Starting phenix.real_space_refine on Fri Mar 14 02:43:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rhb_19174/03_2025/8rhb_19174.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rhb_19174/03_2025/8rhb_19174.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rhb_19174/03_2025/8rhb_19174.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rhb_19174/03_2025/8rhb_19174.map" model { file = "/net/cci-nas-00/data/ceres_data/8rhb_19174/03_2025/8rhb_19174.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rhb_19174/03_2025/8rhb_19174.cif" } resolution = 3.0 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= 0.002 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: 6 Type Number sf(0) Gaussians P 8 5.49 5 Mg 2 5.21 5 S 64 5.16 5 C 5981 2.51 5 N 1625 2.21 5 O 1859 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9539 Number of models: 1 Model: "" Number of chains: 9 Chain: "B" Number of atoms: 3351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3351 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "K" Number of atoms: 2585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2585 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 8, 'TRANS': 321} Chain: "A" Number of atoms: 3358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3358 Classifications: {'peptide': 428} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Chain: "T" Number of atoms: 43 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 6, 43 Classifications: {'peptide': 6} Link IDs: {'PTRANS': 1, 'TRANS': 4} Chain: "t" Number of atoms: 47 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 6, 47 Classifications: {'peptide': 6} Link IDs: {'PTRANS': 2, 'TRANS': 3} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'TA1': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N AALA T 918 " occ=0.50 ... (3 atoms not shown) pdb=" CB AALA T 918 " occ=0.50 residue: pdb=" N AGLN T 919 " occ=0.50 ... (7 atoms not shown) pdb=" NE2AGLN T 919 " occ=0.50 residue: pdb=" N AILE T 920 " occ=0.50 ... (6 atoms not shown) pdb=" CD1AILE T 920 " occ=0.50 residue: pdb=" N AALA T 921 " occ=0.50 ... (3 atoms not shown) pdb=" CB AALA T 921 " occ=0.50 residue: pdb=" N ALYS T 922 " occ=0.50 ... (7 atoms not shown) pdb=" NZ ALYS T 922 " occ=0.50 residue: pdb=" N APRO T 923 " occ=0.50 ... (5 atoms not shown) pdb=" CD APRO T 923 " occ=0.50 residue: pdb=" N BALA t 921 " occ=0.50 ... (3 atoms not shown) pdb=" CB BALA t 921 " occ=0.50 residue: pdb=" N BLYS t 922 " occ=0.50 ... (7 atoms not shown) pdb=" NZ BLYS t 922 " occ=0.50 residue: pdb=" N BPRO t 923 " occ=0.50 ... (5 atoms not shown) pdb=" CD BPRO t 923 " occ=0.50 residue: pdb=" N BILE t 936 " occ=0.50 ... (6 atoms not shown) pdb=" CD1BILE t 936 " occ=0.50 residue: pdb=" N BARG t 937 " occ=0.50 ... (9 atoms not shown) pdb=" NH2BARG t 937 " occ=0.50 residue: pdb=" N BPRO t 938 " occ=0.50 ... (5 atoms not shown) pdb=" CD BPRO t 938 " occ=0.50 Time building chain proxies: 6.40, per 1000 atoms: 0.67 Number of scatterers: 9539 At special positions: 0 Unit cell: (73.644, 106.134, 111.549, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 64 16.00 P 8 15.00 Mg 2 11.99 O 1859 8.00 N 1625 7.00 C 5981 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.33 Conformation dependent library (CDL) restraints added in 1.3 seconds 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2226 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 9 sheets defined 47.2% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'B' and resid 10 through 29 removed outlier: 3.961A pdb=" N LYS B 19 " --> pdb=" O GLN B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 48 removed outlier: 4.432A pdb=" N LEU B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG B 48 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 81 Processing helix chain 'B' and resid 102 through 108 Processing helix chain 'B' and resid 111 through 128 removed outlier: 4.120A pdb=" N ASP B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N SER B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 161 Processing helix chain 'B' and resid 182 through 198 removed outlier: 3.945A pdb=" N GLN B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLU B 196 " --> pdb=" O HIS B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 216 Processing helix chain 'B' and resid 223 through 239 removed outlier: 3.905A pdb=" N THR B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 260 Processing helix chain 'B' and resid 287 through 296 Processing helix chain 'B' and resid 324 through 339 Processing helix chain 'B' and resid 384 through 401 removed outlier: 3.552A pdb=" N PHE B 388 " --> pdb=" O ILE B 384 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ARG B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 Processing helix chain 'B' and resid 414 through 435 removed outlier: 3.531A pdb=" N PHE B 418 " --> pdb=" O ASP B 414 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 24 Processing helix chain 'K' and resid 57 through 66 Processing helix chain 'K' and resid 66 through 76 removed outlier: 3.630A pdb=" N LYS K 71 " --> pdb=" O LYS K 67 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 96 Processing helix chain 'K' and resid 106 through 122 removed outlier: 3.575A pdb=" N ARG K 110 " --> pdb=" O GLY K 106 " (cutoff:3.500A) Processing helix chain 'K' and resid 175 through 189 removed outlier: 3.611A pdb=" N VAL K 179 " --> pdb=" O SER K 175 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN K 189 " --> pdb=" O GLU K 185 " (cutoff:3.500A) Processing helix chain 'K' and resid 237 through 242 Processing helix chain 'K' and resid 245 through 271 Processing helix chain 'K' and resid 276 through 279 removed outlier: 4.011A pdb=" N ASP K 279 " --> pdb=" O PRO K 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 276 through 279' Processing helix chain 'K' and resid 280 through 286 Processing helix chain 'K' and resid 286 through 292 Processing helix chain 'K' and resid 305 through 307 No H-bonds generated for 'chain 'K' and resid 305 through 307' Processing helix chain 'K' and resid 