113973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.099350 restraints weight = 33525.010| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.61 r_work: 0.3311 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 23544 Z= 0.202 Angle : 0.593 9.341 32338 Z= 0.321 Chirality : 0.045 0.296 3648 Planarity : 0.005 0.052 3820 Dihedral : 19.301 178.064 4189 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.64 % Allowed : 19.84 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.16), residues: 2595 helix: 1.12 (0.20), residues: 741 sheet: 1.07 (0.25), residues: 456 loop : -2.32 (0.13), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 162 TYR 0.020 0.001 TYR F 271 PHE 0.023 0.002 PHE H 273 TRP 0.012 0.001 TRP C 33 HIS 0.004 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00483 (23544) covalent geometry : angle 0.59263 (32338) hydrogen bonds : bond 0.05119 ( 796) hydrogen bonds : angle 4.38841 ( 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 697 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 616 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 ASP cc_start: 0.7594 (t0) cc_final: 0.7360 (t0) REVERT: A 334 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7458 (mp0) REVERT: B 55 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8346 (tp) REVERT: B 229 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.7669 (ttp) REVERT: C 71 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8257 (mm) REVERT: D 17 GLU cc_start: 0.8097 (tt0) cc_final: 0.7864 (tt0) REVERT: D 43 PHE cc_start: 0.8716 (t80) cc_final: 0.8504 (t80) REVERT: D 156 GLU cc_start: 0.7253 (mp0) cc_final: 0.7044 (mp0) REVERT: F 57 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8440 (pp) REVERT: F 83 ASP cc_start: 0.7715 (t0) cc_final: 0.7501 (t0) REVERT: F 247 ASN cc_start: 0.8494 (m-40) cc_final: 0.8284 (t0) REVERT: F 291 LYS cc_start: 0.8361 (tttp) cc_final: 0.7974 (tttp) REVERT: F 315 ASP cc_start: 0.7972 (t0) cc_final: 0.7674 (t0) REVERT: G 165 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7937 (mm-30) REVERT: H 37 PHE cc_start: 0.7761 (t80) cc_final: 0.7476 (t80) REVERT: H 290 PHE cc_start: 0.7814 (OUTLIER) cc_final: 0.7516 (m-10) REVERT: H 315 ASP cc_start: 0.6964 (m-30) cc_final: 0.6716 (m-30) REVERT: M 59 GLU cc_start: 0.7296 (mt-10) cc_final: 0.7093 (mt-10) REVERT: M 74 GLU cc_start: 0.7526 (tt0) cc_final: 0.7248 (tt0) REVERT: M 105 GLU cc_start: 0.7597 (tp30) cc_final: 0.7341 (tp30) REVERT: M 106 ASN cc_start: 0.8557 (t0) cc_final: 0.8296 (m110) REVERT: M 109 GLU cc_start: 0.7676 (pt0) cc_final: 0.7458 (pt0) outliers start: 81 outliers final: 56 residues processed: 638 average time/residue: 0.7460 time to fit residues: 537.7095 Evaluate side-chains 667 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 605 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 78 LYS 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 A residue 294 THR Chi-restraints excluded: chain A residue 332 LYS 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 81 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 229 MET 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 183 VAL 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 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 242 LYS Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 236 ASN Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 135 MET Chi-restraints excluded: chain F residue 234 LEU 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 168 GLU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 286 ILE Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain H residue 50 THR 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 267 ASP Chi-restraints excluded: chain H residue 290 PHE Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 14 ILE Chi-restraints excluded: chain M residue 90 ILE Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 116 ARG 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: 3.9990 chunk 247 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 224 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 215 optimal weight: 4.9990 chunk 178 optimal weight: 5.9990 chunk 127 optimal weight: 0.8980 chunk 183 optimal weight: 6.