Starting phenix.real_space_refine on Wed Feb 14 10:59:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hd0_34668/02_2024/8hd0_34668_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hd0_34668/02_2024/8hd0_34668.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hd0_34668/02_2024/8hd0_34668.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hd0_34668/02_2024/8hd0_34668.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hd0_34668/02_2024/8hd0_34668_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hd0_34668/02_2024/8hd0_34668_updated.pdb" } resolution = 3.11 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= -0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 30 5.16 5 C 5699 2.51 5 N 1682 2.21 5 O 1679 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 302": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9096 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1669 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 210} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1670 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 210} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 1918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 1918 Classifications: {'peptide': 299} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PTRANS': 9, 'TRANS': 289} Unresolved non-hydrogen bonds: 393 Unresolved non-hydrogen angles: 505 Unresolved non-hydrogen dihedrals: 313 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 10, 'TYR:plan': 4, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 14, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 248 Chain: "D" Number of atoms: 1888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 1888 Classifications: {'peptide': 299} Incomplete info: {'truncation_to_alanine': 117} Link IDs: {'PTRANS': 9, 'TRANS': 289} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 425 Unresolved non-hydrogen angles: 547 Unresolved non-hydrogen dihedrals: 337 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 13, 'TYR:plan': 3, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 12, 'PHE:plan': 5, 'GLU:plan': 11, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 264 Chain: "E" Number of atoms: 1889 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 380, 1869 Classifications: {'peptide': 380} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 300} Link IDs: {'PTRANS': 8, 'TRANS': 371} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 1137 Unresolved non-hydrogen angles: 1428 Unresolved non-hydrogen dihedrals: 923 Unresolved non-hydrogen chiralities: 85 Planarities with less than four sites: {'GLN:plan1': 49, 'HIS:plan': 3, 'TYR:plan': 9, 'ASN:plan1': 10, 'TRP:plan': 4, 'ASP:plan': 7, 'ARG%COO:plan': 1, 'PHE:plan': 4, 'GLU:plan': 36, 'ARG:plan': 34} Unresolved non-hydrogen planarities: 704 Conformer: "B" Number of residues, atoms: 380, 1869 Classifications: {'peptide': 380} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 300} Link IDs: {'PTRANS': 8, 'TRANS': 371} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 1137 Unresolved non-hydrogen angles: 1428 Unresolved non-hydrogen dihedrals: 923 Unresolved non-hydrogen chiralities: 85 Planarities with less than four sites: {'GLN:plan1': 49, 'HIS:plan': 3, 'TYR:plan': 9, 'ASN:plan1': 10, 'TRP:plan': 4, 'ASP:plan': 7, 'ARG%COO:plan': 1, 'PHE:plan': 4, 'GLU:plan': 36, 'ARG:plan': 34} Unresolved non-hydrogen planarities: 704 bond proxies already assigned to first conformer: 1844 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AGLU E 233 " occ=0.50 ... (8 atoms not shown) pdb=" CB BGLU E 233 " occ=0.50 residue: pdb=" N AARG E 237 " occ=0.50 ... (8 atoms not shown) pdb=" CB BARG E 237 " occ=0.50 residue: pdb=" N AARG E 262 " occ=0.50 ... (8 atoms not shown) pdb=" CB BARG E 262 " occ=0.50 residue: pdb=" N AVAL E 302 " occ=0.50 ... (8 atoms not shown) pdb=" CB BVAL E 302 " occ=0.50 Time building chain proxies: 6.62, per 1000 atoms: 0.73 Number of scatterers: 9096 At special positions: 0 Unit cell: (68.04, 91.56, 253.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 P 6 15.00 O 1679 8.00 N 1682 7.00 C 5699 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 - 3.50 Amino acid : False - 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: 3.85 Conformation dependent library (CDL) restraints added in 2.7 seconds 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2592 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 47 helices and 10 sheets defined 54.1% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.22 Creating SS restraints... Processing helix chain 'A' and resid 41 through 49 Processing helix chain 'A' and resid 74 through 79 Processing helix chain 'A' and resid 96 through 107 Proline residue: A 103 - end of helix Processing helix chain 'A' and resid 111 through 124 Processing helix chain 'A' and resid 128 through 130 No H-bonds generated for 'chain 'A' and resid 128 through 130' Processing helix chain 'A' and resid 135 through 137 No H-bonds generated for 'chain 'A' and resid 135 through 137' Processing helix chain 'A' and resid 140 through 154 removed outlier: 4.815A pdb=" N ASN A 154 " --> pdb=" O ARG A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 186 removed outlier: 4.436A pdb=" N VAL A 186 " --> pdb=" O GLU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 200 No H-bonds generated for 'chain 'A' and resid 197 through 200' Processing helix chain 'B' and resid 41 through 49 Processing helix chain 