Starting phenix.real_space_refine on Thu Feb 13 22:57:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rhb_19174/02_2025/8rhb_19174.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rhb_19174/02_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_19174/02_2025/8rhb_19174.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rhb_19174/02_2025/8rhb_19174.map" model { file = "/net/cci-nas-00/data/ceres_data/8rhb_19174/02_2025/8rhb_19174.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rhb_19174/02_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 7.97, per 1000 atoms: 0.84 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: 3.11 Conformation dependent library (CDL) restraints added in 1.4 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: 1.14 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: 3.84 Time building geometry restraints manager: 3.66 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: 0.810 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: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 29.940 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.330 ------------------------------------------------------------------------------- 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 : 0.977 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: 1.2119 time to fit residues: 357.2671 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 : 1.108 ------------------------------------------------------------------------------- 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: 0.0980 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: 0.3418 ------------------------------------------------------------------------------- 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 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 = 0.3565 r_free = 0.3565 target = 0.102916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.088577 restraints weight = 18889.450| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 3.42 r_work: 0.3176 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3187 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 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 = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4090 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9741 Z= 0.218 Angle : 0.750 16.118 13221 Z= 0.364 Chirality : 0.046 0.240 1458 Planarity : 0.005 0.082 1708 Dihedral : 15.695 174.525 1465 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.36 % Allowed : 18.59 % Favored : 77.06 % 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: 0.11 (0.24), residues: 1184 helix: 1.34 (0.23), residues: 480 sheet: -0.24 (0.36), residues: 212 loop : -1.02 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP B 21 HIS 0.025 0.002 HIS B 28 PHE 0.012 0.001 PHE B 20 TYR 0.022 0.002 TYR A 103 ARG 0.014 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 206 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 161 time to evaluate : 0.976 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: 0.7047 (tm-30) REVERT: K 59 GLU cc_start: 0.7277 (pm20) cc_final: 0.6728 (tp30) REVERT: A 80 THR cc_start: 0.7009 (OUTLIER) cc_final: 0.6634 (p) REVERT: A 188 ILE cc_start: 0.3385 (OUTLIER) cc_final: 0.3155 (mt) outliers start: 45 outliers final: 9 residues processed: 193 average time/residue: 0.9742 time to fit residues: 205.4766 Evaluate side-chains 141 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 1.036 ------------------------------------------------------------------------------- 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 188 ILE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 344 VAL 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: 3.9990 chunk 79 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 116 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 111 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN B 294 GLN ** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 GLN K 34 GLN K 129 HIS ** K 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 216 ASN 