Starting phenix.real_space_refine on Wed Nov 19 09:03:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6b48_7052/11_2025/6b48_7052.cif Found real_map, /net/cci-nas-00/data/ceres_data/6b48_7052/11_2025/6b48_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6b48_7052/11_2025/6b48_7052.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6b48_7052/11_2025/6b48_7052.map" model { file = "/net/cci-nas-00/data/ceres_data/6b48_7052/11_2025/6b48_7052.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6b48_7052/11_2025/6b48_7052.cif" } 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-2.0-5881/lib/python3.9/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: {'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 11, 'rna3p_pur': 20, 'rna3p_pyr': 19} Link IDs: {'rna2p': 19, 'rna3p': 40} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 6.05, per 1000 atoms: 0.27 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: 1.87 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: 2.58 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: 3.76 Time building geometry restraints manager: 2.52 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: 30668 3.38 - 6.76: 390 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 - 32.19: 12760 32.19 - 64.37: 290 64.37 - 96.56: 33 96.56 - 128.74: 2 128.74 - 160.93: 2 Dihedral angle restraints: 13087 sinusoidal: 5483 harmonic: 7604 Sorted by residual: dihedral pdb=" O4' U M 43 " pdb=" C1' U M 43 " pdb=" N1 U M 43 " pdb=" C2 U M 43 " ideal model delta sinusoidal sigma weight residual 200.00 39.07 160.93 1 1.50e+01 4.44e-03 8.30e+01 dihedral pdb=" O4' U M 21 " pdb=" C1' U M 21 " pdb=" N1 U M 21 " pdb=" C2 U M 21 " ideal model delta sinusoidal sigma weight residual 200.00 48.90 151.10 1 1.50e+01 4.44e-03 8.00e+01 dihedral pdb=" CA ARG A 222 " pdb=" C ARG A 222 " pdb=" N SER A 223 " pdb=" CA SER A 223 " ideal model delta harmonic sigma weight residual 180.00 143.32 36.68 0 5.00e+00 4.00e-02 5.38e+01 ... (remaining 13084 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2727 0.077 - 0.153: 467 0.153 - 0.230: 38 0.230 - 0.307: 6 0.307 - 0.383: 2 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=" CB ILE E 53 " pdb=" CA ILE E 53 " pdb=" CG1 ILE E 53 " pdb=" CG2 ILE E 53 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.91e+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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 23.330 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 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= 0.294 Angle : 0.980 16.907 31091 Z= 0.531 Chirality : 0.057 0.383 3240 Planarity : 0.006 0.081 4040 Dihedral : 13.640 160.929 8511 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 covalent geometry : bond 0.00667 (22852) covalent geometry : angle 0.98004 (31091) hydrogen bonds : bond 0.09569 ( 761) hydrogen bonds : angle 7.22651 ( 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 : 0.829 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: 0.2097 time to fit residues: 125.7773 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 : 0.909 ------------------------------------------------------------------------------- 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: 0.6980 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: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 GLN B 19 ASN 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 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: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.193732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.154592 restraints weight = 36627.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.153771 restraints weight = 30949.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.154871 restraints weight = 21261.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.154145 restraints weight = 15138.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.154768 restraints weight = 16374.742| |-----------------------------------------------------------------------------| r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 22852 Z= 0.117 Angle : 0.609 11.778 31091 Z= 0.321 Chirality : 0.042 0.242 3240 Planarity : 0.005 0.064 4040 Dihedral : 14.725 159.220 4155 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 1.96 % Allowed : 9.76 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.58 (0.14), residues: 2950 helix: -1.25 (0.16), residues: 884 sheet: -2.11 (0.26), residues: 356 loop : -3.21 (0.13), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 98 TYR 0.013 0.001 TYR H 271 