'B' and resid 74 through 77 No H-bonds generated for 'chain 'B' and resid 74 through 77' Processing helix chain 'B' and resid 96 through 107 Proline residue: B 103 - end of helix Processing helix chain 'B' and resid 111 through 123 Processing helix chain 'B' and resid 128 through 130 No H-bonds generated for 'chain 'B' and resid 128 through 130' Processing helix chain 'B' and resid 135 through 137 No H-bonds generated for 'chain 'B' and resid 135 through 137' Processing helix chain 'B' and resid 140 through 154 removed outlier: 5.012A pdb=" N ASN B 154 " --> pdb=" O ARG B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 186 removed outlier: 4.166A pdb=" N VAL B 186 " --> pdb=" O GLU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 201 No H-bonds generated for 'chain 'B' and resid 198 through 201' Processing helix chain 'C' and resid 64 through 78 Processing helix chain 'C' and resid 81 through 106 removed outlier: 3.635A pdb=" N VAL C 90 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU C 97 " --> pdb=" O ILE C 93 " (cutoff:3.500A) Proline residue: C 98 - end of helix removed outlier: 4.186A pdb=" N MET C 103 " --> pdb=" O SER C 99 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL C 104 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR C 105 " --> pdb=" O CYS C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 111 No H-bonds generated for 'chain 'C' and resid 108 through 111' Processing helix chain 'C' and resid 131 through 140 removed outlier: 3.887A pdb=" N ALA C 135 " --> pdb=" O ASP C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 164 removed outlier: 4.489A pdb=" N GLY C 160 " --> pdb=" O ASP C 157 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N GLU C 161 " --> pdb=" O ALA C 158 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE C 162 " --> pdb=" O LEU C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 193 No H-bonds generated for 'chain 'C' and resid 190 through 193' Processing helix chain 'C' and resid 195 through 206 removed outlier: 3.632A pdb=" N THR C 200 " --> pdb=" O GLU C 196 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU C 201 " --> pdb=" O SER C 197 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP C 203 " --> pdb=" O ASN C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 224 No H-bonds generated for 'chain 'C' and resid 222 through 224' Processing helix chain 'C' and resid 230 through 269 removed outlier: 3.680A pdb=" N SER C 235 " --> pdb=" O VAL C 231 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ALA C 236 " --> pdb=" O GLY C 232 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE C 247 " --> pdb=" O VAL C 243 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG C 261 " --> pdb=" O SER C 257 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ASP C 263 " --> pdb=" O PHE C 259 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N SER C 264 " --> pdb=" O ALA C 260 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE C 265 " --> pdb=" O ARG C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 299 Proline residue: C 281 - end of helix removed outlier: 3.511A pdb=" N GLY C 285 " --> pdb=" O PRO C 281 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU C 289 " --> pdb=" O GLY C 285 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU C 296 " --> pdb=" O SER C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 319 removed outlier: 3.925A pdb=" N SER C 310 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA C 311 " --> pdb=" O ARG C 307 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLN C 317 " --> pdb=" O ALA C 313 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL C 318 " --> pdb=" O GLU C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 356 removed outlier: 4.134A pdb=" N LEU C 335 " --> pdb=" O ASP C 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 78 Processing helix chain 'D' and resid 81 through 115 removed outlier: 4.159A pdb=" N LEU D 97 " --> pdb=" O ILE D 93 " (cutoff:3.500A) Proline residue: D 98 - end of helix Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 155 through 163 removed outlier: 4.451A pdb=" N GLY D 160 " --> pdb=" O ASP D 157 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N GLU D 161 " --> pdb=" O ALA D 158 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE D 162 " --> pdb=" O LEU D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 193 No H-bonds generated for 'chain 'D' and resid 190 through 193' Processing helix chain 'D' and resid 195 through 206 removed outlier: 5.036A pdb=" N THR D 200 " --> pdb=" O GLU D 196 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU D 201 " --> pdb=" O SER D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 263 removed outlier: 4.306A pdb=" N SER D 235 " --> pdb=" O VAL D 231 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ASP D 263 " --> pdb=" O PHE D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 270 Processing helix chain 'D' and resid 275 through 318 removed outlier: 3.512A pdb=" N ARG D 280 " --> pdb=" O GLY D 276 " (cutoff:3.500A) Proline residue: D 281 - end of helix removed outlier: 3.789A pdb=" N LEU D 289 " --> pdb=" O GLY D 285 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N SER D 310 " --> pdb=" O LEU D 306 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ALA D 311 " --> pdb=" O ARG D 307 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N VAL D 312 " --> pdb=" O LEU D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 