308 through 324 removed outlier: 4.085A pdb=" N THR K 324 " --> pdb=" O GLN K 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 28 Processing helix chain 'A' and resid 71 through 81 removed outlier: 4.553A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 114 through 128 removed outlier: 3.545A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 161 removed outlier: 5.160A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N SER A 151 " --> pdb=" O SER A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 194 Processing helix chain 'A' and resid 205 through 216 Processing helix chain 'A' and resid 223 through 244 removed outlier: 4.756A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG A 243 " --> pdb=" O THR A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 278 through 282 removed outlier: 3.795A pdb=" N TYR A 282 " --> pdb=" O GLU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.616A pdb=" N GLN A 301 " --> pdb=" O PRO A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 Processing helix chain 'A' and resid 384 through 401 removed outlier: 4.073A pdb=" N LYS A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.849A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 437 removed outlier: 4.243A pdb=" N PHE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 93 through 94 removed outlier: 7.889A pdb=" N VAL B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU B 67 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ILE B 66 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N HIS B 6 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N VAL B 68 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N GLN B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N GLU B 3 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N SER B 140 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N GLN B 133 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ASN B 167 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N PHE B 135 " --> pdb=" O ASN B 167 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N PHE B 169 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU B 137 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N VAL B 171 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N HIS B 139 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N MET B 166 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N TYR B 202 " --> pdb=" O MET B 166 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR B 168 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ILE B 204 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N SER B 170 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N PHE B 267 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N SER B 381 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA B 273 " --> pdb=" O ALA B 375 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N SER B 374 " --> pdb=" O PHE B 319 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N PHE B 319 " --> pdb=" O SER B 374 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N THR B 376 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ALA B 317 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE B 378 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N VAL B 315 " --> pdb=" O ILE B 378 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ASN B 380 " --> pdb=" O LEU B 313 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 6 through 8 Processing sheet with id=AA3, first strand: chain 'K' and resid 10 through 15 removed outlier: 7.476A pdb=" N VAL K 11 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N PHE K 52 " --> pdb=" O VAL K 11 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N CYS K 13 " --> pdb=" O PHE K 52 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 50 through 52 current: chain 'K' and resid 142 through 144 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 142 through 144 current: chain 'K' and resid 222 through 223 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'K' and resid 32 through 34 removed outlier: 3.608A pdb=" N GLN K 34 " --> pdb=" O THR K 38 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR K 38 " --> pdb=" O GLN K 34 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'K' and resid 154 through 157 removed outlier: 4.505A pdb=" N SER K 154 " --> pdb=" O LYS K 166 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 192 through 193 Processing sheet with id=AA7, first strand: chain 'A' and resid 93 through 94 removed outlier: 7.867A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N GLU A 3 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N LEU A 136 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE A 5 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N PHE A 138 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ILE A 7 " --> pdb=" O PHE A 138 " (cutoff:3.500A) removed outlier: 9.779A pdb=" N SER A 165 " --> pdb=" O GLY A 131 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N GLN A 133 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N LEU A 167 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA9, first strand: chain 'A' and resid 269 through 273 removed outlier: 6.809A pdb=" N ALA A 374 " --> pdb=" O TYR A 319 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N TYR A 319 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N CYS A 376 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N LEU A 317 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU A 378 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N CYS A 315 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ASN A 380 " --> pdb=" O MET A 313 " (cutoff:3.500A) 402 hydrogen bonds defined for protein. 1182 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: 3.49 Time building geometry restraints manager: 3.