Starting phenix.real_space_refine on Sat Apr 6 07:22:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kh4_37236/04_2024/8kh4_37236_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kh4_37236/04_2024/8kh4_37236.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kh4_37236/04_2024/8kh4_37236.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kh4_37236/04_2024/8kh4_37236.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kh4_37236/04_2024/8kh4_37236_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kh4_37236/04_2024/8kh4_37236_updated.pdb" } resolution = 3.1 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= 0.001 sd= 0.118 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: 4 Type Number sf(0) Gaussians S 51 5.16 5 C 4814 2.51 5 N 1286 2.21 5 O 1370 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 170": "OE1" <-> "OE2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "B GLU 27": "OE1" <-> "OE2" Residue "B GLU 370": "OE1" <-> "OE2" Residue "D TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 7521 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2048 Classifications: {'peptide': 266} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 10, 'TRANS': 255} Chain breaks: 1 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 1809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1809 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 57 Chain: "C" Number of atoms: 2435 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 336, 2425 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 5, 'ARG:plan': 9, 'ASN:plan1': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 113 Conformer: "B" Number of residues, atoms: 336, 2425 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 5, 'ARG:plan': 9, 'ASN:plan1': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 113 bond proxies already assigned to first conformer: 2458 Chain: "E" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 936 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 265 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 1, 'TRANS': 42} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.70, per 1000 atoms: 0.76 Number of scatterers: 7521 At special positions: 0 Unit cell: (72.36, 95.04, 126.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 51 16.00 O 1370 8.00 N 1286 7.00 C 4814 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 178 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 99 " - pdb=" SG CYS E 107 " distance=2.03 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: 2.90 Conformation dependent library (CDL) restraints added in 1.8 seconds 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1886 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 11 sheets defined 38.6% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 28 through 53 removed outlier: 3.838A pdb=" N ILE A 39 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 58 No H-bonds generated for 'chain 'A' and resid 56 through 58' Processing helix chain 'A' and resid 61 through 79 Processing helix chain 'A' and resid 81 through 90 Processing helix chain 'A' and resid 97 through 130 removed outlier: 3.655A pdb=" N GLY A 119 " --> pdb=" O MET A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 138 No H-bonds generated for 'chain 'A' and resid 135 through 138' Processing helix chain 'A' and resid 141 through 159 removed outlier: 3.593A pdb=" N TRP A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 164 No H-bonds generated for 'chain 'A' and resid 161 through 164' Processing helix chain 'A' and resid 186 through 196 Processing helix chain 'A' and resid 198 through 218 Processing helix chain 'A' and resid 267 through 296 removed outlier: 3.683A pdb=" N PHE A 279 " --> pdb=" O VAL A 275 " (cutoff:3.500A) Proline residue: A 285 - end of helix Processing helix chain 'A' and resid 303 through 326 removed outlier: 4.122A pdb=" N ALA A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Proline residue: A 321 - end of helix Processing helix chain 'A' and resid 329 through 337 Processing helix chain 'B' and resid 13 through 38 Processing helix chain 'B' and resid 53 through 59 Processing helix chain 'B' and resid 266 through 278 