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN A 252 GLN B 18 ASN C 18 ASN ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN D 144 ASN F 63 ASN F 71 ASN F 82 ASN F 149 GLN F 159 HIS G 140 ASN G 252 GLN H 18 ASN H 80 GLN H 186 ASN H 195 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.113809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.099110 restraints weight = 33147.278| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.60 r_work: 0.3309 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 23544 Z= 0.207 Angle : 0.594 9.354 32338 Z= 0.321 Chirality : 0.045 0.235 3648 Planarity : 0.005 0.053 3820 Dihedral : 19.255 178.134 4189 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.73 % Allowed : 19.84 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.16), residues: 2595 helix: 1.17 (0.20), residues: 735 sheet: 1.05 (0.26), residues: 444 loop : -2.27 (0.13), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 162 TYR 0.019 0.001 TYR F 271 PHE 0.045 0.002 PHE H 43 TRP 0.013 0.001 TRP H 149 HIS 0.004 0.001 HIS F 304 Details of bonding type rmsd covalent geometry : bond 0.00497 (23544) covalent geometry : angle 0.59368 (32338) hydrogen bonds : bond 0.05157 ( 796) hydrogen bonds : angle 4.38336 ( 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 685 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 602 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 ASP cc_start: 0.7587 (t0) cc_final: 0.7362 (t0) REVERT: A 334 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7424 (mp0) REVERT: B 55 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8332 (tp) REVERT: B 229 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.7756 (ttp) REVERT: C 71 ILE cc_start: 0.8482 (OUTLIER) cc_final: 0.8251 (mm) REVERT: F 57 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8436 (pp) REVERT: F 247 ASN cc_start: 0.8541 (m-40) cc_final: 0.8325 (t0) REVERT: F 277 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7477 (mtp85) REVERT: F 291 LYS cc_start: 0.8325 (tttp) cc_final: 0.7955 (tttp) REVERT: F 315 ASP cc_start: 0.7975 (t0) cc_final: 0.7678 (t0) REVERT: F 320 MET cc_start: 0.8659 (mtp) cc_final: 0.8440 (mtp) REVERT: G 165 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7908 (mm-30) REVERT: H 37 PHE cc_start: 0.7784 (t80) cc_final: 0.7458 (t80) REVERT: H 290 PHE cc_start: 0.7835 (OUTLIER) cc_final: 0.7561 (m-10) REVERT: H 315 ASP cc_start: 0.6963 (m-30) cc_final: 0.6715 (m-30) REVERT: M 74 GLU cc_start: 0.7525 (tt0) cc_final: 0.7249 (tt0) REVERT: M 105 GLU cc_start: 0.7561 (tp30) cc_final: 0.7316 (tp30) REVERT: M 106 ASN cc_start: 0.8547 (t0) cc_final: 0.8278 (m110) REVERT: M 109 GLU cc_start: 0.7683 (pt0) cc_final: 0.7453 (pt0) outliers start: 83 outliers final: 59 residues processed: 626 average time/residue: 0.7188 time to fit residues: 507.8382 Evaluate side-chains 658 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 592 time to evaluate : 0.891 ------------------------------------------------------------------------------- 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 A residue 294 THR Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain B residue 20 SER 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 140 ASN Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 183 VAL 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 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 242 LYS Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 135 MET Chi-restraints excluded: chain F residue 234 LEU 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 104 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 181 THR 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 267 ASP Chi-restraints excluded: chain G residue 286 ILE Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain H residue 50 THR 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 267 ASP Chi-restraints excluded: chain H residue 290 PHE Chi-restraints excluded: chain M residue 12 THR Chi-restraints excluded: chain M residue 14 ILE Chi-restraints excluded: chain M residue 90 ILE Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 116 ARG 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: 0.4980 chunk 127 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 