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1695 1.32 - 1.44: 2514 1.44 - 1.57: 5417 1.57 - 1.69: 16 1.69 - 1.81: 99 Bond restraints: 9741 Sorted by residual: bond pdb=" O3A ANP K1001 " pdb=" PB ANP K1001 " ideal model delta sigma weight residual 1.700 1.525 0.175 2.00e-02 2.50e+03 7.62e+01 bond pdb=" N3B ANP K1001 " pdb=" PG ANP K1001 " ideal model delta sigma weight residual 1.795 1.668 0.127 2.00e-02 2.50e+03 4.05e+01 bond pdb=" O5' ANP K1001 " pdb=" PA ANP K1001 " ideal model delta sigma weight residual 1.655 1.538 0.117 2.00e-02 2.50e+03 3.41e+01 bond pdb=" O3A ANP K1001 " pdb=" PA ANP K1001 " ideal model delta sigma weight residual 1.613 1.515 0.098 2.00e-02 2.50e+03 2.39e+01 bond pdb=" C5' ANP K1001 " pdb=" O5' ANP K1001 " ideal model delta sigma weight residual 1.409 1.329 0.080 2.00e-02 2.50e+03 1.58e+01 ... (remaining 9736 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.35: 13183 4.35 - 8.69: 30 8.69 - 13.04: 6 13.04 - 17.38: 1 17.38 - 21.73: 1 Bond angle restraints: 13221 Sorted by residual: angle pdb=" C5' ANP K1001 " pdb=" O5' ANP K1001 " pdb=" PA ANP K1001 " ideal model delta sigma weight residual 120.74 99.01 21.73 3.00e+00 1.11e-01 5.25e+01 angle pdb=" C3' ANP K1001 " pdb=" C4' ANP K1001 " pdb=" C5' ANP K1001 " ideal model delta sigma weight residual 116.03 99.88 16.15 3.00e+00 1.11e-01 2.90e+01 angle pdb=" PB ANP K1001 " pdb=" N3B ANP K1001 " pdb=" PG ANP K1001 " ideal model delta sigma weight residual 126.95 114.44 12.51 3.00e+00 1.11e-01 1.74e+01 angle pdb=" C10 TA1 B 502 " pdb=" C18 TA1 B 502 " pdb=" C20 TA1 B 502 " ideal model delta sigma weight residual 104.78 116.29 -11.51 3.00e+00 1.11e-01 1.47e+01 angle pdb=" N VAL A 182 " pdb=" CA VAL A 182 " pdb=" C VAL A 182 " ideal model delta sigma weight residual 111.91 108.81 3.10 8.90e-01 1.26e+00 1.21e+01 ... (remaining 13216 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.05: 5756 34.05 - 68.09: 146 68.09 - 102.14: 6 102.14 - 136.19: 16 136.19 - 170.23: 6 Dihedral angle restraints: 5930 sinusoidal: 2466 harmonic: 3464 Sorted by residual: dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -120.50 -170.23 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -52.39 156.99 1 2.00e+01 2.50e-03 4.61e+01 dihedral pdb=" O5' GTP A 501 " pdb=" O3A GTP A 501 " pdb=" PA GTP A 501 " pdb=" PB GTP A 501 " ideal model delta sinusoidal sigma weight residual 274.12 135.11 139.01 1 2.00e+01 2.50e-03 4.21e+01 ... (remaining 5927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1267 0.066 - 0.131: 182 0.131 - 0.197: 6 0.197 - 0.262: 1 0.262 - 0.328: 2 Chirality restraints: 1458 Sorted by residual: chirality pdb=" C3' ANP K1001 " pdb=" C2' ANP K1001 " pdb=" C4' ANP K1001 " pdb=" O3' ANP K1001 " both_signs ideal model delta sigma weight residual False -2.36 -2.03 -0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" C4' ANP K1001 " pdb=" C3' ANP K1001 " pdb=" C5' ANP K1001 " pdb=" O4' ANP K1001 " both_signs ideal model delta sigma weight residual False -2.45 -2.77 0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" C2' ANP K1001 " pdb=" C1' ANP K1001 " pdb=" C3' ANP K1001 " pdb=" O2' ANP K1001 " both_signs ideal model delta sigma weight residual False -2.72 -2.51 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 1455 not shown) Planarity restraints: 1708 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ANP K1001 " 0.042 2.00e-02 2.50e+03 2.08e-02 1.19e+01 pdb=" C2 ANP K1001 " -0.003 2.00e-02 2.50e+03 pdb=" C4 ANP K1001 " -0.000 2.00e-02 2.50e+03 pdb=" C5 ANP K1001 " 0.001 2.00e-02 2.50e+03 pdb=" C6 ANP K1001 " 0.002 2.00e-02 2.50e+03 pdb=" C8 ANP K1001 " 0.001 2.00e-02 2.50e+03 pdb=" N1 ANP K1001 " 0.002 2.00e-02 2.50e+03 pdb=" N3 ANP K1001 " -0.005 2.00e-02 2.50e+03 pdb=" N6 ANP K1001 " 0.011 2.00e-02 2.50e+03 pdb=" N7 ANP K1001 " 0.002 2.00e-02 2.50e+03 pdb=" N9 ANP K1001 " -0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 324 " 0.026 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO A 325 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 325 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 325 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 88 " 0.025 5.00e-02 4.00e+02 3.72e-02 2.21e+00 pdb=" N PRO A 89 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 89 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 89 " 0.021 5.00e-02 4.00e+02 ... (remaining 1705 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 41 2.43 - 3.05: 6111 3.05 - 3.67: 14367 3.67 - 4.28: 21574 4.28 - 4.90: 36409 Nonbonded interactions: 78502 Sorted by model distance: nonbonded pdb=" O3G GTP A 501 " pdb="MG MG A 502 " model vdw 1.818 2.170 nonbonded pdb=" OG SER K 202 " pdb="MG MG K1002 " model vdw 1.981 2.170 nonbonded pdb=" OG1 THR K 92 " pdb="MG MG K1002 " model vdw 2.167 2.170 nonbonded pdb=" CD GLU A 71 " pdb="MG MG A 502 " model vdw 2.192 2.400 nonbonded pdb=" OG SER A 165 " pdb=" OE1 GLN A 256 " model vdw 2.209 3.040 ... (remaining 78497 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.50 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: 62.920 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.590 Find NCS groups from input model: 0.130 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:56.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 146.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3126 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 : 0.005 0.175 9741 Z= 0.322 Angle : 0.669 21.728 13221 Z= 0.308 Chirality : 0.046 0.328 1458 Planarity : 0.003 0.039 1708 Dihedral : 17.120 170.233 3704 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.00 % Allowed : 10.65 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 0.48 (0.24), residues: 1184 helix: 2.05 (0.24), residues: 468 sheet: -0.39 (0.38), residues: 202 loop : -1.02 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 346 HIS 0.003 0.001 HIS K 129 PHE 0.017 0.001 PHE K 82 TYR 0.011 0.001 TYR B 161 ARG 0.001 0.000 ARG K 25 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 393 GLU cc_start: 0.7090 (tm-30) cc_final: 0.6696 (tm-30) outliers start: 0 outliers final: 2 residues processed: 275 average time/residue: 1.1853 time to fit residues: 349.3503 Evaluate side-chains 147 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 145 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 244 GLU Chi-restraints