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 covalent geometry : bond 0.00244 (22852) covalent geometry : angle 0.60898 (31091) hydrogen bonds : bond 0.03791 ( 761) hydrogen bonds : angle 5.55186 ( 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 344 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 306 time to evaluate : 0.860 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 197 SER cc_start: 0.7682 (m) cc_final: 0.7468 (m) REVERT: A 242 LYS cc_start: 0.9087 (mtpp) cc_final: 0.8760 (mtmt) REVERT: A 247 LYS cc_start: 0.7941 (tppt) cc_final: 0.7135 (mmtt) REVERT: B 27 LEU cc_start: 0.7737 (pp) cc_final: 0.7513 (mm) REVERT: B 94 THR cc_start: 0.8123 (t) cc_final: 0.7598 (m) REVERT: B 215 ASP cc_start: 0.7219 (p0) cc_final: 0.5243 (p0) REVERT: B 263 LEU cc_start: 0.8762 (mm) cc_final: 0.8476 (tp) REVERT: C 323 GLN cc_start: 0.6831 (mt0) cc_final: 0.6017 (mm110) REVERT: D 191 GLU cc_start: 0.6001 (tt0) cc_final: 0.5616 (pm20) REVERT: D 293 LYS cc_start: 0.7409 (mttt) cc_final: 0.6758 (pttt) REVERT: E 110 ASN cc_start: 0.7953 (m110) cc_final: 0.7149 (t0) REVERT: E 271 TYR cc_start: 0.8335 (p90) cc_final: 0.8089 (p90) REVERT: F 303 ASP cc_start: 0.7220 (t0) cc_final: 0.7019 (t0) REVERT: G 197 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7513 (tm-30) REVERT: G 301 LYS cc_start: 0.8274 (mmpt) cc_final: 0.7909 (mmtm) outliers start: 38 outliers final: 16 residues processed: 329 average time/residue: 0.1815 time to fit residues: 89.3705 Evaluate side-chains 253 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 237 time to evaluate : 0.847 ------------------------------------------------------------------------------- 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 245 THR Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain E residue 151 ASN 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 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 88 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 178 optimal weight: 0.9980 chunk 252 optimal weight: 8.9990 chunk 243 optimal weight: 5.9990 chunk 153 optimal weight: 8.9990 chunk 232 optimal weight: 7.9990 chunk 140 optimal weight: 0.2980 chunk 277 optimal weight: 10.0000 chunk 101 optimal weight: 8.9990 chunk 262 optimal weight: 2.9990 chunk 257 optimal weight: 8.9990 chunk 93 optimal weight: 7.9990 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 HIS C 129 GLN C 324 HIS D 256 HIS E 208 HIS E 229 GLN E 241 GLN F 83 ASN F 223 GLN H 164 HIS H 223 GLN H 329 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.189002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.150008 restraints weight = 36336.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.146343 restraints weight = 32607.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.147490 restraints weight = 30124.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.148288 restraints weight = 21419.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.148248 restraints weight = 18264.466| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 22852 Z= 0.176 Angle : 0.629 12.129 31091 Z= 0.329 Chirality : 0.043 0.202 3240 Planarity : 0.004 0.064 4040 Dihedral : 14.554 159.861 4155 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.46 % Favored : 90.51 % Rotamer: Outliers : 2.43 % Allowed : 12.13 % Favored : 85.44 % 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: -3.08 (0.14), residues: 2950 helix: -0.58 (0.17), residues: 881 sheet: -2.08 (0.26), residues: 382 loop : -3.00 (0.14), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 296 TYR 0.013 0.002 TYR C 125 PHE 0.018 0.002 PHE D 304 TRP 0.026 0.002 TRP D 270 HIS 0.008 0.001 HIS D 324 Details of bonding type rmsd covalent geometry : bond 0.00399 (22852) covalent geometry : angle 0.62912 (31091) hydrogen bonds : bond 0.03904 ( 761) hydrogen bonds : angle 5.27478 ( 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 295 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 248 time to evaluate : 0.858 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: 0.7917 (m) cc_final: 0.7710 (m) REVERT: A 242 LYS cc_start: 0.9087 (mtpp) cc_final: 0.8432 (mtmt) REVERT: A 247 LYS cc_start: 0.7973 (tppt) cc_final: 0.7323 (mmtt) REVERT: B 94 THR cc_start: 0.8213 (t) cc_final: 0.7836 (m) REVERT: B 263 LEU cc_start: 0.8767 (mm) cc_final: 0.8432 (tp) REVERT: C 323 GLN cc_start: 0.6831 (mt0) cc_final: 0.5988 (mm110) REVERT: D 16 ARG cc_start: 0.5911 (ttp-110) cc_final: 0.5401 (tmm-80) REVERT: D 191 GLU cc_start: 0.6267 (tt0) cc_final: 0.5742 (pm20) REVERT: D 270 TRP cc_start: 0.5880 (m-90) cc_final: 0.5657 (m-90) REVERT: D 293 LYS