Starting phenix.real_space_refine on Sun Sep 13 10:34:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6b48_7052/09_2026/6b48_7052.cif Found real_map, /net/cci-nas-00/data/ceres_data/6b48_7052/09_2026/6b48_7052.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6b48_7052/09_2026/6b48_7052.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6b48_7052/09_2026/6b48_7052.cif" model { file = "/net/cci-nas-00/data/ceres_data/6b48_7052/09_2026/6b48_7052.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6b48_7052/09_2026/6b48_7052.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6b48_7052/09_2026/6b48_7052.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6b48_7052/09_2026/6b48_7052.map" } resolution = 3.6 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= 0.018 sd= 0.748 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 786 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians Se 5 7.20 5 P 59 5.49 5 S 18 5.16 5 C 13563 2.51 5 N 4184 2.21 5 O 4504 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22333 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 2079 Classifications: {'peptide': 424} Incomplete info: {'backbone_only': 310} Link IDs: {'PTRANS': 24, 'TRANS': 399} Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 1373 Unresolved non-hydrogen angles: 1987 Unresolved non-hydrogen dihedrals: 884 Unresolved non-hydrogen chiralities: 392 Planarities with less than four sites: {'GLN:plan1': 29, 'GLU:plan': 24, 'ARG:plan': 29, 'PHE:plan': 11, 'ASP:plan': 20, 'HIS:plan': 9, 'TRP:plan': 9, 'ASN:plan1': 13, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 726 Chain: "B" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2374 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 23, 'TRANS': 281} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 2272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2272 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 10, 'TRANS': 282} Chain breaks: 2 Chain: "D" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2554 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 2561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2561 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "F" Number of atoms: 2566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2566 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 322} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "G" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2557 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "H" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2554 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "K" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 786 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "L" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 758 Classifications: {'peptide': 189} Incomplete info: {'backbone_only': 173, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 173} Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 806 Unresolved non-hydrogen angles: 1152 Unresolved non-hydrogen dihedrals: 534 Unresolved non-hydrogen chiralities: 219 Planarities with less than four sites: {'ASP:plan': 12, 'HIS:plan': 8, 'TYR:plan': 3, 'ARG:plan': 24, 'GLU:plan': 11, 'PHE:plan': 10, 'GLN:plan1': 9, 'TRP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 414 Chain: "M" Number of atoms: 1272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1272 Classifications: {'RNAv2': 60} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 11, 'rna3p_pur': 20, 'rna3p_pyr': 19} Link IDs: {'rna2p': 19, 'rna3p': 40} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.30, per 1000 atoms: 0.24 Number of scatterers: 22333 At special positions: 0 Unit cell: (131.04, 126.84, 161.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Se 5 33.99 S 18 16.00 P 59 15.00 O 4504 8.00 N 4184 7.00 C 13563 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: 1.94 Conformation dependent library (CDL) restraints added in 1.1 seconds 5900 Ramachandran restraints generated. 2950 Oldfield, 0 Emsley, 2950 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4576 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 40 sheets defined 29.2% alpha, 12.0% beta 1 base pairs and 14 stacking pairs defined. Time for finding SS restraints: 2.15 Creating SS restraints... Processing helix chain 'A' and resid 14 through 27 Processing helix chain 'A' and resid 33 through 48 removed outlier: 4.405A pdb=" N LYS A 39 " --> pdb=" O ASP A 35 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N THR A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 58 removed outlier: 4.247A pdb=" N ALA A 54 " --> pdb=" O GLU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 100 removed outlier: 3.808A pdb=" N LEU A 100 " --> pdb=" O SER A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 123 Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 149 through 161 Processing helix chain 'A' and resid 195 through 211 Processing helix chain 'A' and resid 213 through 222 removed outlier: 3.597A pdb=" N ALA A 217 " --> pdb=" O ASP A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 251 removed outlier: 3.552A pdb=" N ASN A 250 " --> pdb=" O LYS A 247 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE A 251 " --> pdb=" O PRO A 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 247 through 251' Processing helix chain 'A' and resid 294 through 307 Processing helix chain 'A' and resid 314 through 317 Processing helix chain 'A' and resid 318 through 342 removed outlier: 3.724A pdb=" N ALA A 323 " --> pdb=" O ARG A 319 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN A 324 " --> pdb=" O GLN A 320 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 360 Processing helix chain 'A' and resid 386 through 399 Processing helix chain 'A' and resid 408 through 430 removed outlier: 3.834A pdb=" N ALA A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 48 removed outlier: 3.651A pdb=" N PHE B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 135 Processing helix chain 'B' and resid 165 through 180 removed outlier: 3.744A pdb=" N ARG B 178 " --> pdb=" O ARG B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 201 Processing helix chain 'B' and resid 206 through 213 removed outlier: 3.951A pdb=" N LEU B 210 " --> pdb=" O GLU B 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 129 Processing helix chain 'C' and resid 131 through 142 Processing helix chain 'C' and resid 189 through 204 Processing helix chain 'C' and resid 257 through 264 Processing helix chain 'C' and resid 303 through 313 removed outlier: 3.635A pdb=" N LEU C 307 " --> pdb=" O ASP C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 332 Processing helix chain 'D' and resid 31 through 35 removed outlier: 3.865A pdb=" N ASP D 34 " --> pdb=" O ALA D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 70 removed outlier: 4.068A pdb=" N LEU D 67 " --> pdb=" O ASP D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 129 Processing helix chain 'D' and resid 131 through 144 Processing helix chain 'D' and resid 190 through 204 Processing helix chain 'D' and resid 256 through 261 removed outlier: 3.780A pdb=" N ILE D 260 " --> pdb=" O HIS D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 278 Processing helix chain 'D' and resid 303 through 312 Processing helix chain 'D' and resid 319 through 332 Processing helix chain 'E' and resid 32 through 36 removed outlier: 3.587A pdb=" N SER E 36 " --> pdb=" O ARG E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 73 removed outlier: 3.850A pdb=" N SER E 73 " --> pdb=" O ALA E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 129 Processing helix chain 'E' and resid 131 through 144 Processing helix chain 'E' and resid 190 through 204 Processing helix