Starting phenix.real_space_refine on Sun Sep 29 15:10:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b48_7052/09_2024/6b48_7052.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b48_7052/09_2024/6b48_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b48_7052/09_2024/6b48_7052.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b48_7052/09_2024/6b48_7052.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b48_7052/09_2024/6b48_7052.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b48_7052/09_2024/6b48_7052.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.018 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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, 'ASP:plan': 20, 'TYR:plan': 2, 'ASN:plan1': 13, 'TRP:plan': 9, 'HIS:plan': 9, 'PHE:plan': 11, 'GLU:plan': 24, 'ARG:plan': 29} 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: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 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: {'GLU:plan': 1, 'ASP:plan': 3} 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: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 4} 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: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 4} 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: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 4} 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: {'GLU:plan': 1, 'ASP:plan': 3} 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: {'GLN:plan1': 9, 'ASP:plan': 12, 'TYR:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 2, 'HIS:plan': 8, 'PHE:plan': 10, 'GLU:plan': 11, 'ARG:plan': 24} 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: 13.69, per 1000 atoms: 0.61 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: 6.51 Conformation dependent library (CDL) restraints added in 2.9 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: 7.70 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: 6.59 Time building geometry restraints manager: 7.33 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: 30670 3.38 - 6.76: 388 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: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.150 Construct map_model_manager: 0.020 Extract box with map and model: 0.890 Check model and map are aligned: 0.170 Set scattering table: 0.230 Process input model: 55.230 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.180 ------------------------------------------------------------------------------- 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= 0.453 Angle : 0.979 16.907 31091 Z= 0.530 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 : 6.03 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.045 0.005 TRP F 311 HIS 0.019 0.003 HIS H 324 PHE 0.028 0.003 PHE H 216 TYR 0.025 0.003 TYR E 305 ARG 0.014 0.001 ARG G 137 *********************** 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 fitting. rotamer outliers: 2 poor density : 418 time to evaluate : 2.406 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: 0.8159 (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: 0.7047 (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: 0.5436 (pm20) REVERT: D 284 PRO cc_start: 0.8756 (Cg_exo) cc_final: 0.7903 (Cg_endo) REVERT: E 208 HIS cc_start: 0.7098 (t-90) cc_final: 0.6623 (t-90) REVERT: F 214 VAL cc_start: 0.8919 (t) cc_final: 0.8718 (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: 0.8146 (mmtm) REVERT: H 285 TYR cc_start: 0.8029 (m-80) cc_final: 0.7583 (m-80) REVERT: K 31 ARG cc_start: 0.7822 (ptm-80) cc_final: 0.7361 (ptm-80) REVERT: K 78 PRO cc_start: 0.8641 (Cg_exo) cc_final: 0.8429 (Cg_endo) REVERT: K 84 THR cc_start: 0.8831 (p) cc_final: 0.8320 (p) outliers start: 2 outliers final: 0 residues processed: 420 average time/residue: 0.4137 time to fit residues: 249.5247 Evaluate side-chains 235 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 235 time to evaluate : 2.