358 removed outlier: 3.548A pdb=" N ARG D 357 " --> pdb=" O VAL D 353 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N HIS D 358 " --> pdb=" O GLN D 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 50 Processing helix chain 'E' and resid 53 through 122 Processing helix chain 'E' and resid 145 through 149 Processing helix chain 'E' and resid 153 through 216 Processing helix chain 'E' and resid 222 through 246 Processing helix chain 'E' and resid 249 through 270 Processing helix chain 'E' and resid 279 through 285 Processing sheet with id= A, first strand: chain 'A' and resid 23 through 25 Processing sheet with id= B, first strand: chain 'A' and resid 206 through 210 Processing sheet with id= C, first strand: chain 'A' and resid 9 through 11 removed outlier: 6.729A pdb=" N TYR A 11 " --> pdb=" O GLN A 16 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N GLN A 16 " --> pdb=" O TYR A 11 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 23 through 25 Processing sheet with id= E, first strand: chain 'B' and resid 31 through 35 removed outlier: 6.749A pdb=" N ARG B 206 " --> pdb=" O PHE B 32 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N THR B 34 " --> pdb=" O ARG B 206 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LEU B 208 " --> pdb=" O THR B 34 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 81 through 84 removed outlier: 6.584A pdb=" N VAL B 158 " --> pdb=" O GLY B 82 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ILE B 84 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU B 160 " --> pdb=" O ILE B 84 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N THR B 189 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ALA B 161 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU B 191 " --> pdb=" O ALA B 161 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 9 through 11 removed outlier: 6.929A pdb=" N TYR B 11 " --> pdb=" O GLN B 16 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N GLN B 16 " --> pdb=" O TYR B 11 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 322 through 326 Processing sheet with id= I, first strand: chain 'E' and resid 404 through 406 removed outlier: 4.408A pdb=" N ILE E 404 " --> pdb=" O VAL E 411 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 340 through 344 removed outlier: 6.308A pdb=" N VAL E 355 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL E 354 " --> pdb=" O TYR E 366 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL E 356 " --> pdb=" O SER E 364 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER E 364 " --> pdb=" O VAL E 356 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ASP E 362 " --> pdb=" O HIS E 358 " (cutoff:3.500A) 572 hydrogen bonds defined for protein. 1665 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.05 Time building geometry restraints manager: 4.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2854 1.33 - 1.45: 1165 1.45 - 1.57: 5142 1.57 - 1.69: 10 1.69 - 1.81: 52 Bond restraints: 9223 Sorted by residual: bond pdb=" N VAL C 185 " pdb=" CA VAL C 185 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.19e-02 7.06e+03 9.58e+00 bond pdb=" N VAL C 186 " pdb=" CA VAL C 186 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.23e-02 6.61e+03 9.06e+00 bond pdb=" N VAL C 183 " pdb=" CA VAL C 183 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.72e+00 bond pdb=" N ILE C 121 " pdb=" CA ILE C 121 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 8.02e+00 bond pdb=" N ILE C 211 " pdb=" CA ILE C 211 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.96e+00 ... (remaining 9218 not shown) Histogram of bond angle deviations from ideal: 99.10 - 106.08: 165 106.08 - 113.06: 5140 113.06 - 120.04: 3023 120.04 - 127.03: 4232 127.03 - 134.01: 77 Bond angle restraints: 12637 Sorted by residual: angle pdb=" PB ATP B 301 " pdb=" O3B ATP B 301 " pdb=" PG ATP B 301 " ideal model delta sigma weight residual 139.87 129.08 10.79 1.00e+00 1.00e+00 1.16e+02 angle pdb=" PB ATP A 301 " pdb=" O3B ATP A 301 " pdb=" PG ATP A 301 " ideal model delta sigma weight residual 139.87 130.49 9.38 1.00e+00 1.00e+00 8.80e+01 angle pdb=" N ALA C 225 " pdb=" CA ALA C 225 " pdb=" C ALA C 225 " ideal model delta sigma weight residual 114.62 108.03 6.59 1.14e+00 7.69e-01 3.34e+01 angle pdb=" PA ATP B 301 " pdb=" O3A ATP B 301 " pdb=" PB ATP B 301 " ideal model delta sigma weight residual 136.83 131.79 5.04 1.00e+00 1.00e+00 2.54e+01 angle pdb=" N VAL C 100 " pdb=" CA VAL C 100 " pdb=" C VAL C 100 " ideal model delta sigma weight residual 112.96 108.55 4.41 1.00e+00 1.00e+00 1.95e+01 ... (remaining 12632 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.99: 4856 16.99 - 33.98: 379 33.98 - 50.97: 158 50.97 - 67.95: 37 67.95 - 84.94: 8 Dihedral angle restraints: 5438 sinusoidal: 1414 harmonic: 4024 Sorted by residual: dihedral pdb=" CA GLU E 114 " pdb=" C GLU E 114 " pdb=" N ARG E 115 " pdb=" CA ARG E 115 " ideal model delta harmonic sigma weight residual 180.00 153.16 26.84 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA HIS A 195 " pdb=" C HIS A 195 " pdb=" N ASP A 196 " pdb=" CA ASP A 196 " ideal model delta harmonic sigma weight residual 180.00 157.77 22.23 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA SER D 264 " pdb=" C SER D 264 " pdb=" N ILE D 265 " pdb=" CA ILE D 265 " ideal model delta harmonic sigma weight residual 180.00 157.84 22.16 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 5435 