chain 'E' and resid 256 through 264 Processing helix chain 'E' and resid 304 through 312 Processing helix chain 'E' and resid 319 through 332 Processing helix chain 'F' and resid 32 through 36 removed outlier: 3.768A pdb=" N SER F 36 " --> pdb=" O ARG F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 71 removed outlier: 3.604A pdb=" N ILE F 71 " --> pdb=" O LEU F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 129 Processing helix chain 'F' and resid 132 through 144 Processing helix chain 'F' and resid 190 through 204 Processing helix chain 'F' and resid 256 through 264 Processing helix chain 'F' and resid 304 through 312 Processing helix chain 'F' and resid 319 through 332 Processing helix chain 'G' and resid 63 through 72 Processing helix chain 'G' and resid 112 through 129 removed outlier: 3.653A pdb=" N ASP G 116 " --> pdb=" O ALA G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 144 Processing helix chain 'G' and resid 190 through 204 removed outlier: 3.762A pdb=" N SER G 204 " --> pdb=" O ALA G 200 " (cutoff:3.500A) Processing helix chain 'G' and resid 256 through 265 removed outlier: 3.750A pdb=" N ILE G 260 " --> pdb=" O HIS G 256 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG G 265 " --> pdb=" O GLY G 261 " (cutoff:3.500A) Processing helix chain 'G' and resid 304 through 312 Processing helix chain 'G' and resid 319 through 332 Processing helix chain 'H' and resid 32 through 36 Processing helix chain 'H' and resid 63 through 72 removed outlier: 3.591A pdb=" N LEU H 67 " --> pdb=" O ASP H 63 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN H 72 " --> pdb=" O ASP H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 129 Processing helix chain 'H' and resid 131 through 144 Processing helix chain 'H' and resid 190 through 203 Processing helix chain 'H' and resid 256 through 265 removed outlier: 3.733A pdb=" N ARG H 265 " --> pdb=" O GLY H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 303 through 312 removed outlier: 3.611A pdb=" N LEU H 307 " --> pdb=" O ASP H 303 " (cutoff:3.500A) Processing helix chain 'H' and resid 319 through 332 Processing helix chain 'K' and resid 60 through 66 Processing helix chain 'K' and resid 85 through 95 Processing helix chain 'L' and resid 16 through 31 removed outlier: 3.888A pdb=" N LEU L 20 " --> pdb=" O PRO L 16 " (cutoff:3.500A) Processing helix chain 'L' and resid 64 through 69 Processing helix chain 'L' and resid 78 through 82 removed outlier: 3.777A pdb=" N HIS L 82 " --> pdb=" O LEU L 79 " (cutoff:3.500A) Processing helix chain 'L' and resid 108 through 119 removed outlier: 4.639A pdb=" N LEU L 112 " --> pdb=" O ASN L 108 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG L 113 " --> pdb=" O PRO L 109 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 130 Processing sheet with id=AA1, first strand: chain 'A' and resid 189 through 192 removed outlier: 3.676A pdb=" N ARG B 278 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU B 281 " --> pdb=" O ASN B 256 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N LEU B 313 " --> pdb=" O GLU B 308 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU B 308 " --> pdb=" O LEU B 313 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 240 through 242 Processing sheet with id=AA3, first strand: chain 'B' and resid 66 through 68 removed outlier: 6.997A pdb=" N LEU B 105 " --> pdb=" O GLN B 18 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N GLN B 18 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL B 107 " --> pdb=" O SER B 16 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N SER B 16 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N LEU B 109 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ARG B 14 " --> pdb=" O LEU B 109 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 70 through 71 Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 188 removed outlier: 3.847A pdb=" N VAL B 187 " --> pdb=" O GLU B 288 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TRP B 247 " --> pdb=" O TRP B 289 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 12 through 14 Processing sheet with id=AA7, first strand: chain 'C' and resid 174 through 175 Processing sheet with id=AA8, first strand: chain 'D' and resid 12 through 13 removed outlier: 3.619A pdb=" N LEU D 12 " --> pdb=" O PHE D 336 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 19 through 20 removed outlier: 3.886A pdb=" N VAL D 99 " --> pdb=" O VAL D 209 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL D 209 " --> pdb=" O VAL D 99 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 24 through 26 removed outlier: 3.675A pdb=" N ARG D 94 " --> pdb=" O LEU D 24 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL D 99 " --> pdb=" O VAL D 209 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL D 209 " --> pdb=" O VAL D 99 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 46 through 51 Processing sheet with id=AB3, first strand: chain 'D' and resid 82 through 83 removed outlier: 4.577A pdb=" N ALA D 82 " --> pdb=" O VAL D 225 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL D 225 " --> pdb=" O ALA D 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 248 through 249 Processing sheet with id=AB5, first strand: chain 'D' and resid 287 through 288 removed outlier: 3.597A pdb=" N VAL D 288 " --> pdb=" O LYS D 293 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 12 through 14 removed outlier: 3.526A pdb=" N LEU E 12 " --> pdb=" O PHE E 336 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE E 14 " --> pdb=" O GLY E 334 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY E 334 " --> pdb=" O PHE E 14 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 19 through 20 removed outlier: 3.504A pdb=" N VAL E 99 " --> pdb=" O VAL E 209 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N VAL E 209 " --> pdb=" O VAL E 99 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 19 through 20 removed outlier: 5.015A pdb=" N ALA E 253 " --> pdb=" O MET E 25 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA E 252 " --> pdb=" O VAL E 249 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 44 through 50 removed outlier: 3.727A pdb=" N ARG E 45 " --> pdb=" O VAL E 81 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 229 through 230 removed outlier: 4.563A pdb=" N THR E 245 " --> pdb=" O GLU E 230 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 266 through 268 Processing sheet with id=AC3, first strand: chain 'E' and resid 287 through 288 removed outlier: 3.927A pdb=" N VAL E 288 " --> pdb=" O LYS E 293 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS E 293 " --> pdb=" O VAL E 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'F' and resid 12 through 14 Processing sheet with id=AC5, first strand: chain 'F' and resid 19 through 20 removed outlier: 4.353A pdb=" N VAL F 209 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU F 210 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N HIS F 164 " --> pdb=" O ARG F 172 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ARG F 172 " --> pdb=" O HIS F 164 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 19 through 20 removed outlier: 3.789A pdb=" N ARG F 94 " --> pdb=" O LEU F 24 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA F 23 " --> pdb=" O ILE F 255 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE F 255 " --> pdb=" O ALA F 23 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ALA F 253 " --> pdb=" O MET F 25 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA F 252 " --> pdb=" O VAL F 249 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 46 through 51 removed outlier: 3.803A pdb=" N ASN F 75 " --> pdb=" O GLY F 51 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 