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 252 optimal weight: 8.9990 chunk 226 optimal weight: 0.7980 chunk 125 optimal weight: 30.0000 chunk 77 optimal weight: 20.0000 chunk 152 optimal weight: 9.9990 chunk 121 optimal weight: 10.0000 chunk 234 optimal weight: 0.5980 chunk 90 optimal weight: 40.0000 chunk 142 optimal weight: 0.7980 chunk 174 optimal weight: 0.9990 chunk 271 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 GLN B 196 HIS B 269 ASN B 305 HIS C 120 GLN C 129 GLN C 141 ASN C 223 GLN C 324 HIS ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 GLN E 151 ASN E 241 GLN F 55 ASN F 83 ASN F 120 GLN F 127 ASN F 129 GLN G 120 GLN G 129 GLN H 129 GLN H 164 HIS K 37 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 22852 Z= 0.158 Angle : 0.598 12.134 31091 Z= 0.315 Chirality : 0.041 0.218 3240 Planarity : 0.004 0.064 4040 Dihedral : 14.694 158.989 4155 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 1.96 % Allowed : 9.60 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.55 (0.14), residues: 2950 helix: -1.22 (0.16), residues: 890 sheet: -2.10 (0.26), residues: 356 loop : -3.20 (0.13), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 316 HIS 0.006 0.001 HIS G 324 PHE 0.023 0.002 PHE K 46 TYR 0.016 0.001 TYR H 271 ARG 0.008 0.001 ARG H 184 *********************** 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 353 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 315 time to evaluate : 2.431 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: 0.7761 (m) cc_final: 0.7546 (m) REVERT: A 242 LYS cc_start: 0.9166 (mtpp) cc_final: 0.8465 (mtmt) REVERT: A 247 LYS cc_start: 0.8089 (tppt) cc_final: 0.7751 (mmtt) REVERT: B 27 LEU cc_start: 0.7824 (pp) cc_final: 0.7500 (mm) REVERT: B 93 SER cc_start: 0.7690 (p) cc_final: 0.7251 (p) REVERT: B 94 THR cc_start: 0.8215 (t) cc_final: 0.7718 (m) REVERT: B 120 ASP cc_start: 0.8065 (m-30) cc_final: 0.7701 (t0) REVERT: B 263 LEU cc_start: 0.8883 (mm) cc_final: 0.8516 (tp) REVERT: B 310 ASP cc_start: 0.7270 (t70) cc_final: 0.7056 (m-30) REVERT: C 98 ARG cc_start: 0.2538 (ptt180) cc_final: 0.2292 (tpt170) REVERT: C 323 GLN cc_start: 0.6527 (mt0) cc_final: 0.5848 (mm110) REVERT: D 94 ARG cc_start: 0.6597 (ttt-90) cc_final: 0.6263 (ttp-170) REVERT: D 191 GLU cc_start: 0.5943 (tt0) cc_final: 0.5391 (pm20) REVERT: D 283 GLU cc_start: 0.7670 (tt0) cc_final: 0.7297 (tt0) REVERT: D 293 LYS cc_start: 0.7216 (mttt) cc_final: 0.6571 (pttt) REVERT: E 110 ASN cc_start: 0.8094 (m110) cc_final: 0.7225 (t0) REVERT: E 244 LYS cc_start: 0.6494 (OUTLIER) cc_final: 0.5581 (mtpt) REVERT: E 271 TYR cc_start: 0.8353 (p90) cc_final: 0.8081 (p90) REVERT: F 303 ASP cc_start: 0.7345 (t0) cc_final: 0.7112 (t0) REVERT: G 197 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7646 (tm-30) REVERT: G 301 LYS cc_start: 0.8388 (mmpt) cc_final: 0.7991 (mmtm) REVERT: K 51 TYR cc_start: 0.6909 (t80) cc_final: 0.6187 (t80) outliers start: 38 outliers final: 15 residues processed: 338 average time/residue: 0.3713 time to fit residues: 188.4738 Evaluate side-chains 262 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 246 time to evaluate : 2.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain E residue 244 LYS 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 K residue 32 VAL Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 88 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 150 optimal weight: 6.9990 chunk 84 optimal weight: 50.0000 chunk 225 optimal weight: 10.0000 chunk 184 optimal weight: 10.0000 chunk 74 optimal weight: 50.0000 chunk 272 optimal weight: 3.9990 chunk 293 optimal weight: 10.0000 chunk 242 optimal weight: 6.9990 chunk 269 optimal weight: 6.9990 chunk 92 optimal weight: 0.9980 chunk 218 optimal weight: 0.7980 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 HIS B 18 GLN B 19 ASN ** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 GLN E 208 HIS E 229 GLN F 83 ASN F 223 GLN H 164 HIS H 223 GLN H 329 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 22852 Z= 0.290 Angle : 0.639 12.303 31091 Z= 0.332 Chirality : 0.043 0.206 3240 Planarity : 0.004 0.056 4040 Dihedral : 14.539 159.907 4155 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.86 % Favored : 90.10 % Rotamer: Outliers : 2.53 % Allowed : 11.87 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.14), residues: 2950 helix: -0.55 (0.17), residues: 882 sheet: -2.05 (0.26), residues: 383 loop : -2.98 (0.14), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 270 HIS 0.009 0.001 HIS D 324 PHE 0.019 0.002 PHE H 147 TYR 0.013 0.002 TYR C 125 ARG 0.010 0.001 ARG C 296 *********************** 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 307 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 258 time to evaluate : 2.