cc_start: 0.7608 (mttt) cc_final: 0.6821 (pttp) REVERT: E 271 TYR cc_start: 0.8372 (p90) cc_final: 0.8113 (p90) REVERT: E 302 LEU cc_start: 0.8711 (tp) cc_final: 0.8462 (tt) REVERT: F 231 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8138 (tp) REVERT: G 197 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7614 (tm-30) REVERT: G 301 LYS cc_start: 0.8287 (mmpt) cc_final: 0.7976 (mmtm) REVERT: H 329 ASN cc_start: 0.8919 (OUTLIER) cc_final: 0.8048 (t0) outliers start: 47 outliers final: 32 residues processed: 277 average time/residue: 0.1771 time to fit residues: 74.7777 Evaluate side-chains 252 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 218 time to evaluate : 0.845 ------------------------------------------------------------------------------- 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 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 214 VAL 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 124 THR 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 178 optimal weight: 0.9990 chunk 176 optimal weight: 5.9990 chunk 112 optimal weight: 9.9990 chunk 177 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 233 optimal weight: 4.9990 chunk 144 optimal weight: 0.5980 chunk 78 optimal weight: 9.9990 chunk 116 optimal weight: 6.9990 chunk 1 optimal weight: 40.0000 chunk 297 optimal weight: 50.0000 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 164 HIS E 151 ASN E 229 GLN F 83 ASN G 120 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.188390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.147832 restraints weight = 36682.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.146201 restraints weight = 32081.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.147282 restraints weight = 24595.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.146873 restraints weight = 18131.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.147175 restraints weight = 18278.816| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2546 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= 0.183 Angle : 0.620 12.361 31091 Z= 0.324 Chirality : 0.043 0.204 3240 Planarity : 0.004 0.061 4040 Dihedral : 14.451 160.130 4155 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.59 % Favored : 90.37 % Rotamer: Outliers : 3.05 % Allowed : 12.44 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.80 (0.15), residues: 2950 helix: -0.20 (0.18), residues: 877 sheet: -1.97 (0.25), residues: 398 loop : -2.89 (0.14), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 98 TYR 0.017 0.002 TYR D 305 PHE 0.021 0.002 PHE E 226 TRP 0.036 0.002 TRP B 316 HIS 0.008 0.001 HIS D 324 Details of bonding type rmsd covalent geometry : bond 0.00412 (22852) covalent geometry : angle 0.61974 (31091) hydrogen bonds : bond 0.03810 ( 761) hydrogen bonds : angle 5.12348 ( 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 291 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 232 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LYS cc_start: 0.8888 (mtpp) cc_final: 0.8536 (mtmt) REVERT: A 247 LYS cc_start: 0.7987 (tppt) cc_final: 0.7404 (mmtt) REVERT: B 94 THR cc_start: 0.8097 (t) cc_final: 0.7796 (m) REVERT: B 263 LEU cc_start: 0.8785 (mm) cc_final: 0.8456 (tp) REVERT: C 323 GLN cc_start: 0.6821 (mt0) cc_final: 0.5958 (mm110) REVERT: D 191 GLU cc_start: 0.6347 (tt0) cc_final: 0.5751 (pm20) REVERT: D 293 LYS cc_start: 0.7599 (mttt) cc_final: 0.6760 (pttp) REVERT: E 76 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6615 (tt) REVERT: E 271 TYR cc_start: 0.8392 (p90) cc_final: 0.8104 (p90) REVERT: E 302 LEU cc_start: 0.8835 (tp) cc_final: 0.8474 (tt) REVERT: F 231 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8084 (tp) REVERT: G 301 LYS cc_start: 0.8261 (mmpt) cc_final: 0.7974 (mmtm) outliers start: 59 outliers final: 43 residues processed: 269 average time/residue: 0.1677 time to fit residues: 69.9474 Evaluate side-chains 262 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 217 time to evaluate : 0.691 ------------------------------------------------------------------------------- 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 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 214 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 76 LEU 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 54 SER Chi-restraints excluded: chain F residue 124 THR 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 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 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 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: 0.8980 chunk 243 optimal weight: 6.9990 chunk 237 optimal weight: 10.0000 chunk 239 optimal weight: 6.9990 chunk 274 optimal weight: 8.9990 chunk 134 optimal weight: 0.1980 chunk 178 optimal weight: 0.9990 chunk 36 optimal weight: 50.0000 chunk 258 optimal weight: 0.6980 chunk 2 optimal weight: 0.0030 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS B 133 GLN B 282 ASN E 151 ASN F 83 ASN H 241 GLN H 329 ASN K 9 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.194595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.155696 restraints weight = 35982.