266 through 268 Processing sheet with id=AC9, first strand: chain 'G' and resid 12 through 14 removed outlier: 3.760A pdb=" N PHE G 336 " --> pdb=" O LEU G 12 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 19 through 20 Processing sheet with id=AD2, first strand: chain 'G' and resid 19 through 20 removed outlier: 4.303A pdb=" N VAL G 209 " --> pdb=" O VAL G 99 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU G 210 " --> pdb=" O ILE G 165 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ARG G 172 " --> pdb=" O HIS G 164 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 46 through 50 Processing sheet with id=AD4, first strand: chain 'G' and resid 229 through 230 removed outlier: 3.961A pdb=" N THR G 245 " --> pdb=" O GLU G 230 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 248 through 249 Processing sheet with id=AD6, first strand: chain 'G' and resid 266 through 268 Processing sheet with id=AD7, first strand: chain 'H' and resid 108 through 109 removed outlier: 3.735A pdb=" N ALA H 108 " --> pdb=" O ALA H 13 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU H 12 " --> pdb=" O PHE H 336 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLY H 334 " --> pdb=" O PHE H 14 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 170 through 175 removed outlier: 3.899A pdb=" N ARG H 172 " --> pdb=" O HIS H 164 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU H 159 " --> pdb=" O PHE H 216 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE H 165 " --> pdb=" O LEU H 210 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU H 210 " --> pdb=" O ILE H 165 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 49 through 51 Processing sheet with id=AE1, first strand: chain 'H' and resid 266 through 268 Processing sheet with id=AE2, first strand: chain 'K' and resid 6 through 8 removed outlier: 3.969A pdb=" N ARG K 6 " --> pdb=" O VAL K 26 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL K 26 " --> pdb=" O ARG K 6 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 13 through 15 removed outlier: 3.780A pdb=" N PHE K 18 " --> pdb=" O ILE K 15 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 39 through 40 772 hydrogen bonds defined for protein. 2142 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3 hydrogen bonds 6 hydrogen bond angles 0 basepair planarities 1 basepair parallelities 14 stacking parallelities Total time for adding SS restraints: 3.65 Time building geometry restraints manager: 2.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 7830 1.35 - 1.50: 6643 1.50 - 1.65: 8343 1.65 - 1.80: 21 1.80 - 1.95: 15 Bond restraints: 22852 Sorted by residual: bond pdb=" CG1 ILE G 327 " pdb=" CD1 ILE G 327 " ideal model delta sigma weight residual 1.513 1.408 0.105 3.90e-02 6.57e+02 7.25e+00 bond pdb=" CG1 ILE F 327 " pdb=" CD1 ILE F 327 " ideal model delta sigma weight residual 1.513 1.413 0.100 3.90e-02 6.57e+02 6.52e+00 bond pdb=" CG1 ILE D 327 " pdb=" CD1 ILE D 327 " ideal model delta sigma weight residual 1.513 1.418 0.095 3.90e-02 6.57e+02 5.94e+00 bond pdb=" CB ASP K 17 " pdb=" CG ASP K 17 " ideal model delta sigma weight residual 1.516 1.576 -0.060 2.50e-02 1.60e+03 5.82e+00 bond pdb=" CG1 ILE E 327 " pdb=" CD1 ILE E 327 " ideal model delta sigma weight residual 1.513 1.424 0.089 3.90e-02 6.57e+02 5.21e+00 ... (remaining 22847 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.38: 30585 3.38 - 6.76: 473 6.76 - 10.14: 30 10.14 - 13.53: 1 13.53 - 16.91: 2 Bond angle restraints: 31091 Sorted by residual: angle pdb=" C GLU K 8 " pdb=" N ASN K 9 " pdb=" CA ASN K 9 " ideal model delta sigma weight residual 121.54 131.20 -9.66 1.91e+00 2.74e-01 2.56e+01 angle pdb=" C SER A 252 " pdb=" N GLN A 253 " pdb=" CA GLN A 253 " ideal model delta sigma weight residual 121.54 130.82 -9.28 1.91e+00 2.74e-01 2.36e+01 angle pdb=" CA LEU B 181 " pdb=" CB LEU B 181 " pdb=" CG LEU B 181 " ideal model delta sigma weight residual 116.30 133.21 -16.91 3.50e+00 8.16e-02 2.33e+01 angle pdb=" C ASN K 16 " pdb=" N ASP K 17 " pdb=" CA ASP K 17 " ideal model delta sigma weight residual 126.45 134.59 -8.14 1.77e+00 3.19e-01 2.11e+01 angle pdb=" CA LEU H 231 " pdb=" CB LEU H 231 " pdb=" CG LEU H 231 " ideal model delta sigma weight residual 116.30 131.66 -15.36 3.50e+00 8.16e-02 1.93e+01 ... (remaining 31086 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.49: 11766 15.49 - 30.98: 770 30.98 - 46.47: 186 46.47 - 61.96: 102 61.96 - 77.45: 33 Dihedral angle restraints: 12857 sinusoidal: 5253 harmonic: 7604 Sorted by residual: dihedral pdb=" C4' G M 32 " pdb=" C3' G M 32 " pdb=" C2' G M 32 " pdb=" C1' G M 32 " ideal model delta sinusoidal sigma weight residual 36.34 -41.10 77.45 1 3.10e+00 1.04e-01 7.82e+02 dihedral pdb=" C4' C M 31 " pdb=" C3' C M 31 " pdb=" C2' C M 31 " pdb=" C1' C M 31 " ideal model delta sinusoidal sigma weight residual 36.34 -39.13 75.47 1 3.10e+00 1.04e-01 7.48e+02 dihedral pdb=" C4' G M 15 " pdb=" C3' G M 15 " pdb=" C2' G M 15 " pdb=" C1' G M 15 " ideal model delta sinusoidal sigma weight residual 36.35 -38.22 74.56 1 3.10e+00 1.04e-01 7.33e+02 ... (remaining 12854 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2637 0.077 - 0.153: 461 0.153 - 0.230: 68 0.230 - 0.307: 71 0.307 - 0.383: 3 Chirality restraints: 3240 Sorted by residual: chirality pdb=" CB ILE K 15 " pdb=" CA ILE K 15 " pdb=" CG1 ILE K 15 " pdb=" CG2 ILE K 15 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" CB VAL K 49 " pdb=" CA VAL K 49 " pdb=" CG1 VAL K 49 " pdb=" CG2 VAL K 49 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" C3' G M 32 " pdb=" C4' G M 32 " pdb=" O3' G M 32 " pdb=" C2' G M 32 " both_signs ideal model delta sigma weight residual False -2.50 -2.82 0.32 2.00e-01 2.50e+01 2.54e+00 ... (remaining 3237 not shown) Planarity restraints: 4040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 249 " 0.053 5.00e-02 4.00e+02 8.10e-02 1.05e+01 pdb=" N PRO B 250 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO B 250 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 250 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 25 " -0.048 5.00e-02 4.00e+02 7.21e-02 8.32e+00 pdb=" N PRO B 26 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO B 26 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 26 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 263 " 0.027 2.00e-02 2.50e+03 1.70e-02 7.22e+00 pdb=" CG TRP A 263 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP A 263 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP A 263 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 263 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 263 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 263 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 263 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 263 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 263 " 0.007 2.00e-02 2.50e+03 ... (remaining 4037 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3496 2.76 - 3.29: 19674 3.29 - 3.83: 35891 3.83 - 4.36: 40521 4.36 - 4.90: 69553 Nonbonded interactions: 169135 Sorted by model distance: nonbonded pdb=" O PHE H 14 " pdb=" O2' G M 5 " model vdw 2.223 3.040 nonbonded pdb=" O GLU D 283 " pdb=" OH TYR D 325 " model vdw 2.259 3.040 nonbonded pdb=" O PRO A 266 " pdb=" OG1 THR B 28 " model vdw 2.268 3.040 nonbonded pdb=" ND2 ASN D 262 " pdb=" OP2 G M 32 " model vdw 2.299 3.120 nonbonded pdb=" OH TYR D 305 " pdb=" O SER E 54 " model vdw 2.305 3.040 ... (remaining 169130 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 'C' and (resid 6 through 272 or (resid 273 through 275 and (name N or nam \ e CA or name C or name O or name CB )) or resid 276 through 338)) selection = (chain 'D' and (resid 6 through 48 or resid 77 through 231 or resid 244 