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LYS cc_start: 0.8996 (mtpp) cc_final: 0.8510 (mtmt) REVERT: A 247 LYS cc_start: 0.8305 (tppt) cc_final: 0.7744 (mmtt) REVERT: B 18 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7741 (pp30) REVERT: B 27 LEU cc_start: 0.8019 (pp) cc_final: 0.7747 (mp) REVERT: B 94 THR cc_start: 0.8394 (t) cc_final: 0.8012 (m) REVERT: B 120 ASP cc_start: 0.8020 (m-30) cc_final: 0.7667 (t0) REVERT: B 310 ASP cc_start: 0.7343 (t70) cc_final: 0.7094 (m-30) REVERT: C 323 GLN cc_start: 0.6498 (mt0) cc_final: 0.5812 (mm110) REVERT: D 16 ARG cc_start: 0.6190 (ttp-110) cc_final: 0.5529 (tmm-80) REVERT: D 94 ARG cc_start: 0.6633 (ttt-90) cc_final: 0.6219 (ttp-170) REVERT: D 191 GLU cc_start: 0.6265 (tt0) cc_final: 0.5549 (pm20) REVERT: D 270 TRP cc_start: 0.5914 (m-90) cc_final: 0.5103 (m-90) REVERT: D 283 GLU cc_start: 0.7737 (tt0) cc_final: 0.7223 (tt0) REVERT: D 293 LYS cc_start: 0.7500 (mttt) cc_final: 0.6600 (pttp) REVERT: E 271 TYR cc_start: 0.8410 (p90) cc_final: 0.8185 (p90) REVERT: E 302 LEU cc_start: 0.8701 (tp) cc_final: 0.8358 (tt) REVERT: G 301 LYS cc_start: 0.8431 (mmpt) cc_final: 0.8027 (mmtm) outliers start: 49 outliers final: 34 residues processed: 290 average time/residue: 0.3728 time to fit residues: 164.2298 Evaluate side-chains 262 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 227 time to evaluate : 2.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 78 THR 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 216 LEU Chi-restraints excluded: chain B residue 300 ASP 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 255 ILE Chi-restraints excluded: chain D residue 312 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 54 SER 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 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 Chi-restraints excluded: chain K residue 92 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 268 optimal weight: 9.9990 chunk 204 optimal weight: 3.9990 chunk 141 optimal weight: 10.0000 chunk 30 optimal weight: 50.0000 chunk 129 optimal weight: 0.8980 chunk 182 optimal weight: 1.9990 chunk 272 optimal weight: 7.9990 chunk 289 optimal weight: 40.0000 chunk 142 optimal weight: 0.8980 chunk 258 optimal weight: 0.9980 chunk 77 optimal weight: 50.0000 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 HIS ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 HIS E 208 HIS E 229 GLN F 83 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22852 Z= 0.179 Angle : 0.569 11.850 31091 Z= 0.296 Chirality : 0.041 0.194 3240 Planarity : 0.004 0.058 4040 Dihedral : 14.339 159.575 4155 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 2.12 % Allowed : 13.42 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.15), residues: 2950 helix: -0.05 (0.18), residues: 885 sheet: -1.86 (0.25), residues: 394 loop : -2.81 (0.14), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 316 HIS 0.005 0.001 HIS A 188 PHE 0.021 0.002 PHE E 226 TYR 0.017 0.001 TYR D 305 ARG 0.005 0.000 ARG D 98 *********************** 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 290 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 249 time to evaluate : 2.208 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: 0.8211 (tppt) cc_final: 0.7523 (mmtt) REVERT: B 94 THR cc_start: 0.8260 (t) cc_final: 0.7954 (m) REVERT: B 120 ASP cc_start: 0.8055 (m-30) cc_final: 0.7606 (t0) REVERT: B 263 LEU cc_start: 0.8841 (mm) cc_final: 0.8388 (tp) REVERT: B 310 ASP cc_start: 0.7300 (t70) cc_final: 0.7073 (m-30) REVERT: C 323 GLN cc_start: 0.6450 (mt0) cc_final: 0.5753 (mm110) REVERT: D 16 ARG cc_start: 0.6091 (ttp-110) cc_final: 0.5525 (tmm-80) REVERT: D 94 ARG cc_start: 0.6600 (ttt-90) cc_final: 0.6208 (ttp-170) REVERT: D 191 GLU cc_start: 0.6193 (tt0) cc_final: 0.5468 (pm20) REVERT: D 293 LYS cc_start: 0.7448 (mttt) cc_final: 0.6524 (pttp) REVERT: E 271 TYR cc_start: 0.8351 (p90) cc_final: 0.8093 (p90) REVERT: E 302 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8397 (tp) REVERT: G 301 LYS cc_start: 0.8323 (mmpt) cc_final: 0.7996 (mmtm) REVERT: K 46 PHE cc_start: 0.8375 (t80) cc_final: 0.8061 (t80) REVERT: K 90 GLU cc_start: 0.8220 (pt0) cc_final: 0.7926 (pt0) outliers start: 41 outliers final: 27 residues processed: 274 average time/residue: 0.3567 time to fit residues: 148.3922 Evaluate side-chains 252 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 224 time to evaluate : 2.