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1355 0.066 - 0.131: 173 0.131 - 0.197: 28 0.197 - 0.262: 4 0.262 - 0.328: 2 Chirality restraints: 1562 Sorted by residual: chirality pdb=" CB THR C 360 " pdb=" CA THR C 360 " pdb=" OG1 THR C 360 " pdb=" CG2 THR C 360 " both_signs ideal model delta sigma weight residual False 2.55 2.22 0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" CB VAL B 96 " pdb=" CA VAL B 96 " pdb=" CG1 VAL B 96 " pdb=" CG2 VAL B 96 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA LEU C 198 " pdb=" N LEU C 198 " pdb=" C LEU C 198 " pdb=" CB LEU C 198 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 1559 not shown) Planarity restraints: 1674 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS E 110 " 0.022 2.00e-02 2.50e+03 4.44e-02 1.97e+01 pdb=" C LYS E 110 " -0.077 2.00e-02 2.50e+03 pdb=" O LYS E 110 " 0.028 2.00e-02 2.50e+03 pdb=" N ALA E 111 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG D 280 " 0.060 5.00e-02 4.00e+02 9.00e-02 1.29e+01 pdb=" N PRO D 281 " -0.156 5.00e-02 4.00e+02 pdb=" CA PRO D 281 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO D 281 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 104 " -0.015 2.00e-02 2.50e+03 2.97e-02 8.84e+00 pdb=" C ALA E 104 " 0.051 2.00e-02 2.50e+03 pdb=" O ALA E 104 " -0.019 2.00e-02 2.50e+03 pdb=" N LYS E 105 " -0.017 2.00e-02 2.50e+03 ... (remaining 1671 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 113 2.64 - 3.21: 8653 3.21 - 3.77: 14027 3.77 - 4.34: 17727 4.34 - 4.90: 29668 Nonbonded interactions: 70188 Sorted by model distance: nonbonded pdb=" OG SER A 139 " pdb=" OE1 GLU A 142 " model vdw 2.075 2.440 nonbonded pdb=" O ASP A 169 " pdb=" OG SER A 173 " model vdw 2.117 2.440 nonbonded pdb=" NH2 ARG A 79 " pdb=" O GLY D 272 " model vdw 2.215 2.520 nonbonded pdb=" O ASP C 76 " pdb=" OG SER C 79 " model vdw 2.225 2.440 nonbonded pdb=" OH TYR B 11 " pdb=" OG1 THR B 43 " model vdw 2.244 2.440 ... (remaining 70183 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 11 or (resid 12 and (name N or name CA or name C \ or name O or name CB )) or resid 13 through 196 or (resid 197 through 198 and ( \ name N or name CA or name C or name O or name CB )) or resid 199 through 218 or \ resid 301)) selection = (chain 'B' and (resid 1 through 67 or (resid 68 and (name N or name CA or name C \ or name O or name CB )) or resid 69 or (resid 70 and (name N or name CA or name \ C or name O or name CB )) or resid 71 through 218 or resid 301)) } ncs_group { reference = (chain 'C' and ((resid 63 through 65 and (name N or name CA or name C or name O \ or name CB )) or resid 66 through 74 or (resid 75 through 76 and (name N or name \ CA or name C or name O or name CB )) or resid 77 through 220 or (resid 221 thro \ ugh 223 and (name N or name CA or name C or name O or name CB )) or resid 224 th \ rough 226 or (resid 227 and (name N or name CA or name C or name O or name CB )) \ or resid 228 through 229 or (resid 230 through 231 and (name N or name CA or na \ me C or name O or name CB )) or resid 232 or (resid 233 through 234 and (name N \ or name CA or name C or name O or name CB )) or resid 235 through 307 or (resid \ 308 through 319 and (name N or name CA or name C or name O or name CB )) or (res \ id 320 through 326 and (name N or name CA or name C or name O or name CB )) or r \ esid 327 through 331 or (resid 332 and (name N or name CA or name C or name O or \ name CB )) or resid 333 through 353 or (resid 354 and (name N or name CA or nam \ e C or name O or name CB )) or resid 355 through 359 or (resid 360 through 361 a \ nd (name N or name CA or name C or name O or name CB )))) selection = (chain 'D' and (resid 63 through 75 or (resid 76 and (name N or name CA or name \ C or name O or name CB )) or resid 77 through 105 or (resid 106 and (name N or n \ ame CA or name C or name O or name CB )) or resid 107 through 108 or (resid 109 \ through 116 and (name N or name CA or name C or name O or name CB )) or resid 11 \ 7 through 218 or (resid 219 through 223 and (name N or name CA or name C or name \ O or name CB )) or resid 224 through 233 or (resid 234 and (name N or name CA o \ r name C or name O or name CB )) or resid 235 through 256 or (resid 257 and (nam \ e N or name CA or name C or name O or name CB )) or resid 258 through 262 or (re \ sid 263 and (name N or name CA or name C or name O or name CB )) or resid 264 th \ rough 301 or (resid 302 and (name N or name CA or name C or name O or name CB )) \ or resid 303 through 333 or (resid 334 and (name N or name CA or name C or name \ O or name CB )) or resid 335 through 361)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 38.680 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 32.100 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 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 0.063 9223 Z= 0.454 Angle : 0.798 12.378 12637 Z= 0.487 Chirality : 0.050 0.328 1562 Planarity : 0.005 0.090 1674 Dihedral : 16.177 84.942 2846 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.85 % Allowed : 9.62 % Favored : 89.53 % Rotamer: Outliers : 1.47 % Allowed : 27.36 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.94 (0.23), residues: 1416 helix: 0.81 (0.19), residues: 766 sheet: -2.27 (0.51), residues: 68 loop : -2.46 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 345 HIS 0.006 0.001 HIS A 195 PHE 0.018 0.002 PHE B 23 TYR 0.008 0.001 TYR C 68 ARG 0.004 0.001 ARG C 233 