through \ 338)) selection = (chain 'E' and (resid 6 through 48 or resid 77 through 231 or resid 244 through \ 338)) selection = (chain 'F' and (resid 6 through 48 or resid 77 through 231 or resid 244 through \ 338)) selection = (chain 'G' and (resid 6 through 48 or resid 77 through 231 or resid 244 through \ 338)) selection = (chain 'H' and (resid 6 through 48 or resid 77 through 231 or resid 244 through \ 338)) } 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 group one per residue 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.060 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 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 0.105 22852 Z= 0.295 Angle : 1.021 16.907 31091 Z= 0.539 Chirality : 0.070 0.383 3240 Planarity : 0.006 0.081 4040 Dihedral : 13.010 77.446 8281 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 12.07 % Favored : 87.83 % Rotamer: Outliers : 0.10 % Allowed : 3.15 % Favored : 96.75 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.93 (0.12), residues: 2950 helix: -3.03 (0.12), residues: 876 sheet: -2.63 (0.24), residues: 393 loop : -3.72 (0.12), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 137 TYR 0.025 0.003 TYR E 305 PHE 0.028 0.003 PHE H 216 TRP 0.045 0.005 TRP F 311 HIS 0.019 0.003 HIS H 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00672 / 0.30 (22852) covalent geometry : angle 1.02091 / 0.54 (31091) hydrogen bonds : bond 0.09569 / 6.95 ( 761) hydrogen bonds : angle 7.22651 / 5.21 ( 2148) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5900 Ramachandran restraints generated. 2950 Oldfield, 0 Emsley, 2950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5900 Ramachandran restraints generated. 2950 Oldfield, 0 Emsley, 2950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 418 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LYS cc_start: 0.9077 (mtpp) cc_final: 0.8647 (mtmt) REVERT: B 94 THR cc_start: 0.8553 (t) cc_final: 0.8161 (m) REVERT: B 263 LEU cc_start: 0.8911 (mm) cc_final: 0.8595 (tp) REVERT: B 290 LEU cc_start: 0.7581 (mt) cc_final: 0.7376 (mt) REVERT: B 310 ASP cc_start: 0.7289 (t70) cc_final: 0.7045 (m-30) REVERT: C 323 GLN cc_start: 0.6494 (mt0) cc_final: 0.5793 (mm110) REVERT: D 94 ARG cc_start: 0.6704 (ttt-90) cc_final: 0.6388 (ttp-170) REVERT: D 191 GLU cc_start: 0.6048 (tt0) cc_final: 0.5434 (pm20) REVERT: D 284 PRO cc_start: 0.8756 (Cg_exo) cc_final: 0.7900 (Cg_endo) REVERT: E 208 HIS cc_start: 0.7098 (t-90) cc_final: 0.6621 (t-90) REVERT: F 214 VAL cc_start: 0.8919 (t) cc_final: 0.8715 (m) REVERT: F 223 GLN cc_start: 0.7347 (tp-100) cc_final: 0.7133 (mm-40) REVERT: F 301 LYS cc_start: 0.8240 (mmpt) cc_final: 0.7913 (mmtm) REVERT: G 197 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7698 (tm-30) REVERT: G 301 LYS cc_start: 0.8513 (mmpt) cc_final: 0.8143 (mmtm) REVERT: H 285 TYR cc_start: 0.8029 (m-80) cc_final: 0.7582 (m-80) REVERT: K 31 ARG cc_start: 0.7822 (ptm-80) cc_final: 0.7360 (ptm-80) REVERT: K 78 PRO cc_start: 0.8641 (Cg_exo) cc_final: 0.8430 (Cg_endo) REVERT: K 84 THR cc_start: 0.8831 (p) cc_final: 0.8316 (p) outliers start: 2 outliers final: 0 residues processed: 420 average time/residue: 0.1969 time to fit residues: 120.4769 Evaluate side-chains 233 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.0470 chunk 298 optimal weight: 50.0000 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 GLN B 196 HIS B 269 ASN B 305 HIS C 120 GLN C 141 ASN C 223 GLN D 241 GLN E 129 GLN E 151 ASN F 55 ASN F 83 ASN F 120 GLN ** F 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 GLN G 83 ASN G 120 GLN G 129 GLN H 129 GLN H 164 HIS H 329 ASN K 37 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.193703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.155004 restraints weight = 36653.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.154403 restraints weight = 32816.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.155691 restraints weight = 21632.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.155124 restraints weight = 15099.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.155582 restraints weight = 15746.682| |-----------------------------------------------------------------------------| r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22852 Z= 0.130 Angle : 0.833 15.649 31091 Z= 0.380 Chirality : 0.065 0.850 3240 Planarity : 0.004 0.062 4040 Dihedral : 11.270 147.956 3925 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 1.86 % Allowed : 9.96 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.60 (0.14), residues: 2950 helix: -1.28 (0.16), residues: 880 sheet: -2.09 (0.26), residues: 364 loop : -3.22 (0.13), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 184 TYR 0.013 0.001 TYR C 125 PHE 0.023 0.002 PHE K 46 TRP 0.027 0.002 TRP B 316 HIS 0.007 0.001 HIS G 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (22852) covalent geometry : angle 0.83271 / 0.38 (31091) hydrogen bonds : bond 0.03939 / 3.03 ( 761) hydrogen bonds : angle 5.63786 / 4.11 ( 2148) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5900 Ramachandran restraints generated. 2950 Oldfield, 0 Emsley, 2950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5900 Ramachandran restraints generated. 2950 Oldfield, 0 Emsley, 2950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 302 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 SER cc_start: 0.7698 (m) cc_final: 0.7484 (m) REVERT: A 242 LYS cc_start: 0.9068 (mtpp) cc_final: 0.8368 (mtmt) REVERT: A 247 LYS cc_start: 0.7910 (tppt) cc_final: 0.7115 (mmtt) REVERT: B 27 LEU cc_start: 0.7754 (pp) cc_final: 0.7491 (mm) REVERT: B 94 THR cc_start: 0.8135 (t) cc_final: 0.7609 (m) REVERT: B 215 ASP cc_start: 0.7149 (p0) cc_final: 0.5281 (p0) REVERT: B 263 LEU cc_start: 0.8773 (mm) cc_final: 0.8481 (tp) REVERT: C 323 GLN cc_start: 0.6853 (mt0) cc_final: 0.6050 (mm110) REVERT: D 191 GLU cc_start: 0.6043 (tt0) cc_final: 0.5647 (pm20) REVERT: D 293 LYS cc_start: 0.7448 (mttt) cc_final: 0.6728 (pttp) REVERT: E 110 ASN cc_start: 0.7971 (m110) cc_final: 0.7139 (t0) REVERT: E 271 TYR cc_start: 0.8336 (p90) cc_final: 0.8118 (p90) REVERT: F 83 ASN cc_start: 0.8289 (m-40) cc_final: 0.7713 (m110) REVERT: F 303 ASP cc_start: 0.7247 (t0) cc_final: 0.7020 (t0) REVERT: G 197 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7535 (tm-30) REVERT: G 301 LYS cc_start: 0.8315 (mmpt) cc_final: 0.7962 (mmtm) outliers start: 36 outliers final: 18 residues processed: 324 average time/residue: 0.1727 time to fit residues: 84.9744 Evaluate side-chains 245 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 227 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain E residue 151 ASN Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 245 THR Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain G residue 116 ASP Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 329 ASN Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 88 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 178 optimal weight: 0.9990 chunk 252 optimal weight: 3.9990 chunk 243 optimal weight: 8.9990 chunk 153 optimal weight: 8.9990 chunk 232 optimal weight: 0.9980 chunk 140 optimal weight: 0.1980 chunk 277 optimal weight: 50.0000 chunk 101 optimal weight: 5.9990 chunk 262 optimal weight: 0.9990 chunk 257 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 GLN C 324 HIS E 208 HIS ** E 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 223 GLN H 223 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.193830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.156514 restraints weight = 36300.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.153012 restraints weight = 29729.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.154396 restraints weight = 26181.