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 308 through 311 No H-bonds generated for 'chain 'B' and resid 308 through 311' Processing helix chain 'B' and resid 313 through 317 Processing helix chain 'B' and resid 332 through 351 removed outlier: 3.683A pdb=" N ILE B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 390 Processing helix chain 'C' and resid 6 through 25 Processing helix chain 'C' and resid 30 through 35 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'D' and resid 10 through 23 Processing helix chain 'D' and resid 30 through 47 removed outlier: 4.806A pdb=" N LYS D 46 " --> pdb=" O GLU D 42 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N GLU D 47 " --> pdb=" O ALA D 43 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 169 through 172 removed outlier: 3.657A pdb=" N VAL A 179 " --> pdb=" O GLU A 170 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP A 172 " --> pdb=" O MET A 177 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET A 177 " --> pdb=" O ASP A 172 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 359 through 363 removed outlier: 7.416A pdb=" N VAL B 287 " --> pdb=" O TYR B 360 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N HIS B 362 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU B 289 " --> pdb=" O HIS B 362 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA B 243 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN B 218 " --> pdb=" O HIS B 41 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N LEU B 43 " --> pdb=" O ASN B 218 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N HIS B 220 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N LEU B 45 " --> pdb=" O HIS B 220 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N PHE B 222 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.919A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 100 through 105 removed outlier: 7.044A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.706A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 187 through 192 removed outlier: 7.112A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.737A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.271A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY C 306 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 47 through 52 removed outlier: 6.939A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE C 335 " --> pdb=" O SER C 331 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL C 327 " --> pdb=" O TRP C 339 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= K, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.056A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) 381 hydrogen bonds defined for protein. 1101 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: 2.22 Time building geometry restraints manager: 3.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1208 1.29 - 1.42: 2106 1.42 - 1.56: 4303 1.56 - 1.69: 3 1.69 - 1.83: 73 Bond restraints: 7693 Sorted by residual: bond pdb=" CA PHE A 201 " pdb=" C PHE A 201 " ideal model delta sigma weight residual 1.524 1.415 0.109 1.29e-02 6.01e+03 7.08e+01 bond pdb=" CA SER A 62 " pdb=" C SER A 62 " ideal model delta sigma weight residual 1.524 1.426 0.098 1.26e-02 6.30e+03 6.04e+01 bond pdb=" CA VAL A 179 " pdb=" C VAL A 179 " ideal model delta sigma weight residual 1.523 1.427 0.096 1.27e-02 6.20e+03 5.74e+01 bond pdb=" C PHE A 201 " pdb=" O PHE A 201 " ideal model delta sigma weight residual 1.237 1.156 0.080 1.19e-02 7.06e+03 4.57e+01 bond pdb=" N VAL A 179 " pdb=" CA VAL A 179 " ideal model delta sigma weight residual 1.459 1.377 0.082 1.25e-02 6.40e+03 4.26e+01 ... (remaining 7688 not shown) Histogram of bond angle deviations from ideal: 95.51 - 103.62: 84 103.62 - 111.74: 3681 111.74 - 119.85: 3034 119.85 - 127.97: 3623 127.97 - 136.08: 81 Bond angle restraints: 10503 Sorted by residual: angle pdb=" N ARG A 213 " pdb=" CA ARG A 213 " pdb=" C ARG A 213 " ideal model delta sigma weight residual 111.07 100.56 10.51 1.07e+00 8.73e-01 9.65e+01 angle pdb=" N ILE A 211 " pdb=" CA ILE A 211 " pdb=" C ILE A 211 " ideal model delta sigma weight residual 110.62 102.37 8.25 1.02e+00 9.61e-01 6.55e+01 angle pdb=" N ALA D 34 " pdb=" CA ALA D 