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 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 E residue 49 VAL Chi-restraints excluded: chain E residue 251 ASP Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 231 LEU Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain G residue 116 ASP Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain H residue 208 HIS Chi-restraints excluded: chain H residue 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 61 VAL Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 88 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 240 optimal weight: 0.7980 chunk 164 optimal weight: 5.9990 chunk 4 optimal weight: 40.0000 chunk 215 optimal weight: 0.6980 chunk 119 optimal weight: 20.0000 chunk 246 optimal weight: 7.9990 chunk 199 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 147 optimal weight: 7.9990 chunk 259 optimal weight: 6.9990 chunk 72 optimal weight: 20.0000 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 GLN E 129 GLN F 83 ASN G 120 GLN ** K 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 22852 Z= 0.238 Angle : 0.588 11.757 31091 Z= 0.304 Chirality : 0.042 0.204 3240 Planarity : 0.004 0.055 4040 Dihedral : 14.277 159.704 4155 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 2.43 % Allowed : 13.89 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.15), residues: 2950 helix: 0.13 (0.18), residues: 877 sheet: -1.71 (0.26), residues: 385 loop : -2.74 (0.14), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 270 HIS 0.006 0.001 HIS A 188 PHE 0.019 0.002 PHE E 226 TYR 0.012 0.001 TYR A 235 ARG 0.006 0.000 ARG D 98 *********************** 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 278 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 231 time to evaluate : 2.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 LYS cc_start: 0.8228 (tppt) cc_final: 0.7577 (mmtt) REVERT: B 94 THR cc_start: 0.8217 (t) cc_final: 0.7935 (m) REVERT: B 120 ASP cc_start: 0.8058 (m-30) cc_final: 0.7618 (t0) REVERT: B 215 ASP cc_start: 0.7635 (p0) cc_final: 0.6537 (p0) REVERT: B 263 LEU cc_start: 0.8851 (mm) cc_final: 0.8391 (tp) REVERT: B 310 ASP cc_start: 0.7276 (t70) cc_final: 0.7066 (m-30) REVERT: C 323 GLN cc_start: 0.6458 (mt0) cc_final: 0.5742 (mm110) REVERT: D 16 ARG cc_start: 0.6196 (ttp-110) cc_final: 0.5620 (tmm-80) REVERT: D 94 ARG cc_start: 0.6616 (ttt-90) cc_final: 0.6206 (ttp-170) REVERT: D 98 ARG cc_start: 0.7231 (ttp-110) cc_final: 0.6928 (ttp-110) REVERT: D 191 GLU cc_start: 0.6240 (tt0) cc_final: 0.5480 (pm20) REVERT: E 271 TYR cc_start: 0.8395 (p90) cc_final: 0.8144 (p90) REVERT: E 302 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8409 (tt) REVERT: G 301 LYS cc_start: 0.8344 (mmpt) cc_final: 0.8006 (mmtm) REVERT: K 90 GLU cc_start: 0.8253 (pt0) cc_final: 0.7950 (pt0) outliers start: 47 outliers final: 36 residues processed: 260 average time/residue: 0.3634 time to fit residues: 144.7454 Evaluate side-chains 255 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 218 time to evaluate : 2.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 LEU 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 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 297 GLN Chi-restraints excluded: chain D residue 306 THR 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 E residue 302 LEU 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 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 214 VAL Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain K residue 15 ILE Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 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 97 optimal weight: 4.9990 chunk 260 optimal weight: 0.0970 chunk 57 optimal weight: 10.0000 chunk 169 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 289 optimal weight: 50.0000 chunk 240 optimal weight: 7.9990 chunk 133 optimal weight: 0.9980 chunk 24 optimal weight: 10.0000 chunk 95 optimal weight: 7.9990 chunk 151 optimal weight: 10.0000 overall best weight: 3.