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.154767 restraints weight = 20470.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.155008 restraints weight = 17441.066| |-----------------------------------------------------------------------------| r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 22852 Z= 0.114 Angle : 0.688 11.979 31091 Z= 0.328 Chirality : 0.052 0.445 3240 Planarity : 0.004 0.063 4040 Dihedral : 11.137 162.757 3925 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 2.07 % Allowed : 11.77 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.94 (0.14), residues: 2950 helix: -0.47 (0.17), residues: 890 sheet: -1.86 (0.26), residues: 373 loop : -2.95 (0.13), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 98 TYR 0.013 0.001 TYR C 125 PHE 0.020 0.001 PHE D 336 TRP 0.028 0.002 TRP B 316 HIS 0.006 0.001 HIS G 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (22852) covalent geometry : angle 0.68768 / 0.33 (31091) hydrogen bonds : bond 0.03522 / 2.66 ( 761) hydrogen bonds : angle 5.11263 / 3.73 ( 2148) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5900 Ramachandran restraints generated. 2950 Oldfield, 0 Emsley, 2950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5900 Ramachandran restraints generated. 2950 Oldfield, 0 Emsley, 2950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 266 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LYS cc_start: 0.8851 (mtpp) cc_final: 0.8424 (mtmt) REVERT: A 247 LYS cc_start: 0.7772 (tppt) cc_final: 0.7475 (mmtt) REVERT: B 27 LEU cc_start: 0.7593 (pp) cc_final: 0.7353 (mp) REVERT: B 94 THR cc_start: 0.8085 (t) cc_final: 0.7667 (m) REVERT: B 263 LEU cc_start: 0.8705 (mm) cc_final: 0.8436 (tp) REVERT: C 323 GLN cc_start: 0.6771 (mt0) cc_final: 0.5973 (mm110) REVERT: D 16 ARG cc_start: 0.5792 (ttp-110) cc_final: 0.5399 (tmm-80) REVERT: D 191 GLU cc_start: 0.6066 (tt0) cc_final: 0.5637 (pm20) REVERT: D 283 GLU cc_start: 0.7244 (tt0) cc_final: 0.7000 (tt0) REVERT: D 293 LYS cc_start: 0.7532 (mttt) cc_final: 0.6861 (pttt) REVERT: E 271 TYR cc_start: 0.8256 (p90) cc_final: 0.7982 (p90) REVERT: G 301 LYS cc_start: 0.8200 (mmpt) cc_final: 0.7886 (mmtm) outliers start: 40 outliers final: 27 residues processed: 291 average time/residue: 0.1685 time to fit residues: 75.5412 Evaluate side-chains 248 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 221 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 251 ASP Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 245 THR Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain G residue 116 ASP Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain H residue 208 HIS Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 88 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 178 optimal weight: 1.9990 chunk 176 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 177 optimal weight: 7.9990 chunk 114 optimal weight: 7.9990 chunk 233 optimal weight: 6.9990 chunk 144 optimal weight: 10.0000 chunk 78 optimal weight: 50.0000 chunk 116 optimal weight: 7.9990 chunk 1 optimal weight: 40.0000 chunk 297 optimal weight: 50.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 ASN C 229 GLN E 151 ASN E 208 HIS E 229 GLN E 241 GLN F 83 ASN F 127 ASN G 120 GLN H 164 HIS H 329 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.185118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.144581 restraints weight = 36094.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.142351 restraints weight = 33090.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.143998 restraints weight = 26323.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.143861 restraints weight = 18850.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.143973 restraints weight = 17509.974| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 22852 Z= 0.278 Angle : 0.827 12.772 31091 Z= 0.401 Chirality : 0.058 0.591 3240 Planarity : 0.005 0.061 4040 Dihedral : 11.352 172.308 3925 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.69 % Favored : 88.27 % Rotamer: Outliers : 3.30 % Allowed : 12.91 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.91 (0.15), residues: 2950 helix: -0.41 (0.18), residues: 878 sheet: -1.91 (0.26), residues: 398 loop : -2.92 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 296 TYR 0.020 0.002 TYR G 295 PHE 0.023 0.002 PHE H 147 TRP 0.026 0.003 TRP G 30 HIS 0.010 0.002 HIS D 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00638 / 0.28 (22852) covalent geometry : angle 0.82698 / 0.40 (31091) hydrogen bonds : bond 0.04341 / 3.27 ( 761) hydrogen bonds : angle 5.40382 / 3.92 ( 2148) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5900 Ramachandran restraints generated. 2950 Oldfield, 0 Emsley, 2950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5900 Ramachandran restraints generated. 2950 Oldfield, 0 Emsley, 2950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 228 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LYS cc_start: 0.8830 (mtpp) cc_final: 0.8528 (mtmt) REVERT: A 247 LYS cc_start: 0.8128 (tppt) cc_final: 0.7378 (mmtt) REVERT: B 61 ILE cc_start: 0.8478 (mt) cc_final: 0.8237 (mt) REVERT: B 94 THR cc_start: 0.8184 (t) cc_final: 0.7868 (m) REVERT: C 323 GLN cc_start: 0.6854 (mt0) cc_final: 0.6012 (mm110) REVERT: D 256 HIS cc_start: 0.7291 (m170) cc_final: 0.7074 (m-70) REVERT: E 76 LEU cc_start: 0.6992 (OUTLIER) cc_final: 0.6641 (tt) REVERT: E 271 TYR cc_start: 0.8496 (p90) cc_final: 0.8233 (p90) REVERT: G 301 LYS cc_start: 0.8295 (mmpt) cc_final: 0.8011 (mmtm) REVERT: H 329 ASN cc_start: 0.8944 (OUTLIER) cc_final: 0.7952 (t0) REVERT: K 80 ILE cc_start: 0.8714 (tp) cc_final: 0.8486 (tp) REVERT: K 90 GLU cc_start: 0.8210 (pt0) cc_final: 0.7955 (pt0) outliers start: 64 outliers final: 52 residues processed: 272 average time/residue: 0.1636 time to fit residues: 69.6282 Evaluate side-chains 269 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 215 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 151 ASN Chi-restraints excluded: chain E residue 251 ASP Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 231 LEU Chi-restraints excluded: chain F residue 245 THR Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 116 ASP Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain H residue 60 LYS Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain H residue 208 HIS Chi-restraints excluded: chain H residue 212 GLU Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain H residue 329 ASN Chi-restraints excluded: chain K residue 15 ILE Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain K residue 92 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 11 optimal weight: 50.0000 chunk 113 optimal weight: 0.9990 chunk 243 optimal weight: 1.9990 chunk 237 optimal weight: 5.9990 chunk 239 optimal weight: 4.9990 chunk 274 optimal weight: 8.9990 chunk 134 optimal weight: 8.9990 chunk 178 optimal weight: 0.9990 chunk 36 optimal weight: 50.0000 chunk 258 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 ASN G 223 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.190358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.151978 restraints weight = 35658.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.147662 restraints weight = 30228.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.148728 restraints weight = 28509.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.149037 restraints weight = 23893.