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 133 time to evaluate : 1.060 Fit side-chains REVERT: A 71 ASN cc_start: 0.8147 (m-40) cc_final: 0.7845 (t0) REVERT: C 306 LEU cc_start: 0.6695 (mt) cc_final: 0.6360 (pp) outliers start: 9 outliers final: 2 residues processed: 139 average time/residue: 0.3228 time to fit residues: 56.4642 Evaluate side-chains 104 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 102 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 221 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 8.9990 chunk 104 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 55 optimal weight: 8.9990 chunk 108 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 80 optimal weight: 30.0000 chunk 125 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 9223 Z= 0.423 Angle : 0.711 10.056 12637 Z= 0.364 Chirality : 0.044 0.226 1562 Planarity : 0.005 0.060 1674 Dihedral : 9.011 86.884 1549 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.98 % Favored : 91.60 % Rotamer: Outliers : 7.65 % Allowed : 23.13 % Favored : 69.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.67 (0.22), residues: 1416 helix: 1.10 (0.19), residues: 757 sheet: -1.52 (0.59), residues: 60 loop : -2.49 (0.24), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP A 60 HIS 0.005 0.002 HIS B 214 PHE 0.017 0.002 PHE A 23 TYR 0.024 0.002 TYR C 105 ARG 0.005 0.001 ARG A 53 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 115 time to evaluate : 1.070 Fit side-chains REVERT: A 200 ILE cc_start: 0.8604 (pt) cc_final: 0.8309 (pt) REVERT: B 74 VAL cc_start: 0.8205 (OUTLIER) cc_final: 0.7994 (t) REVERT: B 207 MET cc_start: 0.7434 (OUTLIER) cc_final: 0.6874 (tmm) REVERT: C 355 HIS cc_start: 0.7217 (OUTLIER) cc_final: 0.6943 (t-90) REVERT: D 241 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7528 (mp) REVERT: D 268 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.7437 (tt0) outliers start: 47 outliers final: 23 residues processed: 153 average time/residue: 0.2431 time to fit residues: 49.8328 Evaluate side-chains 130 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 102 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 261 ARG Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 355 HIS Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 334 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 69 optimal weight: 0.5980 chunk 38 optimal weight: 0.3980 chunk 104 optimal weight: 9.9990 chunk 85 optimal weight: 20.0000 chunk 34 optimal weight: 0.5980 chunk 125 optimal weight: 30.0000 chunk 135 optimal weight: 50.0000 chunk 111 optimal weight: 10.0000 chunk 124 optimal weight: 30.0000 chunk 42 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 HIS ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.116 9223 Z= 0.999 Angle : 1.020 13.722 12637 Z= 0.513 Chirality : 0.061 0.400 1562 Planarity : 0.007 0.061 1674 Dihedral : 9.469 86.619 1547 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.62 % Favored : 90.95 % Rotamer: Outliers : 10.10 % Allowed : 22.64 % Favored : 67.26 % 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: -1.36 (0.22), residues: 1416 helix: 0.53 (0.18), residues: 755 sheet: -2.34 (0.52), residues: 74 loop : -2.71 (0.23), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.005 TRP A 60 HIS 0.013 0.004 HIS B 89 PHE 0.029 0.004 PHE A 23 TYR 0.019 0.003 TYR C 105 ARG 0.007 0.001 ARG B 206 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 106 time to evaluate : 0.976 Fit side-chains REVERT: A 73 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7814 (tp30) REVERT: A 87 ASP cc_start: 0.8151 (OUTLIER) cc_final: 0.7418 (m-30) REVERT: A 155 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7804 (pttt) REVERT: A 195 HIS cc_start: 0.8987 (OUTLIER) cc_final: 0.8580 (p-80) REVERT: A 200 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8462 (pt) REVERT: A 208 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8344 (mt) REVERT: B 5 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7379 (mt-10) REVERT: B 74 VAL cc_start: 0.8332 (OUTLIER) cc_final: 0.8069 (t) REVERT: B 207 MET cc_start: 0.7793 (OUTLIER) cc_final: 0.7090 (tmm) REVERT: D 241 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7303 (mp) REVERT: D 268 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.7764 (tt0) outliers start: 62 outliers final: 36 residues processed: 156 average time/residue: 0.2234 time to fit residues: 47.7255 Evaluate side-chains 148 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 102 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain B residue 30 MET Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 355 HIS Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 358 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 40.0000 chunk 94 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 13 optimal weight: 0.2980 chunk 59 optimal weight: 0.6980 chunk 84 optimal weight: 20.0000 chunk 125 optimal weight: 0.0040 chunk 133 optimal weight: 50.0000 chunk 119 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 111 optimal weight: 0.8980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9223 Z= 0.273 Angle : 0.593 9.195 12637 Z= 0.311 Chirality : 0.041 0.162 1562 Planarity : 0.004 0.050 1674 Dihedral : 8.246 85.860 1547 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.84 % Favored : 92.74 % Rotamer: Outliers : 6.51 % Allowed : 25.24 % Favored : 68.24 % 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: -0.57 (0.23), residues: 