34 " pdb=" C ALA D 34 " ideal model delta sigma weight residual 111.28 102.51 8.77 1.09e+00 8.42e-01 6.47e+01 angle pdb=" N TYR D 40 " pdb=" CA TYR D 40 " pdb=" C TYR D 40 " ideal model delta sigma weight residual 111.28 102.91 8.37 1.09e+00 8.42e-01 5.90e+01 angle pdb=" C PHE A 199 " pdb=" N PRO A 200 " pdb=" CA PRO A 200 " ideal model delta sigma weight residual 119.05 110.58 8.47 1.11e+00 8.12e-01 5.82e+01 ... (remaining 10498 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.19: 4320 24.19 - 48.38: 190 48.38 - 72.57: 13 72.57 - 96.76: 10 96.76 - 120.95: 1 Dihedral angle restraints: 4534 sinusoidal: 1614 harmonic: 2920 Sorted by residual: dihedral pdb=" CB CYS E 99 " pdb=" SG CYS E 99 " pdb=" SG CYS E 107 " pdb=" CB CYS E 107 " ideal model delta sinusoidal sigma weight residual -86.00 -2.52 -83.48 1 1.00e+01 1.00e-02 8.51e+01 dihedral pdb=" C ASN A 63 " pdb=" N ASN A 63 " pdb=" CA ASN A 63 " pdb=" CB ASN A 63 " ideal model delta harmonic sigma weight residual -122.60 -138.96 16.36 0 2.50e+00 1.60e-01 4.28e+01 dihedral pdb=" N ASN A 63 " pdb=" C ASN A 63 " pdb=" CA ASN A 63 " pdb=" CB ASN A 63 " ideal model delta harmonic sigma weight residual 122.80 139.06 -16.26 0 2.50e+00 1.60e-01 4.23e+01 ... (remaining 4531 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.163: 1181 0.163 - 0.327: 29 0.327 - 0.490: 7 0.490 - 0.653: 4 0.653 - 0.817: 2 Chirality restraints: 1223 Sorted by residual: chirality pdb=" CA ASN A 63 " pdb=" N ASN A 63 " pdb=" C ASN A 63 " pdb=" CB ASN A 63 " both_signs ideal model delta sigma weight residual False 2.51 1.69 0.82 2.00e-01 2.50e+01 1.67e+01 chirality pdb=" CA ALA A 219 " pdb=" N ALA A 219 " pdb=" C ALA A 219 " pdb=" CB ALA A 219 " both_signs ideal model delta sigma weight residual False 2.48 1.77 0.72 2.00e-01 2.50e+01 1.28e+01 chirality pdb=" CA PHE A 174 " pdb=" N PHE A 174 " pdb=" C PHE A 174 " pdb=" CB PHE A 174 " both_signs ideal model delta sigma weight residual False 2.51 1.86 0.65 2.00e-01 2.50e+01 1.06e+01 ... (remaining 1220 not shown) Planarity restraints: 1324 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 235 " 0.066 5.00e-02 4.00e+02 9.76e-02 1.53e+01 pdb=" N PRO C 236 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO C 236 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO C 236 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 213 " -0.018 2.00e-02 2.50e+03 3.44e-02 1.19e+01 pdb=" C ARG A 213 " 0.060 2.00e-02 2.50e+03 pdb=" O ARG A 213 " -0.022 2.00e-02 2.50e+03 pdb=" N VAL A 214 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 57 " 0.015 2.00e-02 2.50e+03 3.01e-02 9.07e+00 pdb=" C TYR A 57 " -0.052 2.00e-02 2.50e+03 pdb=" O TYR A 57 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU A 58 " 0.017 2.00e-02 2.50e+03 ... (remaining 1321 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 134 2.62 - 3.19: 6893 3.19 - 3.76: 12319 3.76 - 4.33: 16978 4.33 - 4.90: 28380 Nonbonded interactions: 64704 Sorted by model distance: nonbonded pdb=" CD2 LEU A 61 " pdb=" CB ALA A 144 " model vdw 2.049 3.880 nonbonded pdb=" OG SER C 74 " pdb=" OD1 ASP C 76 " model vdw 2.150 2.440 nonbonded pdb=" O ILE C 58 " pdb=" OG SER C 316 " model vdw 2.180 2.440 nonbonded pdb=" N VAL A 179 " pdb=" O VAL A 179 " model vdw 2.218 2.496 nonbonded pdb=" NH1 ARG B 228 " pdb=" OD1 ASP C 186 " model vdw 2.219 2.520 ... (remaining 64699 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.38 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: 0.250 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: 1.690 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 25.980 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 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 : 0.009 0.109 7693 Z= 0.568 Angle : 1.014 13.493 10503 Z= 0.632 Chirality : 0.081 0.817 1223 Planarity : 0.007 0.098 1324 Dihedral : 14.018 120.945 2639 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.40 % Allowed : 1.48 % Favored : 98.12 % Cbeta Deviations : 0.95 % 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: 0.62 (0.27), residues: 988 helix: 1.63 (0.26), residues: 402 sheet: 0.16 (0.35), residues: 204 loop : -0.73 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 99 HIS 0.007 0.002 HIS D 44 