excluded: chain A residue 127 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.1980 chunk 88 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 30 optimal weight: 9.9990 chunk 59 optimal weight: 8.9990 chunk 47 optimal weight: 7.9990 chunk 91 optimal weight: 0.0870 chunk 35 optimal weight: 0.0170 chunk 55 optimal weight: 5.9990 chunk 68 optimal weight: 0.4980 chunk 106 optimal weight: 4.9990 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 28 HIS B 206 ASN ** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 ASN K 93 HIS K 129 HIS K 211 ASN ** K 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 327 ASN ** A 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 GLN ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.102813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.088468 restraints weight = 18840.475| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 3.40 r_work: 0.3172 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3179 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3178 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4086 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 : 0.003 0.051 9741 Z= 0.224 Angle : 0.738 15.438 13221 Z= 0.357 Chirality : 0.046 0.235 1458 Planarity : 0.005 0.083 1708 Dihedral : 15.792 174.711 1465 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.07 % Allowed : 18.78 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 0.16 (0.24), residues: 1184 helix: 1.40 (0.24), residues: 480 sheet: -0.24 (0.37), residues: 212 loop : -1.00 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP B 21 HIS 0.026 0.002 HIS B 28 PHE 0.013 0.001 PHE B 377 TYR 0.024 0.002 TYR A 103 ARG 0.015 0.001 ARG B 278 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 157 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 393 GLU cc_start: 0.7582 (tm-30) cc_final: 0.7046 (tm-30) REVERT: K 59 GLU cc_start: 0.7256 (pm20) cc_final: 0.6682 (tp30) REVERT: A 80 THR cc_start: 0.7013 (OUTLIER) cc_final: 0.6640 (p) REVERT: A 431 ASP cc_start: 0.6638 (t0) cc_final: 0.6279 (t70) outliers start: 42 outliers final: 8 residues processed: 187 average time/residue: 0.9951 time to fit residues: 202.6992 Evaluate side-chains 138 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 129 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 248 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 18 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 116 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 111 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 ASN B 293 GLN ** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 ASN ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 GLN ** K 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 18 ASN A 101 ASN A 176 GLN ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.107209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.093140 restraints weight = 19005.724| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 3.46 r_work: 0.3247 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3249 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3249 r_free = 0.3249 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3249 r_free = 0.3249 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3249 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4953 moved from start: 0.5950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9741 Z= 0.264 Angle : 0.776 11.417 13221 Z= 0.388 Chirality : 0.048 0.268 1458 Planarity : 0.006 0.063 1708 Dihedral : 12.341 178.941 1460 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.45 % Allowed : 17.91 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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 (0.24), residues: 1184 helix: 0.71 (0.22), residues: 485 sheet: 0.03 (0.38), residues: 201 loop : -1.00 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 21 HIS 0.020 0.002 HIS B 28 PHE 0.023 0.002 PHE B 377 TYR 0.028 0.002 TYR B 342 ARG 0.012 0.001 ARG B 264 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 177 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 52 TYR cc_start: 0.6001 (m-80) cc_final: 0.5385 (m-80) REVERT: B 185 TYR cc_start: 0.5134 (m-80) cc_final: 0.4845 (m-80) REVERT: B 269 MET cc_start: 0.5680 (OUTLIER) cc_final: 0.4928 (tmt) REVERT: B 306 ASP cc_start: 0.7097 (t0) cc_final: 0.6887 (p0) REVERT: B 393 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7440 (tm-30) REVERT: B 431 GLU cc_start: 0.6182 (tm-30) cc_final: 0.5642 (tt0) REVERT: K 8 ASN cc_start: 0.7565 (p0) cc_final: 0.7058 (p0) REVERT: K 25 ARG cc_start: 0.5771 (OUTLIER) cc_final: 0.5565 (mtm-85) REVERT: K 130 ILE cc_start: 0.0463 (OUTLIER) cc_final: 0.0230 (pp) REVERT: A 176 GLN cc_start: 0.7618 (mm110) cc_final: 0.7178 (mm-40) outliers start: 46 outliers final: 13 residues processed: 207 average time/residue: 1.0464 time to fit residues: 234.9412 Evaluate side-chains 172 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 156 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 139 HIS Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain K residue 25 ARG Chi-restraints excluded: chain K residue 130 ILE Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 296 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 32 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 43 optimal weight: 8.9990 chunk 69 optimal weight: 0.0050 chunk 87 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 85 optimal weight: 20.0000 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 HIS B 294 GLN K 117 ASN K 129 HIS ** K 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.112157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.097033 restraints weight = 18714.881| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 3.45 r_work: 0.3324 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3329 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3329 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5630 moved from start: 0.8065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 9741 Z= 0.281 Angle : 0.771 10.769 