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.109802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.095195 restraints weight = 19264.591| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 3.59 r_work: 0.3272 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3285 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3285 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5485 moved from start: 0.7266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.118 9741 Z= 0.359 Angle : 0.892 11.951 13221 Z= 0.457 Chirality : 0.052 0.307 1458 Planarity : 0.007 0.068 1708 Dihedral : 12.665 177.486 1460 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.14 % Favored : 96.78 % Rotamer: Outliers : 4.84 % Allowed : 17.13 % Favored : 78.03 % 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: -0.69 (0.23), residues: 1184 helix: 0.15 (0.22), residues: 484 sheet: 0.02 (0.39), residues: 192 loop : -1.18 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP A 21 HIS 0.021 0.002 HIS B 28 PHE 0.019 0.003 PHE A 404 TYR 0.034 0.003 TYR A 408 ARG 0.015 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 260 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 210 time to evaluate : 1.007 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 204 ILE cc_start: 0.5805 (mp) cc_final: 0.5048 (mp) REVERT: B 269 MET cc_start: 0.5994 (OUTLIER) cc_final: 0.5305 (tmt) REVERT: B 373 MET cc_start: 0.1886 (ptm) cc_final: 0.1621 (ptm) REVERT: B 393 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7530 (tm-30) REVERT: K 8 ASN cc_start: 0.7679 (p0) cc_final: 0.7203 (p0) REVERT: K 25 ARG cc_start: 0.6204 (OUTLIER) cc_final: 0.5826 (mtm-85) REVERT: K 180 MET cc_start: 0.6310 (OUTLIER) cc_final: 0.5388 (tpt) REVERT: A 2 ARG cc_start: 0.4697 (OUTLIER) cc_final: 0.4328 (mmt180) REVERT: A 94 THR cc_start: 0.4158 (p) cc_final: 0.3870 (t) REVERT: A 176 GLN cc_start: 0.7951 (mm110) cc_final: 0.7428 (mm-40) REVERT: A 230 LEU cc_start: 0.8373 (mm) cc_final: 0.8126 (mm) REVERT: A 280 LYS cc_start: 0.4910 (mtmm) cc_final: 0.4697 (tptt) REVERT: A 318 LEU cc_start: 0.3717 (OUTLIER) cc_final: 0.3346 (tt) outliers start: 50 outliers final: 12 residues processed: 245 average time/residue: 1.0547 time to fit residues: 279.4855 Evaluate side-chains 180 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 163 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 74 LEU Chi-restraints excluded: chain K residue 146 LEU Chi-restraints excluded: chain K residue 180 MET Chi-restraints excluded: chain K residue 297 THR Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 296 PHE Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 355 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 32 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 69 optimal weight: 0.2980 chunk 87 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 chunk 85 optimal weight: 0.0170 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 197 ASN K 93 HIS K 129 HIS K 189 ASN A 101 ASN ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.113938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.098750 restraints weight = 18830.582| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 3.57 r_work: 0.3338 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3341 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3341 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5675 moved from start: 0.8349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 9741 Z= 0.218 Angle : 0.752 11.394 13221 Z= 0.369 Chirality : 0.046 0.243 1458 Planarity : 0.005 0.049 1708 Dihedral : 12.101 164.525 1460 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.84 % Allowed : 21.20 % Favored : 73.96 % 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: -0.15 (0.23), residues: 1184 helix: 0.74 (0.22), residues: 479 sheet: 0.19 (0.38), residues: 199 loop : -0.98 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 21 HIS 0.012 0.001 HIS A 8 PHE 0.025 0.002 PHE K 128 TYR 0.020 0.001 TYR A 312 ARG 0.006 0.001 ARG B 278 *********************** 