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.154573 restraints weight = 34765.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.155948 restraints weight = 24551.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.155894 restraints weight = 18372.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.156279 restraints weight = 17533.083| |-----------------------------------------------------------------------------| r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 22852 Z= 0.100 Angle : 0.537 11.830 31091 Z= 0.280 Chirality : 0.040 0.186 3240 Planarity : 0.004 0.055 4040 Dihedral : 14.162 159.027 4155 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 2.22 % Allowed : 13.58 % Favored : 84.20 % 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: -2.34 (0.15), residues: 2950 helix: 0.28 (0.18), residues: 880 sheet: -1.57 (0.27), residues: 365 loop : -2.70 (0.14), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 137 TYR 0.014 0.001 TYR D 305 PHE 0.020 0.001 PHE E 226 TRP 0.034 0.001 TRP D 270 HIS 0.007 0.001 HIS B 114 Details of bonding type rmsd covalent geometry : bond 0.00209 (22852) covalent geometry : angle 0.53734 (31091) hydrogen bonds : bond 0.03121 ( 761) hydrogen bonds : angle 4.65306 ( 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 315 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 272 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 LYS cc_start: 0.7877 (tppt) cc_final: 0.7674 (mmtt) REVERT: B 94 THR cc_start: 0.8043 (t) cc_final: 0.7682 (m) REVERT: B 263 LEU cc_start: 0.8656 (mm) cc_final: 0.8389 (tp) REVERT: C 323 GLN cc_start: 0.6702 (mt0) cc_final: 0.5901 (mm110) REVERT: D 191 GLU cc_start: 0.6111 (tt0) cc_final: 0.5664 (pm20) REVERT: D 271 TYR cc_start: 0.4279 (p90) cc_final: 0.3721 (p90) REVERT: D 293 LYS cc_start: 0.7560 (mttt) cc_final: 0.6784 (pttt) REVERT: E 271 TYR cc_start: 0.8212 (p90) cc_final: 0.7643 (p90) REVERT: F 83 ASN cc_start: 0.8463 (m-40) cc_final: 0.8036 (m110) REVERT: G 301 LYS cc_start: 0.8125 (mmpt) cc_final: 0.7840 (mmtm) REVERT: K 90 GLU cc_start: 0.8146 (pt0) cc_final: 0.7858 (pt0) outliers start: 43 outliers final: 26 residues processed: 298 average time/residue: 0.1828 time to fit residues: 81.7360 Evaluate side-chains 251 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 225 time to evaluate : 0.902 ------------------------------------------------------------------------------- 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 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 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 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 60 LYS 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 32 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: 7.9990 chunk 201 optimal weight: 5.9990 chunk 219 optimal weight: 8.9990 chunk 60 optimal weight: 9.9990 chunk 248 optimal weight: 9.9990 chunk 270 optimal weight: 9.9990 chunk 220 optimal weight: 4.9990 chunk 208 optimal weight: 6.9990 chunk 5 optimal weight: 30.0000 chunk 70 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS B 269 ASN B 282 ASN D 256 HIS H 241 GLN H 329 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.184821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.144430 restraints weight = 35865.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.142607 restraints weight = 35384.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.144097 restraints weight = 27732.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.144003 restraints weight = 19310.