13221 Z= 0.388 Chirality : 0.047 0.275 1458 Planarity : 0.006 0.086 1708 Dihedral : 12.156 167.307 1460 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.65 % Allowed : 19.26 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.03 (0.24), residues: 1184 helix: 0.98 (0.23), residues: 478 sheet: 0.03 (0.38), residues: 203 loop : -0.97 (0.26), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 21 HIS 0.017 0.002 HIS B 139 PHE 0.027 0.002 PHE K 128 TYR 0.017 0.002 TYR A 408 ARG 0.007 0.001 ARG B 369 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 216 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 108 TYR cc_start: 0.7719 (t80) cc_final: 0.7126 (t80) REVERT: B 218 LYS cc_start: 0.8560 (mmmm) cc_final: 0.8303 (mmmm) REVERT: B 269 MET cc_start: 0.6662 (OUTLIER) cc_final: 0.6092 (tmt) REVERT: B 393 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7632 (tm-30) REVERT: B 400 ARG cc_start: 0.6973 (mtm-85) cc_final: 0.6653 (tmt170) REVERT: K 22 GLU cc_start: 0.6546 (mp0) cc_final: 0.6264 (mp0) REVERT: K 95 MET cc_start: 0.7489 (tmm) cc_final: 0.7190 (tpp) REVERT: K 180 MET cc_start: 0.6541 (OUTLIER) cc_final: 0.5520 (tpt) REVERT: A 176 GLN cc_start: 0.7933 (mm110) cc_final: 0.7414 (mm-40) REVERT: A 230 LEU cc_start: 0.8328 (mm) cc_final: 0.8076 (mm) REVERT: A 280 LYS cc_start: 0.5136 (mtmm) cc_final: 0.4867 (tptt) REVERT: A 377 MET cc_start: 0.3392 (ptm) cc_final: 0.2835 (pmm) outliers start: 48 outliers final: 17 residues processed: 243 average time/residue: 1.1216 time to fit residues: 297.4645 Evaluate side-chains 187 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 PHE Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain K residue 180 MET Chi-restraints excluded: chain K residue 250 GLU Chi-restraints excluded: chain A residue 21 TRP Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 296 PHE Chi-restraints excluded: chain A residue 355 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 80 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 4 optimal weight: 0.0570 chunk 88 optimal weight: 10.0000 chunk 104 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 overall best weight: 1.9502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 93 HIS K 117 ASN ** K 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 216 ASN K 221 GLN K 308 ASN ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.118167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.103331 restraints weight = 19844.088| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 3.66 r_work: 0.3409 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3413 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3413 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6858 moved from start: 1.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 9741 Z= 0.363 Angle : 0.953 13.557 13221 Z= 0.489 Chirality : 0.052 0.190 1458 Planarity : 0.007 0.135 1708 Dihedral : 11.807 134.609 1460 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.32 % Favored : 95.59 % Rotamer: Outliers : 6.00 % Allowed : 22.17 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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 (0.23), residues: 1184 helix: 0.33 (0.22), residues: 484 sheet: -0.39 (0.37), residues: 184 loop : -1.13 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.005 TRP A 21 HIS 0.012 0.002 HIS K 129 PHE 0.028 0.003 PHE A 67 TYR 0.042 0.003 TYR A 408 ARG 0.007 0.001 ARG B 278 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 271 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 ASN cc_start: 0.8495 (t0) cc_final: 0.8157 (t0) REVERT: B 123 ARG cc_start: 0.8130 (ptm-80) cc_final: 0.7231 (ptp90) REVERT: B 166 MET cc_start: 0.4680 (OUTLIER) cc_final: 0.4419 (tpt) REVERT: B 218 LYS cc_start: 0.8632 (mmmm) cc_final: 0.8407 (mmmm) REVERT: B 230 LEU cc_start: 0.9155 (mt) cc_final: 0.8943 (mt) REVERT: B 377 PHE cc_start: 0.7712 (t80) cc_final: 0.7052 (t80) REVERT: B 393 GLU cc_start: 0.8376 (tm-30) cc_final: 0.7912 (tm-30) REVERT: B 400 ARG cc_start: 0.8012 (mtm-85) cc_final: 0.7213 (tmt170) REVERT: B 422 GLU cc_start: 0.6990 (tm-30) cc_final: 0.6651 (tp30) REVERT: B 433 GLN cc_start: 0.8128 (mm-40) cc_final: 0.7459 (tp-100) REVERT: K 15 PHE cc_start: 0.7662 (m-80) cc_final: 0.7328 (m-80) REVERT: K 119 ILE cc_start: 0.6722 (OUTLIER) cc_final: 0.6431 (tt) REVERT: K 178 GLU cc_start: 0.8769 (mm-30) cc_final: 0.7449 (mp0) REVERT: K 180 MET cc_start: 0.6906 (pp-130) cc_final: 0.6280 (tpt) REVERT: A 97 GLU cc_start: 0.8835 (mp0) cc_final: 0.8464 (mp0) REVERT: A 112 LYS cc_start: 0.8337 (tptp) cc_final: 0.7663 (mtmt) REVERT: A 176 GLN cc_start: 0.8656 (mm110) cc_final: 0.8136 (mm-40) REVERT: A 377 MET cc_start: 0.5629 (ptm) cc_final: 0.5092 (pmm) REVERT: A 393 HIS cc_start: 0.7972 (t70) cc_final: 0.7747 (t-90) outliers start: 62 outliers final: 21 residues processed: 307 average time/residue: 0.9656 time to fit residues: 322.8452 Evaluate side-chains 228 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 205 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 119 ILE Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 238 VAL Chi-restraints excluded: chain K residue 297 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 376 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 85 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 63 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 90 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 HIS ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 ASN B 349 ASN B 350 ASN K 125 ASN K 129 HIS ** K 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.115887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.100600 restraints weight = 19365.389| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 3.65 r_work: 0.3373 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3376 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3375 r_free = 0.3375 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3375 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 1.