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.149358 restraints weight = 20191.732| |-----------------------------------------------------------------------------| r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 22852 Z= 0.140 Angle : 0.695 14.088 31091 Z= 0.333 Chirality : 0.051 0.389 3240 Planarity : 0.004 0.057 4040 Dihedral : 11.069 171.726 3925 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 3.10 % Allowed : 13.94 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.55 (0.15), residues: 2950 helix: 0.02 (0.18), residues: 878 sheet: -1.77 (0.26), residues: 397 loop : -2.76 (0.14), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 98 TYR 0.017 0.001 TYR D 305 PHE 0.016 0.002 PHE D 304 TRP 0.034 0.002 TRP B 316 HIS 0.006 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (22852) covalent geometry : angle 0.69474 / 0.33 (31091) hydrogen bonds : bond 0.03529 / 2.66 ( 761) hydrogen bonds : angle 4.97800 / 3.63 ( 2148) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5900 Ramachandran restraints generated. 2950 Oldfield, 0 Emsley, 2950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5900 Ramachandran restraints generated. 2950 Oldfield, 0 Emsley, 2950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 238 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 GLU cc_start: 0.7361 (pm20) cc_final: 0.7093 (pm20) REVERT: A 247 LYS cc_start: 0.8065 (tppt) cc_final: 0.7440 (mmtt) REVERT: B 94 THR cc_start: 0.8058 (t) cc_final: 0.7750 (m) REVERT: B 263 LEU cc_start: 0.8747 (mm) cc_final: 0.8336 (tp) REVERT: C 323 GLN cc_start: 0.6642 (mt0) cc_final: 0.5838 (mm110) REVERT: D 16 ARG cc_start: 0.5804 (ttp-110) cc_final: 0.5439 (tmm-80) REVERT: D 191 GLU cc_start: 0.6408 (tt0) cc_final: 0.5776 (pm20) REVERT: D 244 LYS cc_start: 0.4783 (mtpm) cc_final: 0.4422 (tptp) REVERT: E 271 TYR cc_start: 0.8398 (p90) cc_final: 0.8115 (p90) REVERT: F 12 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8477 (mt) REVERT: G 301 LYS cc_start: 0.8189 (mmpt) cc_final: 0.7938 (mmtm) REVERT: K 90 GLU cc_start: 0.8166 (pt0) cc_final: 0.7895 (pt0) outliers start: 60 outliers final: 36 residues processed: 274 average time/residue: 0.1707 time to fit residues: 71.8732 Evaluate side-chains 258 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 221 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 251 ASP Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 245 THR Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain G residue 116 ASP Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain H residue 60 LYS Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain H residue 208 HIS Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain K residue 15 ILE Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 88 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 281 optimal weight: 20.0000 chunk 173 optimal weight: 3.9990 chunk 201 optimal weight: 4.9990 chunk 219 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 248 optimal weight: 7.9990 chunk 270 optimal weight: 0.0070 chunk 220 optimal weight: 3.9990 chunk 208 optimal weight: 4.9990 chunk 5 optimal weight: 30.0000 chunk 70 optimal weight: 5.9990 overall best weight: 2.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 GLN F 83 ASN ** H 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 329 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.189259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.149440 restraints weight = 35683.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.148184 restraints weight = 30104.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.149475 restraints weight = 23195.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.148859 restraints weight = 17047.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.149151 restraints weight = 15996.036| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 22852 Z= 0.151 Angle : 0.685 15.352 31091 Z= 0.328 Chirality : 0.050 0.387 3240 Planarity : 0.004 0.055 4040 Dihedral : 10.999 173.291 3925 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 2.84 % Allowed : 14.87 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.39 (0.15), residues: 2950 helix: 0.17 (0.18), residues: 878 sheet: -1.71 (0.26), residues: 390 loop : -2.66 (0.14), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 31 TYR 0.014 0.001 TYR D 114 PHE 0.021 0.002 PHE K 46 TRP 0.028 0.002 TRP A 263 HIS 0.005 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (22852) covalent geometry : angle 0.68541 / 0.33 (31091) hydrogen bonds : bond 0.03475 / 2.62 ( 761) hydrogen bonds : angle 4.83987 / 3.53 ( 2148) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5900 Ramachandran restraints generated. 2950 Oldfield, 0 Emsley, 2950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5900 Ramachandran restraints generated. 2950 Oldfield, 0 Emsley, 2950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 234 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 LYS cc_start: 0.8024 (tppt) cc_final: 0.7431 (mmtt) REVERT: B 94 THR cc_start: 0.8146 (t) cc_final: 0.7834 (m) REVERT: B 263 LEU cc_start: 0.8737 (mm) cc_final: 0.8320 (tp) REVERT: C 323 GLN cc_start: 0.6643 (mt0) cc_final: 0.5819 (mm110) REVERT: D 191 GLU cc_start: 0.6289 (tt0) cc_final: 0.5751 (pm20) REVERT: D 244 LYS cc_start: 0.4594 (mtpm) cc_final: 0.4340 (tptp) REVERT: E 271 TYR cc_start: 0.8334 (p90) cc_final: 0.8030 (p90) REVERT: G 301 LYS cc_start: 0.8200 (mmpt) cc_final: 0.7921 (mmtm) REVERT: H 329 ASN cc_start: 0.8756 (OUTLIER) cc_final: 0.7941 (t0) REVERT: K 90 GLU cc_start: 0.8165 (pt0) cc_final: 0.7921 (pt0) outliers start: 55 outliers final: 41 residues processed: 267 average time/residue: 0.1616 time to fit residues: 67.9084 Evaluate side-chains 255 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 213 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain E residue 251 ASP Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 245 THR Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 280 ILE Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain G residue 116 ASP Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain H residue 60 LYS Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain H residue 208 HIS Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain H residue 329 ASN Chi-restraints excluded: chain K residue 15 ILE Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 88 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 195 optimal weight: 5.9990 chunk 162 optimal weight: 2.9990 chunk 119 optimal weight: 20.0000 chunk 125 optimal weight: 10.0000 chunk 149 optimal weight: 10.0000 chunk 267 optimal weight: 6.9990 chunk 291 optimal weight: 50.0000 chunk 97 optimal weight: 50.0000 chunk 246 optimal weight: 6.9990 chunk 41 optimal weight: 50.0000 chunk 56 optimal weight: 0.0060 overall best weight: 4.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 ASN ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 329 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.186827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.147177 restraints weight = 35590.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.145018 restraints weight = 31518.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.146434 restraints weight = 26616.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.146488 restraints weight = 18612.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.146686 restraints weight = 17228.215| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 22852 Z= 0.207 Angle : 0.725 15.097 31091 Z= 0.350 Chirality : 0.053 0.416 3240 Planarity : 0.004 0.053 4040 Dihedral : 11.081 174.977 3925 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.31 % Favored : 89.66 % Rotamer: Outliers : 2.89 % Allowed : 15.23 % Favored : 81.88 % 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 are not related in a simple way. whole: -2.41 (0.15), residues: 2950 helix: 0.12 (0.18), residues: 878 sheet: -1.66 (0.27), residues: 384 loop : -2.67 (0.14), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 31 TYR 0.013 0.002 TYR G 295 PHE 0.020 0.002 PHE E 226 TRP 0.027 0.002 TRP A 263 HIS 0.007 0.001 HIS D 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.21 (22852) covalent geometry : angle 0.72547 / 0.35 (31091) hydrogen bonds : bond 0.03764 / 2.83 ( 761) hydrogen bonds : angle 4.93413 / 3.59 ( 2148) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5900 Ramachandran restraints generated. 