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.144204 restraints weight = 18066.631| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 22852 Z= 0.266 Angle : 0.696 11.782 31091 Z= 0.361 Chirality : 0.046 0.223 3240 Planarity : 0.004 0.057 4040 Dihedral : 14.361 160.220 4155 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.29 % Favored : 88.68 % Rotamer: Outliers : 3.56 % Allowed : 14.66 % Favored : 81.78 % 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: -2.59 (0.15), residues: 2950 helix: 0.00 (0.18), residues: 882 sheet: -1.85 (0.26), residues: 388 loop : -2.78 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 45 TYR 0.019 0.002 TYR G 295 PHE 0.022 0.002 PHE H 147 TRP 0.031 0.003 TRP A 263 HIS 0.008 0.002 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00609 (22852) covalent geometry : angle 0.69606 (31091) hydrogen bonds : bond 0.04099 ( 761) hydrogen bonds : angle 5.11593 ( 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 279 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 210 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LYS cc_start: 0.8928 (mtmt) cc_final: 0.8659 (mtpt) REVERT: A 247 LYS cc_start: 0.8154 (tppt) cc_final: 0.7542 (mmtt) REVERT: B 94 THR cc_start: 0.8205 (t) cc_final: 0.7914 (m) REVERT: C 323 GLN cc_start: 0.6789 (mt0) cc_final: 0.5953 (mm110) REVERT: E 271 TYR cc_start: 0.8433 (p90) cc_final: 0.8088 (p90) REVERT: G 301 LYS cc_start: 0.8251 (mmpt) cc_final: 0.7948 (mmtm) REVERT: H 258 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.8683 (pt0) REVERT: H 329 ASN cc_start: 0.8863 (OUTLIER) cc_final: 0.8027 (t0) REVERT: K 90 GLU cc_start: 0.8160 (pt0) cc_final: 0.7906 (pt0) outliers start: 69 outliers final: 50 residues processed: 256 average time/residue: 0.1711 time to fit residues: 67.8797 Evaluate side-chains 251 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 199 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL 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 97 ILE Chi-restraints excluded: chain B residue 108 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 282 ASN 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 210 LEU 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 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 12 LEU 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 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 G residue 18 LEU Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain H residue 8 THR 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 258 GLN 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 88 ILE Chi-restraints excluded: chain K residue 92 VAL Chi-restraints excluded: chain K residue 96 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 195 optimal weight: 1.9990 chunk 162 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 149 optimal weight: 8.9990 chunk 267 optimal weight: 6.9990 chunk 291 optimal weight: 50.0000 chunk 97 optimal weight: 50.0000 chunk 246 optimal weight: 1.9990 chunk 41 optimal weight: 50.0000 chunk 56 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 114 HIS B 282 ASN D 256 HIS F 83 ASN G 223 GLN H 329 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.187794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.147319 restraints weight = 35782.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.144945 restraints weight = 31776.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.146596 restraints weight = 25016.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.146282 restraints weight = 18094.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.146458 restraints weight = 18133.171| |-----------------------------------------------------------------------------| r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 22852 Z= 0.159 Angle : 0.610 15.243 31091 Z= 0.316 Chirality : 0.042 0.202 3240 Planarity : 0.004 0.053 4040 Dihedral : 14.266 159.855 4155 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 3.05 % Allowed : 15.90 % Favored : 81.05 % 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: -2.37 (0.15), residues: 2950 helix: 0.19 (0.18), residues: 883 sheet: -1.56 (0.27), residues: 370 loop : -2.68 (0.14), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 98 TYR 0.012 0.001 TYR G 271 PHE 0.022 0.002 PHE K 46 TRP 0.046 0.002 TRP B 316 HIS 0.006 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00363 (22852) covalent geometry : angle 0.61017 (31091) hydrogen bonds : bond 0.03501 ( 761) hydrogen bonds : angle 4.87011 ( 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 278 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 219 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 PHE cc_start: 0.5524 (p90) cc_final: 0.5298 (p90) REVERT: A 234 GLU cc_start: 0.7424 (pm20) cc_final: 0.7124 (pm20) REVERT: A 247 LYS cc_start: 0.8096 (tppt) cc_final: 0.7509 (mmtt) REVERT: B 94 THR cc_start: 0.8095 (t) cc_final: 0.7850 (m) REVERT: C 323 GLN cc_start: 0.6733 (mt0) cc_final: 0.5885 (mm110) REVERT: D 293 LYS cc_start: 0.7653 (mttt) cc_final: 0.7288 (mptt) REVERT: E 212 