238 optimal weight: 0.0970 chunk 263 optimal weight: 6.9990 chunk 5 optimal weight: 0.0370 chunk 208 optimal weight: 0.9990 chunk 187 optimal weight: 0.6980 chunk 209 optimal weight: 0.4980 chunk 16 optimal weight: 0.0030 chunk 185 optimal weight: 2.9990 overall best weight: 0.2266 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN A 252 GLN B 18 ASN B 80 GLN B 250 HIS C 18 ASN D 18 ASN D 144 ASN F 159 HIS G 140 ASN G 252 GLN H 18 ASN H 80 GLN H 178 ASN H 195 GLN H 256 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.118497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.103754 restraints weight = 33634.979| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.63 r_work: 0.3381 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 23544 Z= 0.104 Angle : 0.534 9.804 32338 Z= 0.287 Chirality : 0.041 0.205 3648 Planarity : 0.005 0.051 3820 Dihedral : 19.090 178.774 4189 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.38 % Allowed : 21.64 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.16), residues: 2595 helix: 1.34 (0.20), residues: 740 sheet: 1.08 (0.24), residues: 484 loop : -2.17 (0.14), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 162 TYR 0.018 0.001 TYR G 138 PHE 0.020 0.001 PHE H 273 TRP 0.011 0.001 TRP F 208 HIS 0.004 0.000 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00224 (23544) covalent geometry : angle 0.53372 (32338) hydrogen bonds : bond 0.03347 ( 796) hydrogen bonds : angle 3.94650 ( 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 658 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 605 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 259 ARG cc_start: 0.8296 (mtm-85) cc_final: 0.7906 (ttm170) REVERT: A 267 ASP cc_start: 0.7522 (t0) cc_final: 0.7313 (t0) REVERT: B 55 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8345 (tp) REVERT: C 12 LEU cc_start: 0.8792 (mp) cc_final: 0.8587 (mt) REVERT: C 71 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.8143 (mm) REVERT: D 156 GLU cc_start: 0.7208 (mp0) cc_final: 0.7006 (mp0) REVERT: F 57 ILE cc_start: 0.8677 (OUTLIER) cc_final: 0.8440 (pp) REVERT: F 247 ASN cc_start: 0.8519 (m-40) cc_final: 0.8305 (t0) REVERT: F 291 LYS cc_start: 0.8298 (tttp) cc_final: 0.7953 (tttp) REVERT: F 315 ASP cc_start: 0.7992 (t0) cc_final: 0.7643 (t0) REVERT: F 320 MET cc_start: 0.8645 (mtp) cc_final: 0.8422 (mtp) REVERT: G 93 ILE cc_start: 0.8710 (mt) cc_final: 0.8402 (tt) REVERT: G 165 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7844 (mm-30) REVERT: G 309 GLU cc_start: 0.7845 (tt0) cc_final: 0.7589 (mt-10) REVERT: H 37 PHE cc_start: 0.7559 (t80) cc_final: 0.7312 (t80) REVERT: H 290 PHE cc_start: 0.7857 (OUTLIER) cc_final: 0.7603 (m-10) REVERT: H 315 ASP cc_start: 0.6749 (m-30) cc_final: 0.6501 (m-30) REVERT: M 59 GLU cc_start: 0.7288 (mt-10) cc_final: 0.7082 (mp0) REVERT: M 74 GLU cc_start: 0.7474 (tt0) cc_final: 0.7183 (tt0) REVERT: M 109 GLU cc_start: 0.7651 (pt0) cc_final: 0.7400 (pt0) outliers start: 53 outliers final: 26 residues processed: 618 average time/residue: 0.6392 time to fit residues: 447.7040 Evaluate side-chains 619 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 589 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 104 GLU 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 205 GLU Chi-restraints excluded: chain D residue 284 ARG Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 184 GLN Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain G residue 18 ASN Chi-restraints excluded: chain G residue 29 GLU Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 212 THR 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 290 PHE Chi-restraints excluded: chain M residue 90 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 157 optimal weight: 2.9990 chunk 246 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 225 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 228 optimal weight: 0.0570 chunk 206 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.5304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN A 208 ASN A 252 GLN B 18 ASN B 75 ASN B 140 ASN C 18 ASN ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN D 144 ASN F 51 ASN F 159 HIS G 140 ASN H 18 ASN ** H 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 