2950 Oldfield, 0 Emsley, 2950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5900 Ramachandran restraints generated. 2950 Oldfield, 0 Emsley, 2950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 220 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 GLU cc_start: 0.7087 (pm20) cc_final: 0.6578 (pm20) REVERT: A 247 LYS cc_start: 0.8044 (tppt) cc_final: 0.7487 (mmtt) REVERT: B 94 THR cc_start: 0.8150 (t) cc_final: 0.7858 (m) REVERT: B 99 GLU cc_start: 0.7531 (pt0) cc_final: 0.7260 (pt0) REVERT: B 263 LEU cc_start: 0.8770 (mm) cc_final: 0.8339 (tp) REVERT: C 184 ARG cc_start: 0.2316 (mtp-110) cc_final: 0.1585 (ptt90) REVERT: C 323 GLN cc_start: 0.6675 (mt0) cc_final: 0.5817 (mm110) REVERT: D 191 GLU cc_start: 0.6351 (tt0) cc_final: 0.5767 (pm20) REVERT: E 271 TYR cc_start: 0.8350 (p90) cc_final: 0.8018 (p90) REVERT: G 301 LYS cc_start: 0.8202 (mmpt) cc_final: 0.7909 (mmtm) REVERT: K 90 GLU cc_start: 0.8159 (pt0) cc_final: 0.7895 (pt0) outliers start: 56 outliers final: 47 residues processed: 254 average time/residue: 0.1625 time to fit residues: 64.6785 Evaluate side-chains 257 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 210 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain E residue 251 ASP Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 245 THR Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 280 ILE Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 116 ASP Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain H residue 60 LYS Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain H residue 208 HIS Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain H residue 329 ASN Chi-restraints excluded: chain K residue 15 ILE Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain K residue 96 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 64 optimal weight: 30.0000 chunk 78 optimal weight: 9.9990 chunk 88 optimal weight: 20.0000 chunk 44 optimal weight: 0.2980 chunk 35 optimal weight: 50.0000 chunk 85 optimal weight: 50.0000 chunk 123 optimal weight: 9.9990 chunk 8 optimal weight: 30.0000 chunk 20 optimal weight: 40.0000 chunk 238 optimal weight: 0.9990 chunk 150 optimal weight: 0.0030 overall best weight: 4.2596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 ASN ** H 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 329 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.186791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.146794 restraints weight = 35654.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.144462 restraints weight = 35025.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.145860 restraints weight = 27608.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.145981 restraints weight = 19864.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.146123 restraints weight = 18385.019| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 22852 Z= 0.196 Angle : 0.720 16.148 31091 Z= 0.347 Chirality : 0.052 0.397 3240 Planarity : 0.004 0.051 4040 Dihedral : 11.063 175.183 3925 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 3.10 % Allowed : 15.44 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.15), residues: 2950 helix: 0.16 (0.18), residues: 878 sheet: -1.65 (0.27), residues: 386 loop : -2.64 (0.14), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 98 TYR 0.012 0.002 TYR G 295 PHE 0.022 0.002 PHE E 226 TRP 0.050 0.002 TRP B 316 HIS 0.006 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.20 (22852) covalent geometry : angle 0.72010 / 0.35 (31091) hydrogen bonds : bond 0.03681 / 2.78 ( 761) hydrogen bonds : angle 4.91749 / 3.58 ( 2148) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5900 Ramachandran restraints generated. 2950 Oldfield, 0 Emsley, 2950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5900 Ramachandran restraints generated. 2950 Oldfield, 0 Emsley, 2950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 217 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 GLU cc_start: 0.7252 (pm20) cc_final: 0.6894 (pm20) REVERT: A 242 LYS cc_start: 0.8991 (mtpt) cc_final: 0.8480 (mtmt) REVERT: A 247 LYS cc_start: 0.8030 (tppt) cc_final: 0.7507 (mmtt) REVERT: B 94 THR cc_start: 0.8134 (t) cc_final: 0.7856 (m) REVERT: B 99 GLU cc_start: 0.7544 (pt0) cc_final: 0.7239 (pt0) REVERT: B 263 LEU cc_start: 0.8786 (mm) cc_final: 0.8354 (tp) REVERT: C 184 ARG cc_start: 0.2343 (mtp-110) cc_final: 0.1583 (ptt90) REVERT: C 323 GLN cc_start: 0.6667 (mt0) cc_final: 0.5811 (mm110) REVERT: D 152 ARG cc_start: 0.4705 (ttt-90) cc_final: 0.2458 (ttp-110) REVERT: D 191 GLU cc_start: 0.6362 (tt0) cc_final: 0.5776 (pm20) REVERT: E 271 TYR cc_start: 0.8315 (p90) cc_final: 0.7984 (p90) REVERT: G 301 LYS cc_start: 0.8195 (mmpt) cc_final: 0.7904 (mmtm) REVERT: H 25 MET cc_start: 0.8185 (mtp) cc_final: 0.7980 (mtm) REVERT: K 29 LEU cc_start: 0.7310 (OUTLIER) cc_final: 0.7066 (mp) REVERT: K 90 GLU cc_start: 0.8156 (pt0) cc_final: 0.7894 (pt0) outliers start: 60 outliers final: 51 residues processed: 251 average time/residue: 0.1689 time to fit residues: 66.1670 Evaluate side-chains 257 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 205 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain E residue 251 ASP Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 87 ASP Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 245 THR Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 280 ILE Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 116 ASP Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain H residue 60 LYS Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain H residue 208 HIS Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 280 ILE Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain H residue 329 ASN Chi-restraints excluded: chain K residue 15 ILE Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain K residue 96 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 54 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 207 optimal weight: 5.9990 chunk 92 optimal weight: 50.0000 chunk 230 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 74 optimal weight: 50.0000 chunk 231 optimal weight: 0.8980 chunk 198 optimal weight: 0.9990 chunk 236 optimal weight: 6.9990 chunk 220 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 GLN ** E 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 HIS F 83 ASN H 83 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.193270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.155242 restraints weight = 35532.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.150122 restraints weight = 29958.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.151368 restraints weight = 26008.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.151788 restraints weight = 21135.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.151964 restraints weight = 19385.138| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 22852 Z= 0.110 Angle : 0.649 16.568 31091 Z= 0.310 Chirality : 0.048 0.362 3240 Planarity : 0.003 0.048 4040 Dihedral : 10.809 172.044 3925 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 2.22 % Allowed : 16.42 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.16), residues: 2950 helix: 0.48 (0.18), residues: 881 sheet: -1.39 (0.28), residues: 366 loop : -2.48 (0.14), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 98 TYR 0.016 0.001 TYR K 51 PHE 0.020 0.001 PHE E 226 TRP 0.027 0.001 TRP E 39 HIS 0.005 0.001 HIS H 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (22852) covalent geometry : angle 0.64919 / 0.31 (31091) hydrogen bonds : bond 0.03200 / 2.40 ( 761) hydrogen bonds : angle 4.59787 / 3.37 ( 2148) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5900 Ramachandran restraints generated. 