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.7138 (pp20) REVERT: E 271 TYR cc_start: 0.8352 (p90) cc_final: 0.8039 (p90) REVERT: G 301 LYS cc_start: 0.8243 (mmpt) cc_final: 0.7957 (mmtm) REVERT: H 329 ASN cc_start: 0.8913 (OUTLIER) cc_final: 0.8189 (t0) REVERT: K 90 GLU cc_start: 0.8177 (pt0) cc_final: 0.7890 (pt0) outliers start: 59 outliers final: 46 residues processed: 256 average time/residue: 0.1589 time to fit residues: 63.5832 Evaluate side-chains 257 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 209 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL 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 126 ILE Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 300 ASP 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 255 ILE Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain E residue 212 GLU 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 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 F residue 289 THR Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 75 ASN Chi-restraints excluded: chain G residue 96 THR 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 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 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 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 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: 0.8980 chunk 78 optimal weight: 30.0000 chunk 88 optimal weight: 40.0000 chunk 44 optimal weight: 8.9990 chunk 35 optimal weight: 50.0000 chunk 85 optimal weight: 6.9990 chunk 123 optimal weight: 20.0000 chunk 8 optimal weight: 30.0000 chunk 20 optimal weight: 6.9990 chunk 238 optimal weight: 7.9990 chunk 150 optimal weight: 6.9990 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 114 HIS B 282 ASN D 256 HIS D 323 GLN F 83 ASN H 329 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.185204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.144799 restraints weight = 35480.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.143443 restraints weight = 29467.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.144468 restraints weight = 21889.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.143942 restraints weight = 16060.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.144267 restraints weight = 16450.647| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 22852 Z= 0.252 Angle : 0.686 16.330 31091 Z= 0.355 Chirality : 0.045 0.217 3240 Planarity : 0.004 0.053 4040 Dihedral : 14.351 159.960 4155 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.69 % Favored : 88.27 % Rotamer: Outliers : 3.56 % Allowed : 15.75 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.52 (0.15), residues: 2950 helix: 0.05 (0.18), residues: 881 sheet: -1.60 (0.27), residues: 375 loop : -2.79 (0.14), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 98 TYR 0.016 0.002 TYR G 295 PHE 0.022 0.002 PHE H 147 TRP 0.060 0.003 TRP B 316 HIS 0.008 0.002 HIS H 324 Details of bonding type rmsd covalent geometry : bond 0.00577 (22852) covalent geometry : angle 0.68645 (31091) hydrogen bonds : bond 0.03921 ( 761) hydrogen bonds : angle 5.06891 ( 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 276 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 207 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 PHE cc_start: 0.5515 (p90) cc_final: 0.5286 (p90) REVERT: A 234 GLU cc_start: 0.7511 (pm20) cc_final: 0.7271 (pm20) REVERT: A 247 LYS cc_start: 0.8091 (tppt) cc_final: 0.7552 (mmtt) REVERT: B 94 THR cc_start: 0.8247 (t) cc_final: 0.7999 (m) REVERT: C 184 ARG cc_start: 0.2340 (mtp-110) cc_final: 0.1539 (ptt90) REVERT: C 323 GLN cc_start: 0.6715 (mt0) cc_final: 0.5865 (mm110) REVERT: D 293 LYS cc_start: 0.7679 (mttt) cc_final: 0.6520 (mtmt) REVERT: E 212 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7285 (pp20) REVERT: E 271 TYR cc_start: 0.8428 (p90) cc_final: 0.8090 (p90) REVERT: G 301 LYS cc_start: 0.8255 (mmpt) cc_final: 0.7945 (mmtm) REVERT: H 329 ASN cc_start: 0.8931 (OUTLIER) cc_final: 0.8119 (t0) REVERT: K 90 GLU cc_start: 0.8132 (pt0) cc_final: 0.7855 (pt0) outliers start: 69 outliers final: 56 residues processed: 252 average time/residue: 0.1605 time to fit residues: 63.2291 Evaluate side-chains 256 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 198 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL 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 114 HIS Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 282 ASN 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 25 MET Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 212 GLU 