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 ASN ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2923 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= 0.271 Angle : 0.604 15.495 31091 Z= 0.312 Chirality : 0.042 0.206 3240 Planarity : 0.004 0.053 4040 Dihedral : 14.257 159.855 4155 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 3.10 % Allowed : 13.99 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.15), residues: 2950 helix: 0.17 (0.18), residues: 879 sheet: -1.74 (0.26), residues: 402 loop : -2.68 (0.14), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 316 HIS 0.006 0.001 HIS A 188 PHE 0.018 0.002 PHE D 216 TYR 0.012 0.001 TYR G 271 ARG 0.005 0.000 ARG E 150 *********************** 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 296 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 236 time to evaluate : 2.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LYS cc_start: 0.8946 (mtmt) cc_final: 0.8735 (mtmt) REVERT: A 247 LYS cc_start: 0.8218 (tppt) cc_final: 0.7632 (mmtt) REVERT: B 94 THR cc_start: 0.8205 (t) cc_final: 0.7954 (m) REVERT: B 120 ASP cc_start: 0.8072 (m-30) cc_final: 0.7625 (t0) REVERT: B 263 LEU cc_start: 0.8870 (mm) cc_final: 0.8395 (tp) REVERT: B 310 ASP cc_start: 0.7342 (t70) cc_final: 0.7098 (m-30) REVERT: C 323 GLN cc_start: 0.6455 (mt0) cc_final: 0.5717 (mm110) REVERT: D 94 ARG cc_start: 0.6641 (ttt-90) cc_final: 0.6253 (ttp-170) REVERT: D 191 GLU cc_start: 0.6334 (tt0) cc_final: 0.5533 (pm20) REVERT: D 293 LYS cc_start: 0.7584 (mttt) cc_final: 0.7149 (mptt) REVERT: E 271 TYR cc_start: 0.8427 (p90) cc_final: 0.8125 (p90) REVERT: E 302 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8425 (tt) REVERT: F 223 GLN cc_start: 0.7449 (mm-40) cc_final: 0.7071 (mm-40) REVERT: G 301 LYS cc_start: 0.8350 (mmpt) cc_final: 0.7997 (mmtm) REVERT: K 90 GLU cc_start: 0.8243 (pt0) cc_final: 0.7931 (pt0) outliers start: 60 outliers final: 45 residues processed: 275 average time/residue: 0.3604 time to fit residues: 150.6928 Evaluate side-chains 263 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 217 time to evaluate : 2.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU 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 245 THR Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 306 THR 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 E residue 302 LEU 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 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 18 LEU 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 208 HIS Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain K residue 15 ILE Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 88 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 278 optimal weight: 50.0000 chunk 32 optimal weight: 50.0000 chunk 164 optimal weight: 2.9990 chunk 211 optimal weight: 0.9990 chunk 163 optimal weight: 0.9980 chunk 243 optimal weight: 10.0000 chunk 161 optimal weight: 6.9990 chunk 288 optimal weight: 0.9980 chunk 180 optimal weight: 4.9990 chunk 175 optimal weight: 4.9990 chunk 133 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 ASN D 297 GLN F 83 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 22852 Z= 0.158 Angle : 0.546 11.297 31091 Z= 0.283 Chirality : 0.040 0.194 3240 Planarity : 0.003 0.050 4040 Dihedral : 14.114 159.315 4155 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 2.22 % Allowed : 15.02 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.16), residues: 2950 helix: 0.48 (0.19), residues: 880 sheet: -1.38 (0.27), residues: 375 loop : -2.56 (0.14), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP D 270 HIS 0.005 0.001 HIS G 324 PHE 0.020 0.001 PHE K 46 TYR 0.013 0.001 TYR K 51 ARG 0.007 0.000 ARG D 98 *********************** 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 282 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 239 time to evaluate : 2.211 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: 0.8088 (tppt) cc_final: 0.7474 (mmtt) REVERT: B 94 THR cc_start: 0.8169 (t) cc_final: 0.7873 (m) REVERT: B 120 ASP cc_start: 0.8046 (m-30) cc_final: 0.7607 (t0) REVERT: B 161 MET cc_start: 0.3575 (OUTLIER) cc_final: 0.3266 (ttt) REVERT: B 263 LEU cc_start: 0.8759 (mm) cc_final: 0.8302 (tp) REVERT: B 310 ASP cc_start: 0.7257 (t70) cc_final: 0.7043 (m-30) REVERT: C 323 GLN cc_start: 0.6271 (mt0) cc_final: 0.5599 (mm110) REVERT: D 94 ARG cc_start: 0.6583 (ttt-90) cc_final: 0.6196 (ttp-170) REVERT: D 98 ARG cc_start: 0.7126 (ttp-110) cc_final: 0.6746 (ttp-110) REVERT: D 191 GLU cc_start: 0.6228 (tt0) cc_final: 0.5457 (pm20) REVERT: D 271 TYR cc_start: 0.3804 (p90) cc_final: 0.3245 (p90) REVERT: D 293 LYS cc_start: 0.7450 (mttt) cc_final: 0.7130 (mptt) REVERT: E 271 TYR cc_start: 0.8254 (p90) cc_final: 0.7664 (p90) REVERT: E 302 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8397 (tp) REVERT: G 277 LEU cc_start: 0.6799 (mp) cc_final: 0.6469 (tt) REVERT: G 301 LYS cc_start: 0.8277 (mmpt) cc_final: 0.7927 (mmtm) REVERT: K 90 GLU cc_start: 0.8199 (pt0) cc_final: 0.7874 (pt0) outliers start: 43 outliers final: 33 residues processed: 266 average time/residue: 0.3488 time to fit residues: 141.8274 Evaluate side-chains 251 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 216 time to evaluate : 2.