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 251 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 201 time to evaluate : 1.032 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: B 269 MET cc_start: 0.6622 (mmm) cc_final: 0.5984 (tmt) REVERT: B 376 THR cc_start: 0.1125 (OUTLIER) cc_final: 0.0507 (p) REVERT: B 393 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7548 (tm-30) REVERT: K 18 LEU cc_start: 0.6901 (tt) cc_final: 0.6534 (tm) REVERT: K 23 VAL cc_start: 0.5713 (p) cc_final: 0.5479 (p) REVERT: K 180 MET cc_start: 0.6678 (OUTLIER) cc_final: 0.5774 (tpt) REVERT: A 94 THR cc_start: 0.4444 (p) cc_final: 0.4081 (t) REVERT: A 176 GLN cc_start: 0.7753 (mm110) cc_final: 0.7339 (mm-40) REVERT: A 230 LEU cc_start: 0.8357 (mm) cc_final: 0.8107 (mm) REVERT: A 408 TYR cc_start: 0.6930 (m-80) cc_final: 0.6621 (m-80) outliers start: 50 outliers final: 21 residues processed: 235 average time/residue: 0.9378 time to fit residues: 241.6534 Evaluate side-chains 191 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 168 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 PHE 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 288 VAL Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain K residue 180 MET Chi-restraints excluded: chain K residue 192 VAL Chi-restraints excluded: chain K residue 250 GLU Chi-restraints excluded: chain K residue 297 THR Chi-restraints excluded: chain K residue 299 VAL Chi-restraints excluded: chain K residue 311 GLU Chi-restraints excluded: chain A residue 92 LEU 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 195 LEU Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 431 ASP 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: 0.8980 chunk 60 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 84 optimal weight: 0.1980 chunk 70 optimal weight: 9.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 78 ASN K 117 ASN K 125 ASN ** K 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 342 GLN ** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.114922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.100051 restraints weight = 19105.084| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 3.56 r_work: 0.3378 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3360 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3360 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6204 moved from start: 1.0030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 9741 Z= 0.265 Angle : 0.763 9.563 13221 Z= 0.376 Chirality : 0.048 0.246 1458 Planarity : 0.005 0.048 1708 Dihedral : 11.692 150.964 1460 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 4.26 % Allowed : 24.59 % Favored : 71.15 % 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: -0.22 (0.23), residues: 1184 helix: 0.73 (0.22), residues: 488 sheet: -0.05 (0.35), residues: 201 loop : -1.01 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP A 21 HIS 0.011 0.001 HIS A 8 PHE 0.023 0.002 PHE A 404 TYR 0.034 0.002 TYR A 103 ARG 0.026 0.001 ARG B 158 *********************** 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 250 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 206 time to evaluate : 1.087 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 108 TYR cc_start: 0.8594 (t80) cc_final: 0.8383 (m-80) REVERT: B 147 SER cc_start: 0.8223 (p) cc_final: 0.7912 (p) REVERT: B 166 MET cc_start: 0.3975 (OUTLIER) cc_final: 0.3237 (tpt) REVERT: B 185 TYR cc_start: 0.7007 (m-80) cc_final: 0.6391 (m-80) REVERT: B 205 ASP cc_start: 0.5262 (OUTLIER) cc_final: 0.4937 (OUTLIER) REVERT: B 269 MET cc_start: 0.6577 (OUTLIER) cc_final: 0.6364 (tmt) REVERT: B 376 THR cc_start: 0.1631 (OUTLIER) cc_final: 0.1054 (p) REVERT: B 393 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7589 (tm-30) REVERT: B 400 ARG cc_start: 0.7541 (mtm-85) cc_final: 0.6923 (tmt170) REVERT: K 157 GLU cc_start: 0.5968 (OUTLIER) cc_final: 0.5756 (tp30) REVERT: K 180 MET cc_start: 0.6782 (OUTLIER) cc_final: 0.6114 (tpt) REVERT: K 282 MET cc_start: 0.7749 (mmp) cc_final: 0.7359 (mmm) REVERT: A 2 ARG cc_start: 0.4853 (OUTLIER) cc_final: 0.4616 (mmt180) REVERT: A 97 GLU cc_start: 0.8856 (mp0) cc_final: 0.8599 (mp0) REVERT: A 176 GLN cc_start: 0.8195 (mm110) cc_final: 0.7680 (mm-40) REVERT: A 230 LEU cc_start: 0.8620 (mm) cc_final: 0.8393 (mm) REVERT: A 377 MET cc_start: 0.5295 (ptt) cc_final: 0.4787 (pmm) outliers start: 44 outliers final: 22 residues processed: 236 average time/residue: 0.9042 time to fit residues: 233.7660 Evaluate side-chains 201 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 173 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 PHE Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 241 CYS 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 371 LEU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain K residue 81 ILE Chi-restraints excluded: chain K residue 157 GLU Chi-restraints excluded: chain K residue 180 MET Chi-restraints excluded: chain K residue 192 VAL Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain K residue 250 GLU Chi-restraints excluded: chain K residue 299 VAL Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 21 TRP Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 431 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 85 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 342 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.116894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.101735 restraints weight = 19353.343| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 3.62 r_work: 0.3387 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3389 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3389 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 1.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 9741 Z= 0.311 Angle : 0.872 14.978 13221 Z= 0.430 Chirality : 0.050 0.228 1458 Planarity : 0.005 0.047 1708 Dihedral : 11.120 129.464 1460 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 5.91 % Allowed : 25.94 % Favored : 68.15 % 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: -0.26 (0.23), residues: 1184 helix: 0.68 (0.23), residues: 489 sheet: -0.09 (0.35), residues: 184 loop : -0.98 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP A 21 HIS 0.013 0.002 HIS B 229 PHE 0.034 0.002 PHE K 82 TYR 0.025 0.002 TYR A 408 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 297 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 236 time to evaluate : 1.106 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 105 LYS cc_start: 0.7990 (tptt) cc_final: 0.7788 (tptp) REVERT: B 131 CYS cc_start: 0.5808 (t) cc_final: 0.5275 (t) REVERT: B 218 LYS cc_start: 0.8527 (mmmm) cc_final: 0.8248 (mmmm) REVERT: B 269 MET cc_start: 0.7459 (OUTLIER) cc_final: 0.7053 (tmt) REVERT: B 376 THR cc_start: 0.3472 (OUTLIER) cc_final: 0.3215 (m) REVERT: B 393 GLU cc_start: 0.8337 (tm-30) cc_final: 0.7801 (tm-30) REVERT: B 400 ARG cc_start: 0.7996 (mtm-85) cc_final: 0.7359 (tmt170) REVERT: B 413 MET cc_start: 0.7682 (mmp) cc_final: 0.7236 (mpm) REVERT: B 422 GLU cc_start: 0.7017 (tm-30) cc_final: 0.6672 (tp30) REVERT: K 101 ASP cc_start: 0.7443 (t70) cc_final: 0.7229 (t0) REVERT: K 131 LYS cc_start: 0.7500 (OUTLIER) cc_final: 0.7077 (ttpt) REVERT: K 170 GLU cc_start: 0.7961 (tp30) cc_final: 0.7282 (mm-30) REVERT: K 180 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.7080 (tpt) REVERT: K 300 ILE cc_start: 0.8548 (OUTLIER) cc_final: 0.8324 (pp) REVERT: A 2 ARG cc_start: 0.5090 (OUTLIER) cc_final: 0.4179 (mmt180) REVERT: A 97 GLU cc_start: 0.8986 (mp0) cc_final: 0.8548 (mp0) REVERT: A 112 LYS cc_start: 0.8457 (tptp) cc_final: 0.8011 (ttpp) REVERT: A 176 GLN cc_start: 0.8491 (mm110) cc_final: 0.7995 (mm110) REVERT: A 234 ILE cc_start: 0.7494 (mt) cc_final: 0.7205 (mt) REVERT: A 329 ASN cc_start: 0.8280 (m-40) cc_final: 0.8078 (m-40) REVERT: A 377 MET cc_start: 0.6076 (ptt) cc_final: 0.4663 (tmm) outliers start: 61 outliers final: 22 residues processed: 274 average time/residue: 0.8859 time to fit residues: 266.0267 Evaluate side-chains 228 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 