2950 Oldfield, 0 Emsley, 2950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5900 Ramachandran restraints generated. 2950 Oldfield, 0 Emsley, 2950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 238 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 GLU cc_start: 0.7307 (pm20) cc_final: 0.6957 (pm20) REVERT: A 242 LYS cc_start: 0.9005 (mtpt) cc_final: 0.8600 (mtmt) REVERT: A 247 LYS cc_start: 0.7895 (tppt) cc_final: 0.7364 (mmtt) REVERT: B 94 THR cc_start: 0.7951 (t) cc_final: 0.7683 (m) REVERT: B 99 GLU cc_start: 0.7512 (pt0) cc_final: 0.7237 (pt0) REVERT: B 263 LEU cc_start: 0.8642 (mm) cc_final: 0.8263 (tp) REVERT: C 184 ARG cc_start: 0.2365 (mtp-110) cc_final: 0.1534 (ptt90) REVERT: C 323 GLN cc_start: 0.6560 (mt0) cc_final: 0.5759 (mm110) REVERT: D 16 ARG cc_start: 0.6054 (ttp-110) cc_final: 0.5430 (tmm-80) REVERT: D 191 GLU cc_start: 0.6397 (tt0) cc_final: 0.5629 (pm20) REVERT: E 271 TYR cc_start: 0.8189 (p90) cc_final: 0.7498 (p90) REVERT: G 301 LYS cc_start: 0.8105 (mmpt) cc_final: 0.7877 (mmtm) REVERT: H 25 MET cc_start: 0.8085 (mtp) cc_final: 0.7866 (mtp) REVERT: K 90 GLU cc_start: 0.8194 (pt0) cc_final: 0.7859 (pt0) outliers start: 43 outliers final: 33 residues processed: 263 average time/residue: 0.1619 time to fit residues: 66.2621 Evaluate side-chains 238 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 205 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 TRP Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 87 ASP Chi-restraints excluded: chain F residue 245 THR Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain G residue 75 ASN Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 60 LYS Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain H residue 208 HIS Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 280 ILE Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain K residue 15 ILE Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain K residue 96 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 138 optimal weight: 20.0000 chunk 16 optimal weight: 8.9990 chunk 266 optimal weight: 20.0000 chunk 200 optimal weight: 6.9990 chunk 76 optimal weight: 9.9990 chunk 122 optimal weight: 40.0000 chunk 217 optimal weight: 9.9990 chunk 159 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 243 optimal weight: 8.9990 chunk 126 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 323 GLN E 151 ASN ** E 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 ASN ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.181404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.141669 restraints weight = 36080.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.139373 restraints weight = 33562.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.141170 restraints weight = 26661.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.141120 restraints weight = 18486.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.141289 restraints weight = 17278.728| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 22852 Z= 0.303 Angle : 0.844 15.966 31091 Z= 0.409 Chirality : 0.057 0.468 3240 Planarity : 0.005 0.050 4040 Dihedral : 11.241 178.817 3925 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 12.17 % Favored : 87.80 % Rotamer: Outliers : 2.43 % Allowed : 16.57 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.15), residues: 2950 helix: 0.05 (0.18), residues: 877 sheet: -1.62 (0.27), residues: 379 loop : -2.65 (0.14), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 296 TYR 0.019 0.002 TYR B 304 PHE 0.026 0.002 PHE D 304 TRP 0.049 0.003 TRP B 316 HIS 0.009 0.002 HIS D 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00697 / 0.30 (22852) covalent geometry : angle 0.84416 / 0.41 (31091) hydrogen bonds : bond 0.04276 / 3.21 ( 761) hydrogen bonds : angle 5.19318 / 3.78 ( 2148) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5900 Ramachandran restraints generated. 2950 Oldfield, 0 Emsley, 2950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5900 Ramachandran restraints generated. 2950 Oldfield, 0 Emsley, 2950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 210 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 LYS cc_start: 0.8014 (tppt) cc_final: 0.7491 (mmtt) REVERT: B 94 THR cc_start: 0.8264 (t) cc_final: 0.8005 (m) REVERT: B 99 GLU cc_start: 0.7566 (pt0) cc_final: 0.7267 (pt0) REVERT: C 323 GLN cc_start: 0.6714 (mt0) cc_final: 0.5865 (mm110) REVERT: D 152 ARG cc_start: 0.4748 (ttt-90) cc_final: 0.2616 (ttp-110) REVERT: D 191 GLU cc_start: 0.6367 (tt0) cc_final: 0.5792 (pm20) REVERT: E 271 TYR cc_start: 0.8412 (p90) cc_final: 0.8033 (p90) REVERT: G 301 LYS cc_start: 0.8283 (mmpt) cc_final: 0.7997 (mmtm) REVERT: K 29 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.7130 (mp) REVERT: K 90 GLU cc_start: 0.8106 (pt0) cc_final: 0.7854 (pt0) outliers start: 47 outliers final: 38 residues processed: 242 average time/residue: 0.1581 time to fit residues: 59.9252 Evaluate side-chains 236 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 197 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 151 ASN Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 87 ASP Chi-restraints excluded: chain F residue 245 THR Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain H residue 208 HIS Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 280 ILE Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain K residue 15 ILE Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain K residue 92 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 141 optimal weight: 6.9990 chunk 11 optimal weight: 50.0000 chunk 215 optimal weight: 0.9990 chunk 175 optimal weight: 0.7980 chunk 252 optimal weight: 4.9990 chunk 66 optimal weight: 0.0470 chunk 140 optimal weight: 9.9990 chunk 279 optimal weight: 0.0770 chunk 239 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 253 optimal weight: 0.8980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 323 GLN E 151 ASN F 83 ASN ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.183464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.143908 restraints weight = 35861.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.141277 restraints weight = 34630.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.142674 restraints weight = 27393.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.142976 restraints weight = 20058.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.143168 restraints weight = 18777.423| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.299 22852 Z= 0.234 Angle : 0.947 59.199 31091 Z= 0.491 Chirality : 0.057 0.648 3240 Planarity : 0.005 0.110 4040 Dihedral : 11.259 178.968 3925 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 12.03 % Favored : 87.93 % Rotamer: Outliers : 2.07 % Allowed : 17.14 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.15), residues: 2950 helix: 0.09 (0.18), residues: 871 sheet: -1.68 (0.27), residues: 384 loop : -2.65 (0.14), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.001 ARG K 31 TYR 0.017 0.002 TYR B 304 PHE 0.026 0.002 PHE D 304 TRP 0.043 0.003 TRP B 316 HIS 0.010 0.002 HIS E 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.23 (22852) covalent geometry : angle 0.94660 / 0.49 (31091) hydrogen bonds : bond 0.04153 / 3.11 ( 761) hydrogen bonds : angle 5.17025 / 3.76 ( 2148) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3484.27 seconds wall clock time: 61 minutes 33.80 seconds (3693.80 seconds total)