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 54 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 18 LEU 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 8 THR Chi-restraints excluded: chain H residue 18 LEU 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 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 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 88 ILE Chi-restraints excluded: chain K residue 92 VAL 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: 6.9990 chunk 2 optimal weight: 0.5980 chunk 207 optimal weight: 7.9990 chunk 92 optimal weight: 20.0000 chunk 230 optimal weight: 0.9980 chunk 51 optimal weight: 20.0000 chunk 74 optimal weight: 50.0000 chunk 231 optimal weight: 7.9990 chunk 198 optimal weight: 0.5980 chunk 236 optimal weight: 6.9990 chunk 220 optimal weight: 0.8980 overall best weight: 2.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 HIS B 282 ASN D 323 GLN F 83 ASN ** H 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.189440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.149065 restraints weight = 35594.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.148360 restraints weight = 31425.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.149309 restraints weight = 21800.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.148667 restraints weight = 15906.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.149027 restraints weight = 16723.286| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22852 Z= 0.128 Angle : 0.599 17.144 31091 Z= 0.307 Chirality : 0.042 0.195 3240 Planarity : 0.004 0.049 4040 Dihedral : 14.224 159.211 4155 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 2.74 % Allowed : 16.57 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.20 (0.15), residues: 2950 helix: 0.38 (0.18), residues: 876 sheet: -1.45 (0.27), residues: 380 loop : -2.61 (0.14), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 265 TYR 0.015 0.001 TYR K 51 PHE 0.026 0.001 PHE K 46 TRP 0.040 0.002 TRP B 316 HIS 0.015 0.001 HIS B 114 Details of bonding type rmsd covalent geometry : bond 0.00289 (22852) covalent geometry : angle 0.59902 (31091) hydrogen bonds : bond 0.03323 ( 761) hydrogen bonds : angle 4.75957 ( 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 276 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 223 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 PHE cc_start: 0.5576 (p90) cc_final: 0.5369 (p90) REVERT: A 247 LYS cc_start: 0.7964 (tppt) cc_final: 0.7452 (mmtt) REVERT: B 94 THR cc_start: 0.8072 (t) cc_final: 0.7832 (m) REVERT: B 263 LEU cc_start: 0.8742 (mm) cc_final: 0.8284 (tp) REVERT: C 184 ARG cc_start: 0.2260 (mtp-110) cc_final: 0.1530 (ptt90) REVERT: C 323 GLN cc_start: 0.6580 (mt0) cc_final: 0.5778 (mm110) REVERT: D 191 GLU cc_start: 0.6291 (tt0) cc_final: 0.5733 (pm20) REVERT: D 293 LYS cc_start: 0.7506 (mttt) cc_final: 0.6363 (mtmt) REVERT: E 212 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.7181 (pp20) REVERT: F 68 ASP cc_start: 0.7160 (m-30) cc_final: 0.6694 (m-30) REVERT: G 301 LYS cc_start: 0.8195 (mmpt) cc_final: 0.7870 (mmtm) REVERT: K 90 GLU cc_start: 0.8133 (pt0) cc_final: 0.7859 (pt0) outliers start: 53 outliers final: 39 residues processed: 257 average time/residue: 0.1602 time to fit residues: 63.9819 Evaluate side-chains 250 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 210 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 255 ILE 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 212 GLU 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 59 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 18 LEU Chi-restraints excluded: chain G residue 75 ASN Chi-restraints excluded: chain G residue 96 THR 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 213 VAL 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 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: 9.9990 chunk 16 optimal weight: 9.9990 chunk 266 optimal weight: 20.0000 chunk 200 optimal weight: 0.0370 chunk 76 optimal weight: 9.9990 chunk 122 optimal weight: 40.0000 chunk 217 optimal weight: 10.0000 chunk 159 optimal weight: 0.3980 chunk 29 optimal weight: 7.9990 chunk 243 optimal weight: 10.0000 chunk 126 optimal weight: 3.9990 overall best weight: 4.4864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 HIS B 282 ASN D 323 GLN F 83 ASN ** H 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.186140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.146683 restraints weight = 35786.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.146488 restraints weight = 36774.