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9741 Z= 0.271 Angle : 0.810 12.698 13221 Z= 0.401 Chirality : 0.048 0.207 1458 Planarity : 0.005 0.071 1708 Dihedral : 11.360 140.500 1460 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.07 % Allowed : 28.94 % Favored : 66.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.42 (0.23), residues: 1184 helix: 0.54 (0.22), residues: 493 sheet: -0.06 (0.39), residues: 185 loop : -1.13 (0.25), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 21 HIS 0.008 0.001 HIS B 28 PHE 0.028 0.002 PHE A 404 TYR 0.012 0.002 TYR B 342 ARG 0.009 0.001 ARG K 295 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 217 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 ASN cc_start: 0.8585 (t0) cc_final: 0.8193 (t160) REVERT: B 123 ARG cc_start: 0.8233 (ptm-80) cc_final: 0.7760 (ptp90) REVERT: B 166 MET cc_start: 0.5911 (OUTLIER) cc_final: 0.5557 (mmt) REVERT: B 218 LYS cc_start: 0.8762 (mmmm) cc_final: 0.8539 (mmmm) REVERT: B 235 MET cc_start: 0.7181 (tmm) cc_final: 0.6534 (ttm) REVERT: B 259 MET cc_start: 0.7944 (mmt) cc_final: 0.7625 (mmt) REVERT: B 325 MET cc_start: 0.7117 (mmm) cc_final: 0.6853 (mpp) REVERT: B 393 GLU cc_start: 0.8338 (tm-30) cc_final: 0.7912 (tm-30) REVERT: B 400 ARG cc_start: 0.8216 (mtm-85) cc_final: 0.7450 (tmt170) REVERT: B 422 GLU cc_start: 0.7205 (tm-30) cc_final: 0.6759 (tp30) REVERT: K 53 GLN cc_start: 0.7525 (pp30) cc_final: 0.7270 (tm130) REVERT: K 171 ARG cc_start: 0.7013 (OUTLIER) cc_final: 0.6382 (ttp-170) REVERT: K 180 MET cc_start: 0.7392 (pp-130) cc_final: 0.6871 (tpt) REVERT: K 277 TYR cc_start: 0.8184 (m-80) cc_final: 0.7795 (m-80) REVERT: A 112 LYS cc_start: 0.8685 (tptp) cc_final: 0.8174 (ttpt) REVERT: A 176 GLN cc_start: 0.8555 (mm110) cc_final: 0.8133 (mm110) REVERT: A 234 ILE cc_start: 0.8073 (mt) cc_final: 0.7756 (mt) REVERT: A 377 MET cc_start: 0.5913 (ptm) cc_final: 0.5156 (pmm) outliers start: 42 outliers final: 16 residues processed: 245 average time/residue: 1.0026 time to fit residues: 266.6465 Evaluate side-chains 203 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 185 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 224 TYR Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 171 ARG Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 355 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 24 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 80 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 106 optimal weight: 9.9990 chunk 56 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 ASN K 117 ASN K 129 HIS ** K 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 11 GLN A 101 ASN ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.111486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.095459 restraints weight = 22185.002| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 4.00 r_work: 0.3293 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3300 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3300 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 1.6169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 9741 Z= 0.281 Angle : 0.860 10.836 13221 Z= 0.425 Chirality : 0.049 0.268 1458 Planarity : 0.006 0.060 1708 Dihedral : 10.715 136.420 1460 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.56 % Favored : 96.36 % Rotamer: Outliers : 3.58 % Allowed : 30.78 % Favored : 65.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.66 (0.23), residues: 1184 helix: 0.22 (0.22), residues: 513 sheet: -0.48 (0.36), residues: 195 loop : -1.04 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 21 HIS 0.007 0.002 HIS B 28 PHE 0.021 0.002 PHE K 82 TYR 0.023 0.002 TYR B 185 ARG 0.012 0.001 ARG B 243 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 241 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 ASN cc_start: 0.8849 (t0) cc_final: 0.8434 (t160) REVERT: B 75 MET cc_start: 0.8120 (ppp) cc_final: 0.7848 (ttm) REVERT: B 83 PHE cc_start: 0.8188 (m-80) cc_final: 0.7726 (t80) REVERT: B 123 ARG cc_start: 0.8434 (ptm-80) cc_final: 0.8100 (ptp-110) REVERT: B 124 LYS cc_start: 0.9042 (tppp) cc_final: 0.8623 (tppp) REVERT: B 218 LYS cc_start: 0.8856 (mmmm) cc_final: 0.8617 (mmmm) REVERT: B 325 MET cc_start: 0.7360 (mmm) cc_final: 0.6825 (mpp) REVERT: B 326 LYS cc_start: 0.7966 (tptp) cc_final: 0.7763 (tppp) REVERT: B 330 GLU cc_start: 0.7937 (pt0) cc_final: 0.7609 (pp20) REVERT: B 342 TYR cc_start: 0.7806 (OUTLIER) cc_final: 0.7497 (t80) REVERT: B 393 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8056 (tm-30) REVERT: B 422 GLU cc_start: 0.7688 (tm-30) cc_final: 0.7096 (tp30) REVERT: K 53 GLN cc_start: 0.7600 (pp30) cc_final: 0.7318 (tm130) REVERT: K 168 CYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8129 (p) REVERT: K 178 GLU cc_start: 0.9153 (mm-30) cc_final: 0.8403 (mt-10) REVERT: A 15 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.8127 (mp10) REVERT: A 69 ASP cc_start: 0.7884 (t0) cc_final: 0.7521 (t0) REVERT: A 98 ASP cc_start: 0.8778 (p0) cc_final: 0.8344 (p0) REVERT: A 112 LYS cc_start: 0.8965 (tptp) cc_final: 0.8478 (mtpm) REVERT: A 176 GLN cc_start: 0.8860 (mm110) cc_final: 0.8544 (mm110) REVERT: A 211 ASP cc_start: 0.8414 (m-30) cc_final: 0.8058 (m-30) REVERT: A 269 LEU cc_start: 0.7729 (pt) cc_final: 0.7499 (pp) REVERT: A 293 ASN cc_start: 0.8078 (m-40) cc_final: 0.7707 (m-40) REVERT: A 297 GLU cc_start: 0.7657 (mm-30) cc_final: 0.6985 (mm-30) REVERT: A 377 MET cc_start: 0.6685 (ptm) cc_final: 0.6440 (ptp) outliers start: 37 outliers final: 16 residues processed: 266 average time/residue: 1.2483 time to fit residues: 361.0181 Evaluate side-chains 232 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 213 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 168 CYS Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 390 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 74 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 12 optimal weight: 0.0770 chunk 40 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 111 optimal weight: 8.