200 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 248 LEU 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 371 LEU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 385 GLN Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain K residue 128 PHE Chi-restraints excluded: chain K residue 131 LYS Chi-restraints excluded: chain K residue 133 SER Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 180 MET Chi-restraints excluded: chain K residue 300 ILE Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 431 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 24 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 59 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 chunk 80 optimal weight: 0.6980 chunk 4 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 125 ASN K 129 HIS ** K 253 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 = 0.3767 r_free = 0.3767 target = 0.116455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.100642 restraints weight = 19963.452| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 3.74 r_work: 0.3365 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3371 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3371 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 1.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9741 Z= 0.237 Angle : 0.811 12.795 13221 Z= 0.395 Chirality : 0.048 0.424 1458 Planarity : 0.005 0.040 1708 Dihedral : 10.659 142.020 1460 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.07 % Allowed : 31.17 % Favored : 64.76 % 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: -0.10 (0.23), residues: 1184 helix: 0.79 (0.23), residues: 493 sheet: 0.07 (0.35), residues: 183 loop : -0.91 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 21 HIS 0.005 0.001 HIS A 8 PHE 0.016 0.002 PHE K 82 TYR 0.018 0.002 TYR B 161 ARG 0.005 0.001 ARG B 123 *********************** 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 254 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 212 time to evaluate : 1.011 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 83 PHE cc_start: 0.7224 (m-80) cc_final: 0.6961 (t80) REVERT: B 123 ARG cc_start: 0.8332 (ttp80) cc_final: 0.7932 (ptp-110) REVERT: B 218 LYS cc_start: 0.8660 (mmmm) cc_final: 0.8446 (mmmm) REVERT: B 247 GLN cc_start: 0.8621 (mm110) cc_final: 0.8374 (tp40) REVERT: B 323 MET cc_start: 0.6335 (pmm) cc_final: 0.5826 (pmm) REVERT: B 325 MET cc_start: 0.7311 (mpp) cc_final: 0.6479 (mpt) REVERT: B 393 GLU cc_start: 0.8303 (tm-30) cc_final: 0.7725 (tm-30) REVERT: B 398 MET cc_start: 0.8100 (tmm) cc_final: 0.5283 (tpt) REVERT: B 422 GLU cc_start: 0.7094 (tm-30) cc_final: 0.6682 (tp30) REVERT: K 53 GLN cc_start: 0.7473 (pp30) cc_final: 0.7220 (tm-30) REVERT: K 131 LYS cc_start: 0.7361 (OUTLIER) cc_final: 0.7062 (ttpt) REVERT: K 162 VAL cc_start: 0.8513 (p) cc_final: 0.8296 (t) REVERT: K 170 GLU cc_start: 0.8228 (tp30) cc_final: 0.7536 (mm-30) REVERT: K 277 TYR cc_start: 0.8016 (m-80) cc_final: 0.7537 (m-80) REVERT: A 2 ARG cc_start: 0.5695 (OUTLIER) cc_final: 0.4767 (mmt180) REVERT: A 112 LYS cc_start: 0.8728 (tptp) cc_final: 0.7939 (mtpt) REVERT: A 176 GLN cc_start: 0.8527 (mm110) cc_final: 0.8029 (mm110) REVERT: A 234 ILE cc_start: 0.7844 (mt) cc_final: 0.7529 (mt) REVERT: A 329 ASN cc_start: 0.8345 (m-40) cc_final: 0.8134 (m-40) outliers start: 42 outliers final: 18 residues processed: 241 average time/residue: 0.9953 time to fit residues: 260.6288 Evaluate side-chains 205 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 185 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 385 GLN Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 131 LYS Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain K residue 261 LEU Chi-restraints excluded: chain K residue 300 ILE Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 158 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 Chi-restraints excluded: chain A residue 431 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 74 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 