1416 helix: 1.28 (0.19), residues: 755 sheet: -2.01 (0.55), residues: 74 loop : -2.50 (0.24), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 345 HIS 0.006 0.001 HIS C 358 PHE 0.022 0.002 PHE C 247 TYR 0.015 0.001 TYR C 105 ARG 0.003 0.000 ARG A 150 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 95 time to evaluate : 1.026 Fit side-chains REVERT: A 73 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7563 (mm-30) REVERT: A 183 PHE cc_start: 0.8473 (OUTLIER) cc_final: 0.7609 (t80) REVERT: A 195 HIS cc_start: 0.8223 (OUTLIER) cc_final: 0.7812 (p-80) REVERT: A 200 ILE cc_start: 0.8584 (pt) cc_final: 0.8170 (pt) REVERT: B 94 ARG cc_start: 0.8101 (mtp85) cc_final: 0.7894 (mtp180) REVERT: B 203 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.8229 (mmt90) REVERT: B 207 MET cc_start: 0.7516 (OUTLIER) cc_final: 0.6883 (tmm) REVERT: D 241 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7578 (mp) REVERT: D 268 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.7582 (tt0) REVERT: D 330 PHE cc_start: 0.4571 (OUTLIER) cc_final: 0.3398 (t80) outliers start: 40 outliers final: 25 residues processed: 128 average time/residue: 0.2583 time to fit residues: 43.9034 Evaluate side-chains 125 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 92 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 203 ARG Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 330 PHE Chi-restraints excluded: chain D residue 334 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 55 optimal weight: 50.0000 chunk 113 optimal weight: 9.9990 chunk 92 optimal weight: 0.0270 chunk 0 optimal weight: 0.9990 chunk 68 optimal weight: 0.2980 chunk 119 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9223 Z= 0.268 Angle : 0.594 8.872 12637 Z= 0.308 Chirality : 0.041 0.163 1562 Planarity : 0.004 0.048 1674 Dihedral : 8.165 89.360 1547 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.12 % Favored : 92.45 % Rotamer: Outliers : 7.49 % Allowed : 24.59 % Favored : 67.92 % 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: -0.18 (0.23), residues: 1416 helix: 1.55 (0.19), residues: 754 sheet: -1.26 (0.60), residues: 62 loop : -2.32 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 345 HIS 0.006 0.001 HIS C 358 PHE 0.019 0.002 PHE D 247 TYR 0.005 0.001 TYR B 205 ARG 0.002 0.000 ARG C 233 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 95 time to evaluate : 1.081 Fit side-chains REVERT: A 83 MET cc_start: 0.7839 (OUTLIER) cc_final: 0.7432 (tpt) REVERT: A 90 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8381 (pp) REVERT: B 203 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.8207 (mmt90) REVERT: B 207 MET cc_start: 0.7421 (OUTLIER) cc_final: 0.6802 (tmm) REVERT: C 95 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8573 (tt) REVERT: C 269 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8182 (tttp) REVERT: D 241 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7565 (mp) REVERT: D 268 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.7503 (tt0) REVERT: D 330 PHE cc_start: 0.4515 (OUTLIER) cc_final: 0.3310 (t80) outliers start: 46 outliers final: 28 residues processed: 132 average time/residue: 0.2530 time to fit residues: 44.6589 Evaluate side-chains 134 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 97 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 203 ARG Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 269 LYS Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 330 PHE Chi-restraints excluded: chain D residue 334 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 50.0000 chunk 26 optimal weight: 0.0170 chunk 78 optimal weight: 20.0000 chunk 32 optimal weight: 0.6980 chunk 133 optimal weight: 50.0000 chunk 110 optimal weight: 30.0000 chunk 61 optimal weight: 0.9980 chunk 11 optimal weight: 0.2980 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 128 optimal weight: 10.0000 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9223 Z= 0.252 Angle : 0.570 11.128 12637 Z= 0.294 Chirality : 0.040 0.180 1562 Planarity : 0.003 0.047 1674 Dihedral : 7.994 87.255 1547 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.77 % Favored : 92.81 % Rotamer: Outliers : 8.14 % Allowed : 24.76 % Favored : 67.10 % 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: 0.05 (0.23), residues: 1416 helix: 1.78 (0.19), residues: 749 sheet: -1.61 (0.57), residues: 75 loop : -2.16 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 345 HIS 0.005 0.001 HIS A 195 PHE 0.026 0.001 PHE C 247 TYR 0.004 0.001 TYR B 205 ARG 0.009 0.000 ARG D 262 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 93 time to evaluate : 0.986 Fit side-chains REVERT: A 73 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7690 (mm-30) REVERT: A 90 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8352 (pp) REVERT: A 123 ASP cc_start: 0.7462 (OUTLIER) cc_final: 0.7261 (t0) REVERT: A 183 PHE cc_start: 0.8484 (OUTLIER) cc_final: 0.7643 (t80) REVERT: B 207 MET cc_start: 0.7394 (OUTLIER) cc_final: 0.6825 (tmm) REVERT: C 95 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8549 (tt) REVERT: C 269 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8182 (tttp) REVERT: D 241 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7551 (mp) REVERT: D 268 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7480 (tt0) REVERT: D 330 PHE cc_start: 0.4416 (OUTLIER) cc_final: 0.3243 (t80) outliers start: 50 outliers final: 31 residues processed: 134 average time/residue: 0.2485 time to fit residues: 44.5781 Evaluate side-chains 134 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 93 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 269 LYS Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 330 PHE Chi-restraints excluded: chain D residue 334 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 0.6980 chunk 76 optimal weight: 7.9990 chunk 97 optimal weight: 8.9990 chunk 75 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 chunk 74 optimal weight: 1.9990 chunk 133 optimal weight: 50.0000 chunk 83 optimal weight: 30.0000 chunk 81 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 82 optimal weight: 8.