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 167 ASN B 350 ASN B 394 GLN K 129 HIS ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.111248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.095624 restraints weight = 21517.821| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 3.81 r_work: 0.3294 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3302 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3302 r_free = 0.3302 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3302 r_free = 0.3302 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3302 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 1.6510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9741 Z= 0.227 Angle : 0.808 12.846 13221 Z= 0.395 Chirality : 0.048 0.175 1458 Planarity : 0.005 0.041 1708 Dihedral : 10.518 140.012 1460 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.39 % Allowed : 33.79 % Favored : 62.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.38 (0.23), residues: 1184 helix: 0.49 (0.22), residues: 506 sheet: -0.21 (0.37), residues: 192 loop : -0.97 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 21 HIS 0.014 0.001 HIS B 229 PHE 0.021 0.002 PHE B 214 TYR 0.033 0.002 TYR B 224 ARG 0.010 0.001 ARG B 215 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 226 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 ASN cc_start: 0.8757 (t0) cc_final: 0.8268 (t160) REVERT: B 75 MET cc_start: 0.8107 (ppp) cc_final: 0.7497 (mtp) REVERT: B 83 PHE cc_start: 0.8259 (m-80) cc_final: 0.7796 (t80) REVERT: B 110 GLU cc_start: 0.8946 (mm-30) cc_final: 0.8637 (tp30) REVERT: B 124 LYS cc_start: 0.9012 (tppp) cc_final: 0.8608 (tppp) REVERT: B 284 ARG cc_start: 0.6918 (ptm-80) cc_final: 0.6634 (ptm-80) REVERT: B 325 MET cc_start: 0.7054 (mmm) cc_final: 0.6628 (mpp) REVERT: B 330 GLU cc_start: 0.8139 (pt0) cc_final: 0.7864 (pp20) REVERT: B 393 GLU cc_start: 0.8474 (tm-30) cc_final: 0.7995 (tm-30) REVERT: B 394 GLN cc_start: 0.7546 (OUTLIER) cc_final: 0.7296 (pt0) REVERT: B 422 GLU cc_start: 0.7678 (tm-30) cc_final: 0.7120 (tp30) REVERT: K 12 MET cc_start: 0.7006 (OUTLIER) cc_final: 0.6741 (ppp) REVERT: K 15 PHE cc_start: 0.8350 (m-80) cc_final: 0.7750 (m-80) REVERT: K 135 PHE cc_start: 0.9210 (p90) cc_final: 0.9001 (p90) REVERT: K 168 CYS cc_start: 0.8414 (t) cc_final: 0.8172 (p) REVERT: K 170 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8362 (tt0) REVERT: K 178 GLU cc_start: 0.9078 (mm-30) cc_final: 0.8352 (mt-10) REVERT: K 244 GLU cc_start: 0.7210 (pp20) cc_final: 0.6875 (pm20) REVERT: A 69 ASP cc_start: 0.7748 (t0) cc_final: 0.7440 (t0) REVERT: A 98 ASP cc_start: 0.8853 (p0) cc_final: 0.8404 (p0) REVERT: A 112 LYS cc_start: 0.9026 (tptp) cc_final: 0.8445 (mtpm) REVERT: A 113 GLU cc_start: 0.8439 (mm-30) cc_final: 0.7903 (mp0) REVERT: A 176 GLN cc_start: 0.8937 (mm110) cc_final: 0.8708 (mm110) REVERT: A 211 ASP cc_start: 0.8393 (m-30) cc_final: 0.8004 (m-30) REVERT: A 227 LEU cc_start: 0.7842 (mp) cc_final: 0.7628 (mp) outliers start: 35 outliers final: 18 residues processed: 252 average time/residue: 0.9351 time to fit residues: 256.9733 Evaluate side-chains 224 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 204 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain K residue 12 MET Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 252 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 43 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 75 optimal weight: 6.9990 chunk 77 optimal weight: 8.9990 chunk 91 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 ASN ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 ASN B 385 GLN K 129 HIS ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.106542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.090420 restraints weight = 20872.036| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 3.74 r_work: 0.3233 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3236 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3236 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 1.7464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9741 Z= 0.267 Angle : 0.881 13.820 13221 Z= 0.427 Chirality : 0.051 0.363 1458 Planarity : 0.005 0.053 1708 Dihedral : 10.289 138.228 1460 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.19 % Allowed : 35.53 % Favored : 61.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.56 (0.23), residues: 1184 helix: 0.32 (0.22), residues: 506 sheet: -0.27 (0.36), residues: 194 loop : -1.05 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 21 HIS 0.005 0.001 HIS A 28 PHE 0.019 0.002 PHE K 82 TYR 0.018 0.002 TYR B 185 ARG 0.010 0.001 ARG B 243 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 226 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 ASN cc_start: 0.8750 (t0) cc_final: 0.8302 (t160) REVERT: B 110 GLU cc_start: 0.8973 (mm-30) cc_final: 0.8721 (tp30) REVERT: B 160 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8604 (tm-30) REVERT: B 259 MET cc_start: 0.8463 (mmm) cc_final: 0.8256 (mmm) REVERT: B 325 MET cc_start: 0.7234 (mmm) cc_final: 0.6680 (mpp) REVERT: B 330 GLU cc_start: 0.8244 (pt0) cc_final: 0.7915 (pp20) REVERT: B 342 TYR cc_start: 0.7676 (OUTLIER) cc_final: 0.7462 (t80) REVERT: B 393 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8122 (tm-30) REVERT: B 398 MET cc_start: 0.8142 (tmm) cc_final: 0.4694 (mmt) REVERT: K 25 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7507 (ptt90) REVERT: K 53 GLN cc_start: 0.7735 (pp30) cc_final: 0.7447 (tm-30) REVERT: K 58 GLN cc_start: 0.6150 (pm20) cc_final: 0.5725 (mt0) REVERT: K 170 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8405 (tt0) REVERT: K 178 GLU cc_start: 0.9156 (mm-30) cc_final: 0.8520 (mt-10) REVERT: K 187 LYS cc_start: 0.8846 (ttpp) cc_final: 0.8537 (tttp) REVERT: K 244 GLU cc_start: 0.7532 (pp20) cc_final: 0.7261 (pm20) REVERT: A 51 THR cc_start: 0.8579 (m) cc_final: 0.8177 (p) REVERT: A 52 PHE cc_start: 0.8897 (m-80) cc_final: 0.8543 (m-80) REVERT: A 69 ASP cc_start: 0.7907 (t0) cc_final: 0.7566 (t0) REVERT: A 70 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7310 (mm) REVERT: A 98 ASP cc_start: 0.8932 (p0) cc_final: 