29 optimal weight: 0.0270 chunk 28 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 chunk 90 optimal weight: 0.9990 overall best weight: 1.4044 ------------------------------------------------------------------------------- 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 50 ASN B 350 ASN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 125 ASN ** K 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 8 HIS ** 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 = 0.3739 r_free = 0.3739 target = 0.114561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.098385 restraints weight = 20868.371| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 3.88 r_work: 0.3327 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3332 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3331 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 1.5270 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= 0.270 Angle : 0.890 14.736 13221 Z= 0.428 Chirality : 0.052 0.530 1458 Planarity : 0.005 0.046 1708 Dihedral : 10.633 134.324 1460 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.48 % Allowed : 32.53 % Favored : 63.99 % 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: -0.27 (0.23), residues: 1184 helix: 0.54 (0.22), residues: 502 sheet: -0.00 (0.35), residues: 183 loop : -0.92 (0.26), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 21 HIS 0.013 0.002 HIS B 28 PHE 0.027 0.002 PHE K 82 TYR 0.022 0.002 TYR B 185 ARG 0.009 0.001 ARG B 400 *********************** 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 277 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 241 time to evaluate : 1.051 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 43 GLN cc_start: 0.7104 (mt0) cc_final: 0.6855 (mt0) REVERT: B 50 ASN cc_start: 0.8972 (m-40) cc_final: 0.8701 (m-40) REVERT: B 131 CYS cc_start: 0.8722 (m) cc_final: 0.8505 (m) REVERT: B 218 LYS cc_start: 0.8788 (mmmm) cc_final: 0.8514 (mmmm) REVERT: B 235 MET cc_start: 0.7141 (tmm) cc_final: 0.6848 (ttm) REVERT: B 269 MET cc_start: 0.7045 (ptm) cc_final: 0.6661 (ptp) REVERT: B 302 MET cc_start: 0.3549 (tmm) cc_final: 0.3001 (tmm) REVERT: B 315 VAL cc_start: 0.7977 (OUTLIER) cc_final: 0.7752 (t) REVERT: B 393 GLU cc_start: 0.8343 (tm-30) cc_final: 0.7779 (tm-30) REVERT: B 394 GLN cc_start: 0.7151 (OUTLIER) cc_final: 0.6865 (tt0) REVERT: B 413 MET cc_start: 0.8146 (mmp) cc_final: 0.7798 (mpm) REVERT: B 422 GLU cc_start: 0.7468 (tm-30) cc_final: 0.6972 (tp30) REVERT: B 433 GLN cc_start: 0.8133 (tm-30) cc_final: 0.7607 (tm-30) REVERT: K 12 MET cc_start: 0.6986 (ppp) cc_final: 0.6316 (pmm) REVERT: K 53 GLN cc_start: 0.7592 (pp30) cc_final: 0.7358 (tm-30) REVERT: K 135 PHE cc_start: 0.8959 (p90) cc_final: 0.8709 (p90) REVERT: K 170 GLU cc_start: 0.8523 (tp30) cc_final: 0.7875 (mm-30) REVERT: K 185 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8170 (tp30) REVERT: K 277 TYR cc_start: 0.8142 (m-80) cc_final: 0.7617 (m-80) REVERT: A 2 ARG cc_start: 0.6166 (OUTLIER) cc_final: 0.5065 (mmt180) REVERT: A 97 GLU cc_start: 0.8947 (mp0) cc_final: 0.8506 (mp0) REVERT: A 112 LYS cc_start: 0.8889 (tptp) cc_final: 0.8436 (mtmt) REVERT: A 119 LEU cc_start: 0.8477 (tt) cc_final: 0.8244 (tp) REVERT: A 175 PRO cc_start: 0.8798 (Cg_exo) cc_final: 0.8447 (Cg_endo) REVERT: A 176 GLN cc_start: 0.8735 (mm110) cc_final: 0.8229 (mm110) REVERT: A 230 LEU cc_start: 0.9172 (mm) cc_final: 0.8739 (tm) REVERT: A 234 ILE cc_start: 0.8126 (mt) cc_final: 0.7866 (mt) REVERT: A 269 LEU cc_start: 0.8021 (pt) cc_final: 0.7676 (pp) REVERT: A 296 PHE cc_start: 0.7900 (m-80) cc_final: 0.7637 (m-80) REVERT: A 311 LYS cc_start: 0.6514 (tptt) cc_final: 0.6259 (tptp) REVERT: A 329 ASN cc_start: 0.8517 (m-40) cc_final: 0.8315 (m-40) REVERT: A 377 MET cc_start: 0.6467 (ptt) cc_final: 0.6231 (pmt) REVERT: A 393 HIS cc_start: 0.8129 (t70) cc_final: 0.7920 (t-90) outliers start: 36 outliers final: 16 residues processed: 266 average time/residue: 0.9165 time to fit residues: 267.2651 Evaluate side-chains 236 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 