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.147819 restraints weight = 24639.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.146988 restraints weight = 18025.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.147400 restraints weight = 17254.515| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 22852 Z= 0.202 Angle : 0.659 16.930 31091 Z= 0.338 Chirality : 0.044 0.210 3240 Planarity : 0.004 0.051 4040 Dihedral : 14.253 159.191 4155 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.05 % Favored : 88.95 % Rotamer: Outliers : 2.79 % Allowed : 16.68 % Favored : 80.54 % 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: -2.30 (0.15), residues: 2950 helix: 0.29 (0.18), residues: 880 sheet: -1.55 (0.27), residues: 384 loop : -2.67 (0.14), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 98 TYR 0.016 0.002 TYR G 295 PHE 0.019 0.002 PHE H 147 TRP 0.045 0.002 TRP B 316 HIS 0.007 0.001 HIS D 256 Details of bonding type rmsd covalent geometry : bond 0.00467 (22852) covalent geometry : angle 0.65931 (31091) hydrogen bonds : bond 0.03685 ( 761) hydrogen bonds : angle 4.86533 ( 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 263 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 209 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 GLU cc_start: 0.7203 (pm20) cc_final: 0.6770 (pm20) REVERT: A 247 LYS cc_start: 0.7946 (tppt) cc_final: 0.7432 (mmtt) REVERT: B 94 THR cc_start: 0.8102 (t) cc_final: 0.7877 (m) REVERT: C 184 ARG cc_start: 0.2352 (mtp-110) cc_final: 0.1514 (ptt90) REVERT: C 323 GLN cc_start: 0.6721 (mt0) cc_final: 0.5903 (mm110) REVERT: D 191 GLU cc_start: 0.6285 (tt0) cc_final: 0.5773 (pm20) REVERT: D 293 LYS cc_start: 0.7541 (mttt) cc_final: 0.7255 (mptt) REVERT: G 301 LYS cc_start: 0.8173 (mmpt) cc_final: 0.7868 (mmtm) REVERT: K 90 GLU cc_start: 0.8073 (pt0) cc_final: 0.7803 (pt0) outliers start: 54 outliers final: 50 residues processed: 244 average time/residue: 0.1557 time to fit residues: 59.4932 Evaluate side-chains 249 residues out of total 2418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 199 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 114 HIS Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 282 ASN 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 25 MET Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 193 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 54 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 288 VAL Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 96 THR 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 77 GLN 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 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 88 ILE Chi-restraints excluded: chain K residue 92 VAL 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 141 optimal weight: 5.9990 chunk 11 optimal weight: 50.0000 chunk 215 optimal weight: 7.9990 chunk 175 optimal weight: 0.9980 chunk 252 optimal weight: 8.9990 chunk 66 optimal weight: 0.6980 chunk 140 optimal weight: 0.8980 chunk 279 optimal weight: 9.9990 chunk 239 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 253 optimal weight: 0.0070 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 HIS B 282 ASN D 323 GLN F 83 ASN H 83 ASN ** H 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.191230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.151760 restraints weight = 35512.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.151255 restraints weight = 32468.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.152864 restraints weight = 21299.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.152117 restraints weight = 14770.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.152645 restraints weight = 15329.065| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 22852 Z= 0.107 Angle : 0.590 17.471 31091 Z= 0.299 Chirality : 0.041 0.190 3240 Planarity : 0.003 0.047 4040 Dihedral : 14.137 158.676 4155 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 2.27 % Allowed : 17.55 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.16), residues: 2950 helix: 0.60 (0.19), residues: 878 sheet: -1.27 (0.28), residues: 372 loop : -2.51 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 98 TYR 0.018 0.001 TYR K 51 PHE 0.028 0.001 PHE K 46 TRP 0.033 0.001 TRP B 316 HIS 0.005 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00242 (22852) covalent geometry : angle 0.59001 (31091) hydrogen bonds : bond 0.03151 ( 761) hydrogen bonds : angle 4.62511 ( 2148) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3558.87 seconds wall clock time: 62 minutes 17.92 seconds (3737.92 seconds total)