0.8476 (p0) REVERT: A 112 LYS cc_start: 0.8994 (tptp) cc_final: 0.8715 (mtpm) REVERT: A 113 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8008 (mp0) REVERT: A 123 ARG cc_start: 0.9007 (ppp80) cc_final: 0.8714 (tmm-80) REVERT: A 155 GLU cc_start: 0.8940 (tm-30) cc_final: 0.8523 (pp20) REVERT: A 211 ASP cc_start: 0.8561 (m-30) cc_final: 0.8338 (m-30) outliers start: 33 outliers final: 16 residues processed: 249 average time/residue: 1.2426 time to fit residues: 336.6891 Evaluate side-chains 222 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 202 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 HIS Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 229 HIS Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain K residue 25 ARG Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 252 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 41 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 21 optimal weight: 0.0040 chunk 46 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 HIS B 167 ASN B 350 ASN B 385 GLN K 129 HIS ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.107220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.091397 restraints weight = 22084.919| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 3.85 r_work: 0.3240 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3245 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3245 r_free = 0.3245 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3245 r_free = 0.3245 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3245 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 1.7837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9741 Z= 0.234 Angle : 0.844 12.811 13221 Z= 0.412 Chirality : 0.049 0.303 1458 Planarity : 0.005 0.044 1708 Dihedral : 10.181 137.368 1460 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.52 % Allowed : 36.50 % Favored : 60.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.47 (0.23), residues: 1184 helix: 0.44 (0.22), residues: 502 sheet: -0.41 (0.36), residues: 203 loop : -0.96 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 21 HIS 0.004 0.001 HIS B 229 PHE 0.022 0.002 PHE B 83 TYR 0.023 0.001 TYR B 185 ARG 0.011 0.001 ARG A 215 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 221 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 ASN cc_start: 0.8774 (t0) cc_final: 0.8335 (t160) REVERT: B 110 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8783 (tp30) REVERT: B 325 MET cc_start: 0.7183 (mmm) cc_final: 0.6736 (mpp) REVERT: B 369 ARG cc_start: 0.6669 (mpp-170) cc_final: 0.6443 (mmm-85) REVERT: B 393 GLU cc_start: 0.8597 (tm-30) cc_final: 0.8189 (tm-30) REVERT: B 422 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7546 (tm-30) REVERT: K 25 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.7494 (ptt90) REVERT: K 53 GLN cc_start: 0.7428 (pp30) cc_final: 0.7185 (tm-30) REVERT: K 58 GLN cc_start: 0.6192 (pm20) cc_final: 0.5949 (mt0) REVERT: K 170 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8551 (mm-30) REVERT: K 178 GLU cc_start: 0.9140 (mm-30) cc_final: 0.8503 (mt-10) REVERT: K 187 LYS cc_start: 0.8936 (ttpp) cc_final: 0.8650 (tttp) REVERT: K 197 MET cc_start: 0.8545 (mtm) cc_final: 0.8238 (mpt) REVERT: K 244 GLU cc_start: 0.7569 (pp20) cc_final: 0.7292 (pm20) REVERT: A 51 THR cc_start: 0.8745 (m) cc_final: 0.8312 (p) REVERT: A 52 PHE cc_start: 0.8940 (m-80) cc_final: 0.8623 (m-80) REVERT: A 61 HIS cc_start: 0.7679 (m90) cc_final: 0.7358 (m90) REVERT: A 69 ASP cc_start: 0.7967 (t0) cc_final: 0.7670 (t0) REVERT: A 70 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7379 (OUTLIER) REVERT: A 98 ASP cc_start: 0.8889 (p0) cc_final: 0.8474 (p0) REVERT: A 112 LYS cc_start: 0.8902 (tptp) cc_final: 0.8655 (mtmt) REVERT: A 113 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8089 (mp0) REVERT: A 123 ARG cc_start: 0.9015 (ppp80) cc_final: 0.8704 (ptm160) REVERT: A 155 GLU cc_start: 0.8844 (tm-30) cc_final: 0.8475 (pp20) REVERT: A 203 MET cc_start: 0.8719 (mmp) cc_final: 0.8512 (mmp) REVERT: A 211 ASP cc_start: 0.8559 (m-30) cc_final: 0.8229 (m-30) outliers start: 26 outliers final: 17 residues processed: 239 average time/residue: 0.9295 time to fit residues: 242.6676 Evaluate side-chains 219 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 201 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 HIS Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 229 HIS Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain K residue 25 ARG Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 252 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 3 optimal weight: 8.9990 chunk 53 optimal weight: 0.6980 chunk 112 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 30 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 115 optimal weight: 7.9990 chunk 106 optimal weight: 0.3980 chunk 86 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 350 ASN B 385 GLN K 129 HIS ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.103098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.087265 restraints weight = 23175.195| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 3.93 r_work: 0.3154 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3164 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3164 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 1.8883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 9741 Z= 0.282 Angle : 0.896 15.419 13221 Z= 0.439 Chirality : 0.051 0.283 1458 Planarity : 0.005 0.054 1708 Dihedral : 10.162 136.469 1460 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.13 % Allowed : 37.75 % Favored : 60.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.63 (0.23), residues: 1184 helix: 0.31 (0.22), residues: 504 sheet: -0.45 (0.35), residues: 206 loop : -1.09 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 21 HIS 0.004 0.001 HIS B 229 PHE 0.021 0.002 PHE K 82 TYR 0.024 0.002 TYR B 185 ARG 0.009 0.001 ARG K 50 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7060.40 seconds wall clock time: 125 minutes 37.66 seconds (7537.66 seconds total)