217 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 28 HIS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 385 GLN Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 431 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 43 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 chunk 91 optimal weight: 0.0980 chunk 94 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 37 optimal weight: 0.0980 chunk 81 optimal weight: 0.5980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 380 ASN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 ASN ** 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 = 0.3755 r_free = 0.3755 target = 0.115896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.100294 restraints weight = 20307.103| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 3.74 r_work: 0.3346 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3350 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3350 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 1.5633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9741 Z= 0.224 Angle : 0.866 12.859 13221 Z= 0.414 Chirality : 0.050 0.525 1458 Planarity : 0.005 0.052 1708 Dihedral : 10.236 139.561 1460 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.81 % Allowed : 33.88 % Favored : 63.31 % 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: -0.18 (0.23), residues: 1184 helix: 0.65 (0.23), residues: 501 sheet: 0.04 (0.35), residues: 187 loop : -0.90 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 21 HIS 0.027 0.002 HIS B 28 PHE 0.020 0.002 PHE B 83 TYR 0.034 0.002 TYR A 357 ARG 0.008 0.001 ARG B 215 *********************** 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 263 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 234 time to evaluate : 1.129 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: B 19 LYS cc_start: 0.8326 (tptp) cc_final: 0.7939 (tppt) REVERT: B 50 ASN cc_start: 0.8754 (m-40) cc_final: 0.8551 (m-40) REVERT: B 75 MET cc_start: 0.7785 (ppp) cc_final: 0.7279 (mtp) REVERT: B 269 MET cc_start: 0.7028 (ptm) cc_final: 0.6726 (ptp) REVERT: B 293 GLN cc_start: 0.7406 (tt0) cc_final: 0.7030 (tp40) REVERT: B 325 MET cc_start: 0.7262 (mpp) cc_final: 0.6017 (mpt) REVERT: B 393 GLU cc_start: 0.8292 (tm-30) cc_final: 0.7804 (tm-30) REVERT: B 413 MET cc_start: 0.7867 (mmp) cc_final: 0.7199 (mpp) REVERT: B 422 GLU cc_start: 0.7489 (tm-30) cc_final: 0.6989 (tp30) REVERT: B 433 GLN cc_start: 0.8166 (tm-30) cc_final: 0.7447 (tp-100) REVERT: K 12 MET cc_start: 0.6989 (ppp) cc_final: 0.6776 (pmm) REVERT: K 53 GLN cc_start: 0.7552 (pp30) cc_final: 0.7313 (tm-30) REVERT: K 170 GLU cc_start: 0.8625 (tp30) cc_final: 0.8251 (mm-30) REVERT: K 178 GLU cc_start: 0.9122 (mm-30) cc_final: 0.8341 (mt-10) REVERT: K 185 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8730 (tp30) REVERT: K 195 THR cc_start: 0.7919 (m) cc_final: 0.7646 (m) REVERT: K 244 GLU cc_start: 0.6892 (pp20) cc_final: 0.6619 (pm20) REVERT: K 277 TYR cc_start: 0.8065 (m-80) cc_final: 0.7567 (m-80) REVERT: K 282 MET cc_start: 0.8585 (mmm) cc_final: 0.8259 (mmm) REVERT: K 300 ILE cc_start: 0.8933 (pt) cc_final: 0.8652 (pp) REVERT: A 2 ARG cc_start: 0.6259 (OUTLIER) cc_final: 0.5127 (mmt180) REVERT: A 22 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7183 (mm-30) REVERT: A 83 TYR cc_start: 0.7757 (m-10) cc_final: 0.7210 (m-10) REVERT: A 97 GLU cc_start: 0.8883 (mp0) cc_final: 0.8643 (mp0) REVERT: A 108 TYR cc_start: 0.8762 (m-80) cc_final: 0.8557 (m-80) REVERT: A 112 LYS cc_start: 0.8953 (tptp) cc_final: 0.8552 (mtmt) REVERT: A 113 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7491 (mp0) REVERT: A 119 LEU cc_start: 0.8576 (tt) cc_final: 0.8361 (tp) REVERT: A 175 PRO cc_start: 0.8825 (Cg_exo) cc_final: 0.8465 (Cg_endo) REVERT: A 176 GLN cc_start: 0.8744 (mm110) cc_final: 0.8276 (mm110) REVERT: A 211 ASP cc_start: 0.7992 (m-30) cc_final: 0.7749 (m-30) REVERT: A 230 LEU cc_start: 0.9133 (mm) cc_final: 0.8677 (tm) REVERT: A 301 GLN cc_start: 0.7546 (tp-100) cc_final: 0.6898 (mm110) REVERT: A 302 