PHE 0.028 0.002 PHE A 65 TYR 0.025 0.002 TYR C 85 ARG 0.008 0.001 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 167 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 327 TRP cc_start: 0.8058 (OUTLIER) cc_final: 0.6682 (m-10) REVERT: B 34 LYS cc_start: 0.7829 (ttpt) cc_final: 0.7618 (tttt) REVERT: B 280 ARG cc_start: 0.8064 (tpt90) cc_final: 0.7821 (ttt90) REVERT: B 317 ARG cc_start: 0.7751 (ptp90) cc_final: 0.7476 (ptp90) REVERT: C 101 MET cc_start: 0.8895 (mtp) cc_final: 0.8644 (mtp) REVERT: C 290 ASP cc_start: 0.6802 (m-30) cc_final: 0.6572 (m-30) REVERT: E 60 TYR cc_start: 0.7386 (m-80) cc_final: 0.7036 (m-80) REVERT: E 80 TYR cc_start: 0.7486 (m-80) cc_final: 0.7066 (m-80) outliers start: 3 outliers final: 0 residues processed: 170 average time/residue: 0.1948 time to fit residues: 44.5264 Evaluate side-chains 150 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 149 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 40 optimal weight: 0.0670 chunk 25 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 88 optimal weight: 0.0970 overall best weight: 0.9920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 GLN ** C 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 ASN E 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7693 Z= 0.215 Angle : 0.593 10.311 10503 Z= 0.311 Chirality : 0.044 0.234 1223 Planarity : 0.005 0.074 1324 Dihedral : 5.739 57.144 1149 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.94 % Allowed : 10.23 % Favored : 88.83 % 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: 0.68 (0.27), residues: 988 helix: 1.82 (0.27), residues: 392 sheet: 0.00 (0.33), residues: 224 loop : -0.70 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 99 HIS 0.003 0.001 HIS B 357 PHE 0.017 0.002 PHE B 212 TYR 0.029 0.002 TYR C 85 ARG 0.006 0.000 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 154 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 280 MET cc_start: 0.7150 (mtp) cc_final: 0.6935 (mtm) REVERT: A 327 TRP cc_start: 0.7624 (OUTLIER) cc_final: 0.6931 (m-10) REVERT: B 266 LEU cc_start: 0.8432 (tp) cc_final: 0.8083 (tp) REVERT: B 274 LYS cc_start: 0.7512 (tttp) cc_final: 0.7274 (ttmt) REVERT: B 280 ARG cc_start: 0.8008 (tpt90) cc_final: 0.7698 (ttt90) REVERT: C 290 ASP cc_start: 0.6805 (m-30) cc_final: 0.6532 (m-30) REVERT: E 60 TYR cc_start: 0.7691 (m-80) cc_final: 0.7361 (m-80) REVERT: E 80 TYR cc_start: 0.7468 (m-80) cc_final: 0.6934 (m-80) REVERT: E 115 TYR cc_start: 0.7835 (t80) cc_final: 0.7543 (t80) outliers start: 7 outliers final: 3 residues processed: 158 average time/residue: 0.2017 time to fit residues: 42.3406 Evaluate side-chains 148 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 144 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 327 TRP Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain B residue 284 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 48 optimal weight: 9.9990 chunk 27 optimal weight: 0.9980 chunk 73 optimal weight: 0.0070 chunk 59 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 78 optimal weight: 0.5980 chunk 87 optimal weight: 0.0270 chunk 30 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 overall best weight: 1.1258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 ASN C 88 ASN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7693 Z= 0.221 Angle : 0.564 10.478 10503 Z= 0.297 Chirality : 0.043 0.165 1223 Planarity : 0.005 0.067 1324 Dihedral : 5.518 55.968 1149 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.88 % Allowed : 11.98 % Favored : 86.14 % 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: 0.83 (0.27), residues: 988 helix: 1.99 (0.27), residues: 391 sheet: 0.03 (0.33), residues: 226 loop : -0.62 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 82 HIS 0.005 0.001 HIS B 220 PHE 0.017 0.001 PHE B 212 TYR 0.024 0.002 TYR C 85 ARG 0.004 0.000 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 151 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 280 MET cc_start: 0.7128 (mtp) cc_final: 0.6897 (mtm) REVERT: A 327 TRP cc_start: 0.7677 (OUTLIER) cc_final: 0.6808 (m-10) REVERT: B 266 LEU cc_start: 0.8539 (tp) cc_final: 0.8238 (tp) REVERT: B 274 LYS cc_start: 0.7518 (tttp) cc_final: 