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 297 GLN Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 54 SER 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 G residue 18 LEU 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 15 ILE Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 88 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 178 optimal weight: 1.9990 chunk 115 optimal weight: 9.9990 chunk 172 optimal weight: 0.0170 chunk 86 optimal weight: 0.0770 chunk 56 optimal weight: 8.9990 chunk 55 optimal weight: 7.9990 chunk 183 optimal weight: 4.9990 chunk 196 optimal weight: 5.9990 chunk 142 optimal weight: 8.9990 chunk 26 optimal weight: 40.0000 chunk 226 optimal weight: 0.9980 overall best weight: 1.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 HIS A 203 HIS ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 ASN C 129 GLN D 297 GLN F 83 ASN ** H 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 22852 Z= 0.170 Angle : 0.546 10.077 31091 Z= 0.280 Chirality : 0.040 0.199 3240 Planarity : 0.003 0.049 4040 Dihedral : 14.045 159.311 4155 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 2.37 % Allowed : 15.44 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.16), residues: 2950 helix: 0.59 (0.19), residues: 880 sheet: -1.28 (0.28), residues: 365 loop : -2.49 (0.14), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP E 39 HIS 0.005 0.001 HIS A 188 PHE 0.017 0.001 PHE D 216 TYR 0.012 0.001 TYR D 114 ARG 0.008 0.000 ARG D 296 *********************** 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 272 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 226 time to evaluate : 2.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 GLU cc_start: 0.7534 (pm20) cc_final: 0.7115 (pm20) REVERT: A 247 LYS cc_start: 0.8027 (tppt) cc_final: 0.7430 (mmtt) REVERT: B 94 THR cc_start: 0.8124 (t) cc_final: 0.7860 (m) REVERT: B 120 ASP cc_start: 0.8029 (m-30) cc_final: 0.7589 (t0) REVERT: B 161 MET cc_start: 0.3609 (OUTLIER) cc_final: 0.3322 (ttt) REVERT: B 263 LEU cc_start: 0.8721 (mm) cc_final: 0.8273 (tp) REVERT: B 310 ASP cc_start: 0.7244 (t70) cc_final: 0.7019 (m-30) REVERT: C 184 ARG cc_start: 0.2482 (mtp-110) cc_final: 0.1582 (ptt90) REVERT: C 323 GLN cc_start: 0.6411 (mt0) cc_final: 0.5690 (mm110) REVERT: D 94 ARG cc_start: 0.6566 (ttt-90) cc_final: 0.6173 (ttp-170) REVERT: D 98 ARG cc_start: 0.7054 (ttp-110) cc_final: 0.6749 (ttp-110) REVERT: D 191 GLU cc_start: 0.6288 (tt0) cc_final: 0.5436 (pm20) REVERT: D 271 TYR cc_start: 0.3694 (p90) cc_final: 0.3177 (p90) REVERT: D 293 LYS cc_start: 0.7490 (mttt) cc_final: 0.7164 (mptt) REVERT: E 302 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8517 (tp) REVERT: F 87 ASP cc_start: 0.6539 (t0) cc_final: 0.6335 (t0) REVERT: G 277 LEU cc_start: 0.6872 (mp) cc_final: 0.6576 (tt) REVERT: G 301 LYS cc_start: 0.8240 (mmpt) cc_final: 0.7873 (mmtm) REVERT: K 90 GLU cc_start: 0.8220 (pt0) cc_final: 0.7898 (pt0) outliers start: 46 outliers final: 41 residues processed: 256 average time/residue: 0.3747 time to fit residues: 149.3064 Evaluate side-chains 248 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 205 time to evaluate : 2.