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 ASN ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.018 0.144 9223 Z= 1.212 Angle : 1.116 14.952 12637 Z= 0.555 Chirality : 0.068 0.424 1562 Planarity : 0.007 0.082 1674 Dihedral : 9.454 87.540 1547 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.48 % Favored : 91.10 % Rotamer: Outliers : 10.91 % Allowed : 23.13 % Favored : 65.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.10 (0.22), residues: 1416 helix: 0.64 (0.19), residues: 759 sheet: -1.80 (0.57), residues: 62 loop : -2.50 (0.23), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.006 TRP A 60 HIS 0.013 0.004 HIS B 89 PHE 0.031 0.004 PHE A 23 TYR 0.015 0.003 TYR B 97 ARG 0.010 0.001 ARG B 185 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 97 time to evaluate : 1.119 Fit side-chains REVERT: A 83 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7592 (ttt) REVERT: A 87 ASP cc_start: 0.8203 (OUTLIER) cc_final: 0.7408 (m-30) REVERT: A 123 ASP cc_start: 0.7696 (OUTLIER) cc_final: 0.7484 (t0) REVERT: A 200 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8532 (pt) REVERT: B 74 VAL cc_start: 0.8350 (OUTLIER) cc_final: 0.8143 (t) REVERT: B 207 MET cc_start: 0.7777 (OUTLIER) cc_final: 0.7083 (tmm) REVERT: C 269 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8204 (tttp) REVERT: C 275 ASP cc_start: 0.7467 (OUTLIER) cc_final: 0.6981 (m-30) REVERT: D 109 ASN cc_start: 0.8230 (OUTLIER) cc_final: 0.7987 (t0) REVERT: D 241 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7297 (mp) REVERT: D 268 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.7781 (tt0) REVERT: D 330 PHE cc_start: 0.4866 (OUTLIER) cc_final: 0.3882 (t80) outliers start: 67 outliers final: 39 residues processed: 151 average time/residue: 0.2179 time to fit residues: 45.4957 Evaluate side-chains 148 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 97 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain B residue 30 MET Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 269 LYS Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 355 HIS Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 330 PHE Chi-restraints excluded: chain D residue 358 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 30.0000 chunk 79 optimal weight: 50.0000 chunk 40 optimal weight: 0.9980 chunk 26 optimal weight: 0.2980 chunk 25 optimal weight: 0.0980 chunk 84 optimal weight: 20.0000 chunk 90 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 12 optimal weight: 0.1980 chunk 104 optimal weight: 10.0000 chunk 120 optimal weight: 50.0000 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9223 Z= 0.233 Angle : 0.592 11.861 12637 Z= 0.308 Chirality : 0.041 0.186 1562 Planarity : 0.004 0.065 1674 Dihedral : 8.303 88.551 1547 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.34 % Favored : 93.23 % Rotamer: Outliers : 6.03 % Allowed : 28.18 % Favored : 65.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.23 (0.23), residues: 1416 helix: 1.49 (0.19), residues: 758 sheet: -1.33 (0.60), residues: 62 loop : -2.34 (0.23), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 345 HIS 0.006 0.001 HIS C 358 PHE 0.024 0.001 PHE C 247 TYR 0.004 0.001 TYR B 205 ARG 0.005 0.001 ARG D 262 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 90 time to evaluate : 1.117 Fit side-chains REVERT: A 195 HIS cc_start: 0.8181 (OUTLIER) cc_final: 0.7861 (p-80) REVERT: B 207 MET cc_start: 0.7539 (OUTLIER) cc_final: 0.6907 (tmm) REVERT: C 95 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8642 (tt) REVERT: C 269 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8192 (tttp) REVERT: D 241 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7432 (mp) REVERT: D 268 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7540 (tt0) outliers start: 37 outliers final: 23 residues processed: 121 average time/residue: 0.2542 time to fit residues: 41.3614 Evaluate side-chains 112 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 83 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 269 LYS Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain D residue 304 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 3.9990 chunk 116 optimal weight: 10.0000 chunk 123 optimal weight: 30.0000 chunk 74 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 97 optimal weight: 8.9990 chunk 38 optimal weight: 0.9990 chunk 112 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 chunk 81 optimal weight: 9.9990 chunk 131 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 268 GLN D 109 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.028 0.221 9223 Z= 1.892 Angle : 1.503 19.589 12637 Z= 0.753 Chirality : 0.093 0.587 1562 Planarity : 0.010 0.123 1674 Dihedral : 10.072 89.741 1547 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.64 % Allowed : 10.04 % Favored : 89.32 % Rotamer: Outliers : 9.61 % Allowed : 24.76 % Favored : 65.64 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.88 (0.21), residues: 1416 helix: -0.10 (0.18), residues: 753 sheet: -1.87 (0.59), residues: 62 loop : -2.74 (0.23), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.008 TRP A 60 HIS 0.021 0.006 HIS A 214 PHE 0.045 0.006 PHE A 23 TYR 0.023 0.005 TYR B 205 ARG 0.015 0.002 ARG B 185 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 94 time to evaluate : 1.064 Fit side-chains REVERT: A 29 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8448 (tt0) REVERT: A 73 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7924 (mm-30) REVERT: A 83 MET cc_start: 0.7923 (OUTLIER) cc_final: 0.7451 (ttt) REVERT: B 207 MET cc_start: 0.7917 (OUTLIER) cc_final: 0.7173 (tmm) REVERT: C 95 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8850 (tt) REVERT: C 269 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8235 (ttmp) REVERT: D 241 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7285 (mp) REVERT: D 268 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.7880 (tt0) REVERT: D 330 PHE cc_start: 0.5017 (OUTLIER) cc_final: 0.4221 (t80) outliers start: 59 outliers final: 37 residues processed: 145 average time/residue: 0.2314 time to fit residues: 45.6675 Evaluate side-chains 139 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 93 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 269 LYS Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 355 HIS Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain D residue 301 SER Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 330 PHE Chi-restraints excluded: chain D residue 358 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 40.0000 chunk 62 optimal weight: 0.6980 chunk 91 optimal weight: 0.5980 chunk 137 optimal weight: 50.0000 chunk 126 optimal weight: 50.0000 chunk 109 optimal weight: 0.9990 chunk 11 optimal weight: 0.0980 chunk 84 optimal weight: 20.0000 chunk 67 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 116 optimal weight: 50.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.4427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 9223 Z= 0.538 Angle : 0.773 11.771 12637 Z= 0.391 Chirality : 0.047 0.260 1562 Planarity : 0.005 0.104 1674 Dihedral : 8.943 88.907 1547 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.12 % Favored : 91.52 % Rotamer: Outliers : 5.70 % Allowed : 28.83 % Favored : 65.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.98 (0.22), residues: 1416 helix: 0.88 (0.19), residues: 754 sheet: -1.97 (0.54), residues: 72 loop : -2.62 (0.23), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP D 345 HIS 0.008 0.002 HIS C 355 PHE 0.021 0.002 PHE C 247 TYR 0.009 0.001 TYR B 205 ARG 0.005 0.001 ARG D 262 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 98 time to evaluate : 1.043 Fit side-chains REVERT: A 200 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8389 (pt) REVERT: B 5 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7348 (mt-10) REVERT: B 207 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.6992 (tmm) REVERT: C 95 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8691 (tt) REVERT: C 269 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8257 (tttp) REVERT: D 241 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7416 (mp) REVERT: D 268 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.7642 (tt0) REVERT: D 330 PHE cc_start: 0.4647 (OUTLIER) cc_final: 0.3747 (t80) outliers start: 35 outliers final: 25 residues processed: 126 average time/residue: 0.2408 time to fit residues: 41.2573 Evaluate side-chains 131 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 99 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 269 LYS Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 330 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 0.3980 chunk 100 optimal weight: 7.9990 chunk 16 optimal weight: 0.0980 chunk 30 optimal weight: 0.6980 chunk 109 optimal weight: 0.4980 chunk 45 optimal weight: 0.9980 chunk 112 optimal weight: 9.9990 chunk 13 optimal weight: 0.0060 chunk 20 optimal weight: 0.1980 chunk 96 optimal weight: 20.0000 chunk 6 optimal weight: 0.8980 overall best weight: 0.2396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.223239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.185785 restraints weight = 31782.653| |-----------------------------------------------------------------------------| r_work (start): 0.4121 rms_B_bonded: 3.34 r_work: 0.3416 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3392 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3392 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9223 Z= 0.187 Angle : 0.566 11.983 12637 Z= 0.292 Chirality : 0.039 0.173 1562 Planarity : 0.004 0.080 1674 Dihedral : 7.930 89.505 1547 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.98 % Favored : 92.66 % Rotamer: Outliers : 3.91 % Allowed : 30.29 % Favored : 65.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.21 (0.23), residues: 1416 helix: 1.66 (0.19), residues: 760 sheet: -1.96 (0.54), residues: 82 loop : -2.49 (0.23), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 345 HIS 0.007 0.001 HIS C 358 PHE 0.021 0.001 PHE C 247 TYR 0.005 0.001 TYR C 102 ARG 0.004 0.000 ARG D 262 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2570.37 seconds wall clock time: 46 minutes 45.31 seconds (2805.31 seconds total)