0.7300 (ttmt) REVERT: B 280 ARG cc_start: 0.8029 (tpt90) cc_final: 0.7535 (tpt90) REVERT: C 111 TYR cc_start: 0.7983 (m-80) cc_final: 0.7759 (m-80) REVERT: C 290 ASP cc_start: 0.6862 (m-30) cc_final: 0.6571 (m-30) REVERT: E 3 GLN cc_start: 0.6035 (mp10) cc_final: 0.5569 (mp10) REVERT: E 50 ASP cc_start: 0.8500 (p0) cc_final: 0.7822 (p0) REVERT: E 80 TYR cc_start: 0.7445 (m-80) cc_final: 0.6892 (m-80) REVERT: E 115 TYR cc_start: 0.7793 (t80) cc_final: 0.7568 (t80) REVERT: D 38 MET cc_start: 0.6562 (mtm) cc_final: 0.6252 (mtp) outliers start: 14 outliers final: 8 residues processed: 161 average time/residue: 0.2022 time to fit residues: 43.7522 Evaluate side-chains 152 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 143 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 327 TRP Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 95 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 0.0970 chunk 66 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 42 optimal weight: 0.0980 chunk 59 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 ASN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7693 Z= 0.181 Angle : 0.543 10.869 10503 Z= 0.285 Chirality : 0.042 0.161 1223 Planarity : 0.004 0.067 1324 Dihedral : 5.366 55.590 1149 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.48 % Allowed : 13.46 % Favored : 85.06 % 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: 0.88 (0.27), residues: 988 helix: 2.08 (0.27), residues: 391 sheet: -0.04 (0.32), residues: 233 loop : -0.61 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 82 HIS 0.004 0.001 HIS B 220 PHE 0.015 0.001 PHE B 212 TYR 0.023 0.002 TYR C 85 ARG 0.003 0.000 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 155 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 280 MET cc_start: 0.7138 (mtp) cc_final: 0.6902 (mtm) REVERT: A 327 TRP cc_start: 0.7623 (OUTLIER) cc_final: 0.6867 (m-10) REVERT: A 338 MET cc_start: 0.7808 (mtp) cc_final: 0.7536 (mtp) REVERT: B 266 LEU cc_start: 0.8519 (tp) cc_final: 0.8221 (tp) REVERT: B 280 ARG cc_start: 0.8025 (tpt90) cc_final: 0.7616 (tpt90) REVERT: C 290 ASP cc_start: 0.6795 (m-30) cc_final: 0.6507 (m-30) REVERT: E 3 GLN cc_start: 0.6203 (mp10) cc_final: 0.5514 (mp10) REVERT: E 50 ASP cc_start: 0.8393 (OUTLIER) cc_final: 0.7724 (p0) REVERT: E 80 TYR cc_start: 0.7444 (m-80) cc_final: 0.6959 (m-80) REVERT: D 38 MET cc_start: 0.6657 (mtm) cc_final: 0.6346 (mtp) outliers start: 11 outliers final: 5 residues processed: 161 average time/residue: 0.1986 time to fit residues: 42.7948 Evaluate side-chains 149 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 142 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 327 TRP Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 95 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 69 optimal weight: 0.0570 chunk 38 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 ASN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7693 Z= 0.178 Angle : 0.538 10.991 10503 Z= 0.282 Chirality : 0.042 0.161 1223 Planarity : 0.004 0.067 1324 Dihedral : 5.238 55.174 1149 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.69 % Allowed : 14.00 % Favored : 83.31 % 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: 0.92 (0.27), residues: 988 helix: 2.16 (0.27), residues: 390 sheet: -0.08 (0.32), residues: 233 loop : -0.58 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 82 HIS 0.004 0.001 HIS B 220 PHE 0.013 0.001 PHE B 212 TYR 0.020 0.002 TYR C 85 ARG 0.004 0.000 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 148 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 327 TRP cc_start: 0.7631 (OUTLIER) cc_final: 0.6871 (m-10) REVERT: B 266 LEU cc_start: 0.8485 (tp) cc_final: 0.8187 (tp) REVERT: B 280 ARG cc_start: 0.8032 (tpt90) cc_final: 0.7640 (tpt90) REVERT: C 111 TYR cc_start: 0.7968 (m-80) cc_final: 0.7713 (m-80) REVERT: C 210 LEU cc_start: 0.7111 (tp) cc_final: 0.6884 (tp) REVERT: C 290 ASP cc_start: 0.6784 (m-30) cc_final: 0.6498 (m-30) REVERT: E 2 VAL cc_start: 0.7673 (OUTLIER) cc_final: 0.7414 (m) REVERT: E 3 GLN cc_start: 0.6208 (mp10) cc_final: 0.5387 (mp10) REVERT: E 50 ASP cc_start: 0.8425 (OUTLIER) cc_final: 0.7797 (p0) REVERT: E 80 TYR cc_start: 0.7421 (m-80) cc_final: 0.6954 (m-80) REVERT: D 38 MET cc_start: 0.6560 (mtm) cc_final: 0.6256 (mtp) outliers start: 20 outliers final: 12 residues processed: 163 average time/residue: 0.1973 time to fit residues: 43.6553 Evaluate side-chains 157 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 142 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 311 TRP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 327 TRP Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 95 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 31 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 chunk 23 optimal weight: 6.9990 chunk 93 optimal weight: 40.0000 chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN B 23 ASN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 GLN E 74 ASN E 84 ASN E 123 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7693 Z= 0.241 Angle : 0.561 11.600 10503 Z= 0.294 Chirality : 0.043 0.161 1223 Planarity : 0.004 0.067 1324 Dihedral : 5.326 55.016 1149 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.36 % Allowed : 15.61 % Favored : 81.02 % 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 (0.27), residues: 988 helix: 2.24 (0.27), residues: 382 sheet: -0.14 (0.31), residues: 238 loop : -0.54 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 82 HIS 0.005 0.001 HIS B 220 PHE 0.017 0.001 PHE E 108 TYR 0.027 0.002 TYR C 85 ARG 0.003 0.000 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 144 time to evaluate : 0.830 Fit side-chains revert: symmetry clash REVERT: A 306 GLU cc_start: 0.7189 (tt0) cc_final: 0.6906 (tt0) REVERT: A 327 TRP cc_start: 0.7631 (OUTLIER) cc_final: 0.6811 (m-10) REVERT: B 38 ARG cc_start: 0.7605 (ttp80) cc_final: 0.6950 (ttp80) REVERT: B 280 ARG cc_start: 0.8071 (tpt90) cc_final: 0.7597 (tpt90) REVERT: C 220 GLN cc_start: 0.6630 (mt0) cc_final: 0.6351 (mt0) REVERT: E 2 VAL cc_start: 0.7630 (OUTLIER) cc_final: 0.7336 (m) REVERT: E 3 GLN cc_start: 0.6299 (mp10) cc_final: 0.5310 (mp10) REVERT: E 50 ASP cc_start: 0.8460 (OUTLIER) cc_final: 0.7826 (p0) REVERT: E 80 TYR cc_start: 0.7437 (m-80) cc_final: 0.6955 (m-80) REVERT: E 98 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.6902 (mtm110) outliers start: 25 outliers final: 13 residues processed: 160 average time/residue: 0.2070 time to fit residues: 44.1203 Evaluate side-chains 162 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 145 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 311 TRP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 327 TRP Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 84 ASN Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 98 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 10 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 93 optimal weight: 30.0000 chunk 58 optimal weight: 0.3980 chunk 56 optimal weight: 0.3980 chunk 43 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 ASN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 GLN E 74 ASN E 84 ASN E 123 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7693 Z= 0.201 Angle : 0.554 11.537 10503 Z= 0.289 Chirality : 0.042 0.163 1223 Planarity : 0.004 0.068 1324 Dihedral : 5.251 54.790 1149 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.56 % Allowed : 17.36 % Favored : 80.08 % 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: 0.96 (0.27), residues: 988 helix: 2.27 (0.27), residues: 382 sheet: -0.15 (0.31), residues: 238 loop : -0.52 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 82 HIS 0.004 0.001 HIS B 220 PHE 0.013 0.001 PHE B 222 TYR 0.024 0.002 TYR C 85 ARG 0.003 0.000 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 144 time to evaluate : 0.846 Fit side-chains revert: symmetry clash REVERT: A 327 TRP cc_start: 0.7625 (OUTLIER) cc_final: 0.6800 (m-10) REVERT: B 23 ASN cc_start: 0.8081 (OUTLIER) cc_final: 0.7835 (t0) REVERT: B 38 ARG cc_start: 0.7566 (ttp80) cc_final: 0.6950 (ttp80) REVERT: B 266 LEU cc_start: 0.8413 (tp) cc_final: 0.8017 (tp) REVERT: B 280 ARG cc_start: 0.8068 (tpt90) cc_final: 0.7610 (tpt90) REVERT: E 50 ASP cc_start: 0.8450 (OUTLIER) cc_final: 0.7803 (p0) REVERT: E 80 TYR cc_start: 0.7427 (m-80) cc_final: 0.6955 (m-80) REVERT: E 98 