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 189 LEU 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 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 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 268 ASP Chi-restraints excluded: chain D residue 297 GLN Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 302 LEU 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 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 G residue 18 LEU 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 77 GLN Chi-restraints excluded: chain H residue 208 HIS Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain H residue 329 ASN Chi-restraints excluded: chain K residue 15 ILE Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain K residue 96 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 262 optimal weight: 2.9990 chunk 276 optimal weight: 4.9990 chunk 251 optimal weight: 1.9990 chunk 268 optimal weight: 8.9990 chunk 161 optimal weight: 4.9990 chunk 116 optimal weight: 10.0000 chunk 210 optimal weight: 0.2980 chunk 82 optimal weight: 20.0000 chunk 242 optimal weight: 10.0000 chunk 253 optimal weight: 2.9990 chunk 267 optimal weight: 5.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 ASN E 208 HIS F 83 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 22852 Z= 0.215 Angle : 0.572 13.552 31091 Z= 0.293 Chirality : 0.041 0.203 3240 Planarity : 0.003 0.046 4040 Dihedral : 14.040 159.361 4155 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 2.63 % Allowed : 15.49 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.16), residues: 2950 helix: 0.59 (0.19), residues: 882 sheet: -1.24 (0.28), residues: 355 loop : -2.48 (0.14), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 316 HIS 0.005 0.001 HIS A 188 PHE 0.018 0.001 PHE K 46 TYR 0.014 0.001 TYR K 51 ARG 0.006 0.000 ARG D 98 *********************** 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 274 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 223 time to evaluate : 2.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 GLU cc_start: 0.7551 (pm20) cc_final: 0.7297 (pm20) REVERT: A 242 LYS cc_start: 0.9119 (mtpt) cc_final: 0.8659 (mtmt) REVERT: A 247 LYS cc_start: 0.7999 (tppt) cc_final: 0.7443 (mmtt) REVERT: B 94 THR cc_start: 0.8126 (t) cc_final: 0.7895 (m) REVERT: B 99 GLU cc_start: 0.7586 (pt0) cc_final: 0.7305 (pt0) REVERT: B 120 ASP cc_start: 0.8027 (m-30) cc_final: 0.7602 (t0) REVERT: B 161 MET cc_start: 0.3773 (OUTLIER) cc_final: 0.3508 (ttt) REVERT: B 263 LEU cc_start: 0.8732 (mm) cc_final: 0.8278 (tp) REVERT: B 310 ASP cc_start: 0.7267 (t70) cc_final: 0.7041 (m-30) REVERT: C 184 ARG cc_start: 0.2504 (mtp-110) cc_final: 0.1590 (ptt90) REVERT: C 323 GLN cc_start: 0.6423 (mt0) cc_final: 0.5685 (mm110) REVERT: D 94 ARG cc_start: 0.6571 (ttt-90) cc_final: 0.6223 (ttp-170) REVERT: D 98 ARG cc_start: 0.7110 (ttp-110) cc_final: 0.6840 (ttp-110) REVERT: D 191 GLU cc_start: 0.6348 (tt0) cc_final: 0.5438 (pm20) REVERT: D 271 TYR cc_start: 0.3737 (p90) cc_final: 0.3203 (p90) REVERT: D 293 LYS cc_start: 0.7477 (mttt) cc_final: 0.7152 (mptt) REVERT: E 302 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8604 (tp) REVERT: G 277 LEU cc_start: 0.6930 (mp) cc_final: 0.6585 (tt) REVERT: G 301 LYS cc_start: 0.8235 (mmpt) cc_final: 0.7863 (mmtm) REVERT: K 90 GLU cc_start: 0.8217 (pt0) cc_final: 0.7897 (pt0) outliers start: 51 outliers final: 42 residues processed: 251 average time/residue: 0.3497 time to fit residues: 134.8418 Evaluate side-chains 258 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 214 time to evaluate : 2.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 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 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 268 ASP Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 302 LEU 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 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 G residue 18 LEU 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 77 GLN Chi-restraints excluded: chain H residue 208 HIS Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain H residue 329 ASN Chi-restraints excluded: chain K residue 15 ILE Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 88 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 176 optimal weight: 0.8980 chunk 283 optimal weight: 20.0000 chunk 173 optimal weight: 7.9990 chunk 134 optimal weight: 0.0010 chunk 197 optimal weight: 0.9980 chunk 297 optimal weight: 50.0000 chunk 274 optimal weight: 6.9990 chunk 237 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 183 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 overall best weight: 1.