178 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 = 0.3617 r_free = 0.3617 target = 0.114305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.099500 restraints weight = 33476.445| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.63 r_work: 0.3316 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 23544 Z= 0.205 Angle : 0.599 10.309 32338 Z= 0.321 Chirality : 0.045 0.209 3648 Planarity : 0.005 0.053 3820 Dihedral : 19.060 178.268 4187 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.93 % Allowed : 22.90 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.16), residues: 2595 helix: 1.37 (0.20), residues: 733 sheet: 1.15 (0.25), residues: 457 loop : -2.13 (0.14), residues: 1405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 162 TYR 0.028 0.002 TYR H 125 PHE 0.030 0.002 PHE H 43 TRP 0.014 0.001 TRP H 149 HIS 0.005 0.001 HIS E 94 Details of bonding type rmsd covalent geometry : bond 0.00492 (23544) covalent geometry : angle 0.59929 (32338) hydrogen bonds : bond 0.05052 ( 796) hydrogen bonds : angle 4.23878 ( 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 646 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 603 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 55 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8329 (tp) REVERT: C 71 ILE cc_start: 0.8462 (OUTLIER) cc_final: 0.8236 (mm) REVERT: F 57 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8445 (pp) REVERT: F 83 ASP cc_start: 0.7682 (t0) cc_final: 0.7481 (t0) REVERT: F 247 ASN cc_start: 0.8556 (m-40) cc_final: 0.8342 (t0) REVERT: F 291 LYS cc_start: 0.8313 (tttp) cc_final: 0.7979 (tttp) REVERT: F 315 ASP cc_start: 0.7950 (t0) cc_final: 0.7631 (t0) REVERT: H 37 PHE cc_start: 0.7745 (t80) cc_final: 0.7455 (t80) REVERT: H 315 ASP cc_start: 0.6952 (m-30) cc_final: 0.6702 (m-30) REVERT: M 74 GLU cc_start: 0.7516 (tt0) cc_final: 0.7227 (tt0) REVERT: M 106 ASN cc_start: 0.8449 (m110) cc_final: 0.8216 (m110) REVERT: M 109 GLU cc_start: 0.7700 (pt0) cc_final: 0.7440 (pt0) outliers start: 43 outliers final: 27 residues processed: 616 average time/residue: 0.6833 time to fit residues: 474.9086 Evaluate side-chains 619 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 589 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 104 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 118 ILE Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 120 GLU 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 212 THR Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain M residue 90 ILE Chi-restraints excluded: chain M residue 98 LEU 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: 3.9990 chunk 64 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 chunk 62 optimal weight: 0.8980 chunk 179 optimal weight: 2.9990 chunk 9 optimal weight: 0.3980 chunk 136 optimal weight: 0.9980 chunk 219 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN A 252 GLN B 18 ASN B 75 ASN C 18 ASN ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN D 144 ASN F 149 GLN F 159 HIS F 335 HIS 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 = 0.3620 r_free = 0.3620 target = 0.114558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.099747 restraints weight = 33555.627| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.62 r_work: 0.3320 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.296 23544 Z= 0.237 Angle : 0.807 59.193 32338 Z= 0.481 Chirality : 0.047 1.118 3648 Planarity : 0.006 0.190 3820 Dihedral : 19.050 178.287 4185 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.66 % Allowed : 23.08 % Favored : 75.26 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.16), residues: 2595 helix: 1.33 (0.20), residues: 733 sheet: 1.15 (0.25), residues: 457 loop : -2.13 (0.14), residues: 1405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 284 TYR 0.023 0.001 TYR H 125 PHE 0.023 0.002 PHE H 273 TRP 0.014 0.001 TRP H 149 HIS 0.004 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00536 (23544) covalent geometry : angle 0.80712 (32338) hydrogen bonds : bond 0.04998 ( 796) hydrogen bonds : angle 4.27034 ( 2422) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10776.18 seconds wall clock time: 183 minutes 26.38 seconds (11006.38 seconds total)