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.6539 (mtm110) REVERT: E 115 TYR cc_start: 0.7828 (t80) cc_final: 0.7490 (t80) outliers start: 19 outliers final: 11 residues processed: 156 average time/residue: 0.2026 time to fit residues: 42.0954 Evaluate side-chains 154 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 139 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 311 TRP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 327 TRP Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 253 TYR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 98 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 55 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 chunk 18 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 73 optimal weight: 9.9990 chunk 85 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 chunk 81 optimal weight: 10.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 ASN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7693 Z= 0.193 Angle : 0.545 11.691 10503 Z= 0.286 Chirality : 0.042 0.164 1223 Planarity : 0.004 0.068 1324 Dihedral : 5.162 54.599 1149 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.56 % Allowed : 17.50 % Favored : 79.95 % 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 (0.27), residues: 988 helix: 2.29 (0.27), residues: 382 sheet: -0.11 (0.31), residues: 238 loop : -0.53 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 82 HIS 0.004 0.001 HIS B 220 PHE 0.013 0.001 PHE B 212 TYR 0.022 0.002 TYR C 85 ARG 0.003 0.000 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 138 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 327 TRP cc_start: 0.7609 (OUTLIER) cc_final: 0.6868 (m-10) REVERT: B 266 LEU cc_start: 0.8435 (tp) cc_final: 0.8074 (tp) REVERT: B 280 ARG cc_start: 0.8068 (tpt90) cc_final: 0.7615 (tpt90) REVERT: C 111 TYR cc_start: 0.8059 (m-80) cc_final: 0.7690 (m-80) REVERT: C 259 GLN cc_start: 0.5739 (pt0) cc_final: 0.5531 (pt0) REVERT: E 3 GLN cc_start: 0.6121 (mp10) cc_final: 0.5424 (mp10) REVERT: E 50 ASP cc_start: 0.8433 (OUTLIER) cc_final: 0.7792 (p0) REVERT: E 80 TYR cc_start: 0.7429 (m-80) cc_final: 0.6963 (m-80) REVERT: E 98 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.6577 (mtm110) REVERT: E 115 TYR cc_start: 0.7819 (t80) cc_final: 0.7473 (t80) outliers start: 19 outliers final: 12 residues processed: 151 average time/residue: 0.2004 time to fit residues: 40.8712 Evaluate side-chains 154 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 139 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 311 TRP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 327 TRP Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 253 TYR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 98 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 37 optimal weight: 0.4980 chunk 68 optimal weight: 0.0070 chunk 26 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 ASN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7693 Z= 0.173 Angle : 0.536 11.515 10503 Z= 0.281 Chirality : 0.042 0.165 1223 Planarity : 0.004 0.068 1324 Dihedral : 5.025 54.299 1149 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.15 % Allowed : 18.44 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.04 (0.27), residues: 988 helix: 2.25 (0.27), residues: 387 sheet: 0.11 (0.32), residues: 225 loop : -0.57 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 82 HIS 0.003 0.001 HIS B 220 PHE 0.012 0.001 PHE B 212 TYR 0.020 0.001 TYR C 85 ARG 0.003 0.000 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 149 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 TRP cc_start: 0.5822 (t-100) cc_final: 0.5232 (t-100) REVERT: A 327 TRP cc_start: 0.7594 (OUTLIER) cc_final: 0.6805 (m-10) REVERT: B 27 GLU cc_start: 0.8090 (tp30) cc_final: 0.7827 (mm-30) REVERT: B 266 LEU cc_start: 0.8487 (tp) cc_final: 0.8111 (tp) REVERT: B 280 ARG cc_start: 0.8089 (tpt90) cc_final: 0.7629 (tpt90) REVERT: C 111 TYR cc_start: 0.8046 (m-80) cc_final: 0.7718 (m-80) REVERT: E 3 GLN cc_start: 0.6106 (mp10) cc_final: 0.5368 (mp10) REVERT: E 50 ASP cc_start: 0.8376 (OUTLIER) cc_final: 0.7796 (p0) REVERT: E 80 TYR cc_start: 0.7513 (m-80) cc_final: 0.7126 (m-80) REVERT: E 98 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.6584 (mtm110) outliers start: 16 outliers final: 13 residues processed: 158 average time/residue: 0.1918 time to fit residues: 40.9819 Evaluate side-chains 161 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 145 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 327 TRP Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 253 TYR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 98 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 56 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 64 optimal weight: 9.9990 chunk 96 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 chunk 59 optimal weight: 0.0570 chunk 47 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 overall best weight: 0.9304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 ASN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 GLN ** E 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7693 Z= 0.196 Angle : 0.550 11.687 10503 Z= 0.288 Chirality : 0.042 0.164 1223 Planarity : 0.004 0.067 1324 Dihedral : 5.042 54.360 1149 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.42 % Allowed : 18.57 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.08 (0.27), residues: 988 helix: 2.24 (0.27), residues: 387 sheet: 0.16 (0.32), residues: 226 loop : -0.51 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 82 HIS 0.004 0.001 HIS B 220 PHE 0.012 0.001 PHE B 222 TYR 0.022 0.002 TYR C 85 ARG 0.003 0.000 ARG E 72 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 141 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 TRP cc_start: 0.5833 (t-100) cc_final: 0.5239 (t-100) REVERT: A 205 LEU cc_start: 0.7968 (tp) cc_final: 0.7467 (tp) REVERT: A 327 TRP cc_start: 0.7563 (OUTLIER) cc_final: 0.6802 (m-10) REVERT: B 266 LEU cc_start: 0.8508 (tp) cc_final: 0.8148 (tp) REVERT: B 280 ARG cc_start: 0.8108 (tpt90) cc_final: 0.7653 (tpt90) REVERT: C 111 TYR cc_start: 0.8107 (m-80) cc_final: 0.7727 (m-80) REVERT: E 3 GLN cc_start: 0.6053 (mp10) cc_final: 0.5283 (mp10) REVERT: E 50 ASP cc_start: 0.8392 (OUTLIER) cc_final: 0.7806 (p0) REVERT: E 80 TYR cc_start: 0.7521 (m-80) cc_final: 0.7179 (m-80) REVERT: E 98 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.6761 (mtm110) outliers start: 18 outliers final: 13 residues processed: 151 average time/residue: 0.1998 time to fit residues: 41.0345 Evaluate side-chains 155 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 139 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 327 TRP Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 98 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 23 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 21 optimal weight: 0.0870 chunk 77 optimal weight: 5.9990 chunk 32 optimal weight: 0.4980 chunk 79 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 14 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 ASN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 GLN ** E 74 ASN ** 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 = 0.4318 r_free = 0.4318 target = 0.195076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.163199 restraints weight = 22863.674| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 5.66 r_work: 0.3640 rms_B_bonded: 5.44 restraints_weight: 2.0000 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3783 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3783 r_free = 0.3783 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3783 r_free = 0.3783 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3783 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7693 Z= 0.175 Angle : 0.540 11.361 10503 Z= 0.284 Chirality : 0.042 0.164 1223 Planarity : 0.004 0.068 1324 Dihedral : 5.004 54.374 1149 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.29 % Allowed : 18.71 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.11 (0.27), residues: 988 helix: 2.29 (0.27), residues: 387 sheet: 0.20 (0.32), residues: 221 loop : -0.54 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 82 HIS 0.003 0.001 HIS B 220 PHE 0.012 0.001 PHE B 340 TYR 0.021 0.001 TYR C 85 ARG 0.003 0.000 ARG E 72 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1931.95 seconds wall clock time: 35 minutes 45.62 seconds (2145.62 seconds total)