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 GLN B 282 ASN E 77 GLN F 83 ASN H 241 GLN ** H 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 22852 Z= 0.153 Angle : 0.544 10.482 31091 Z= 0.280 Chirality : 0.040 0.195 3240 Planarity : 0.003 0.044 4040 Dihedral : 13.969 159.029 4155 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 2.12 % Allowed : 16.26 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.16), residues: 2950 helix: 0.80 (0.19), residues: 875 sheet: -1.12 (0.27), residues: 380 loop : -2.35 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP B 316 HIS 0.004 0.001 HIS G 324 PHE 0.018 0.001 PHE D 216 TYR 0.013 0.001 TYR G 271 ARG 0.006 0.000 ARG D 98 ********************** 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 266 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 225 time to evaluate : 2.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 ARG cc_start: 0.7608 (tpp80) cc_final: 0.7307 (mmt-90) REVERT: A 234 GLU cc_start: 0.7592 (pm20) cc_final: 0.7214 (pm20) REVERT: A 247 LYS cc_start: 0.7862 (tppt) cc_final: 0.7294 (mmtt) REVERT: B 94 THR cc_start: 0.8050 (t) cc_final: 0.7820 (m) REVERT: B 99 GLU cc_start: 0.7535 (pt0) cc_final: 0.7324 (pt0) REVERT: B 120 ASP cc_start: 0.8015 (m-30) cc_final: 0.7593 (t0) REVERT: B 263 LEU cc_start: 0.8698 (mm) cc_final: 0.8236 (tp) REVERT: B 310 ASP cc_start: 0.7191 (t70) cc_final: 0.6979 (m-30) REVERT: C 323 GLN cc_start: 0.6423 (mt0) cc_final: 0.5700 (mm110) REVERT: D 94 ARG cc_start: 0.6557 (ttt-90) cc_final: 0.6184 (ttp-170) REVERT: D 98 ARG cc_start: 0.7085 (ttp-110) cc_final: 0.6774 (ttp-110) REVERT: D 191 GLU cc_start: 0.6270 (tt0) cc_final: 0.5371 (pm20) REVERT: D 293 LYS cc_start: 0.7458 (mttt) cc_final: 0.6198 (mtmt) REVERT: E 77 GLN cc_start: 0.7684 (OUTLIER) cc_final: 0.7461 (pm20) REVERT: E 302 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8489 (tp) REVERT: G 277 LEU cc_start: 0.6866 (mp) cc_final: 0.6546 (tt) REVERT: G 301 LYS cc_start: 0.8181 (mmpt) cc_final: 0.7815 (mmtm) REVERT: H 226 PHE cc_start: 0.8385 (m-80) cc_final: 0.8159 (m-80) REVERT: K 90 GLU cc_start: 0.8205 (pt0) cc_final: 0.7875 (pt0) outliers start: 41 outliers final: 33 residues processed: 251 average time/residue: 0.3591 time to fit residues: 138.1881 Evaluate side-chains 243 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 208 time to evaluate : 2.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 189 LEU 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 306 HIS Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 59 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 G residue 288 VAL Chi-restraints excluded: chain H residue 60 LYS Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain H residue 208 HIS Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain H residue 329 ASN Chi-restraints excluded: chain K residue 15 ILE Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 88 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 188 optimal weight: 0.7980 chunk 252 optimal weight: 3.9990 chunk 72 optimal weight: 0.0470 chunk 218 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 237 optimal weight: 0.2980 chunk 99 optimal weight: 0.9990 chunk 243 optimal weight: 0.0010 chunk 30 optimal weight: 50.0000 chunk 43 optimal weight: 2.9990 overall best weight: 0.4284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 ASN ** C 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 ASN ** H 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.193418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.154226 restraints weight = 35883.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.153609 restraints weight = 32148.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.154373 restraints weight = 22701.517| |-----------------------------------------------------------------------------| r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.226 22852 Z= 0.297 Angle : 0.773 59.200 31091 Z= 0.430 Chirality : 0.042 0.527 3240 Planarity : 0.004 0.174 4040 Dihedral : 13.968 159.031 4155 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 1.76 % Allowed : 16.78 % Favored : 81.47 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.16), residues: 2950 helix: 0.81 (0.19), residues: 875 sheet: -1.11 (0.27), residues: 380 loop : -2.35 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 316 HIS 0.005 0.001 HIS F 324 PHE 0.016 0.001 PHE D 216 TYR 0.039 0.001 TYR C 325 ARG 0.032 0.000 ARG C 296 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4256.76 seconds wall clock time: 76 minutes 51.39 seconds (4611.39 seconds total)