MET cc_start: 0.6955 (tmm) cc_final: 0.5962 (ttm) REVERT: A 311 LYS cc_start: 0.6628 (tptt) cc_final: 0.6250 (tptp) REVERT: A 377 MET cc_start: 0.6321 (ptt) cc_final: 0.6055 (pmt) outliers start: 29 outliers final: 13 residues processed: 254 average time/residue: 0.9015 time to fit residues: 250.9943 Evaluate side-chains 223 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 209 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 THR 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 385 GLN Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain A residue 2 ARG 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 Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 431 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 41 optimal weight: 0.5980 chunk 115 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 HIS B 249 ASN ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 ASN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 GLN K 253 ASN A 216 ASN ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.112018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.095448 restraints weight = 23432.883| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 4.08 r_work: 0.3306 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3312 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3312 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 1.6639 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= 0.245 Angle : 0.896 13.258 13221 Z= 0.433 Chirality : 0.052 0.537 1458 Planarity : 0.005 0.052 1708 Dihedral : 10.077 138.509 1460 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.81 % Allowed : 35.24 % Favored : 61.96 % 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: -0.28 (0.23), residues: 1184 helix: 0.44 (0.22), residues: 501 sheet: 0.17 (0.35), residues: 192 loop : -0.90 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 21 HIS 0.028 0.002 HIS B 28 PHE 0.024 0.002 PHE K 82 TYR 0.019 0.002 TYR A 357 ARG 0.007 0.001 ARG B 400 ********************** 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 269 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 240 time to evaluate : 1.096 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: B 75 MET cc_start: 0.7906 (ppp) cc_final: 0.7455 (mtp) REVERT: B 110 GLU cc_start: 0.8892 (tp30) cc_final: 0.8665 (tp30) REVERT: B 114 LEU cc_start: 0.9304 (mm) cc_final: 0.9084 (tp) REVERT: B 269 MET cc_start: 0.7372 (ptm) cc_final: 0.7093 (ptp) REVERT: B 293 GLN cc_start: 0.7651 (tt0) cc_final: 0.7280 (tp40) REVERT: B 330 GLU cc_start: 0.8057 (pt0) cc_final: 0.7642 (pp20) REVERT: B 393 GLU cc_start: 0.8417 (tm-30) cc_final: 0.7980 (tm-30) REVERT: B 394 GLN cc_start: 0.7573 (OUTLIER) cc_final: 0.7293 (pt0) REVERT: B 413 MET cc_start: 0.8129 (mmp) cc_final: 0.7521 (tpp) REVERT: B 433 GLN cc_start: 0.8328 (tm-30) cc_final: 0.7619 (tp-100) REVERT: K 53 GLN cc_start: 0.7678 (pp30) cc_final: 0.7466 (tm-30) REVERT: K 58 GLN cc_start: 0.6248 (pm20) cc_final: 0.5750 (mt0) REVERT: K 170 GLU cc_start: 0.8684 (tp30) cc_final: 0.8299 (mm-30) REVERT: K 178 GLU cc_start: 0.9174 (mm-30) cc_final: 0.8504 (mt-10) REVERT: K 185 GLU cc_start: 0.9103 (mm-30) cc_final: 0.8621 (tp30) REVERT: K 195 THR cc_start: 0.7800 (m) cc_final: 0.7460 (m) REVERT: K 199 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8207 (tm-30) REVERT: K 244 GLU cc_start: 0.7407 (pp20) cc_final: 0.7111 (pm20) REVERT: K 277 TYR cc_start: 0.8102 (m-80) cc_final: 0.7812 (m-80) REVERT: K 300 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8809 (pp) REVERT: A 2 ARG cc_start: 0.6761 (OUTLIER) cc_final: 0.5669 (mmt180) REVERT: A 22 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7468 (mm-30) REVERT: A 51 THR cc_start: 0.8469 (m) cc_final: 0.8164 (p) REVERT: A 97 GLU cc_start: 0.8851 (mp0) cc_final: 0.8562 (mm-30) REVERT: A 98 ASP cc_start: 0.8833 (p0) cc_final: 0.8251 (p0) REVERT: A 112 LYS cc_start: 0.8984 (tptp) cc_final: 0.8602 (mtmt) REVERT: A 113 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7570 (mp0) REVERT: A 119 LEU cc_start: 0.8787 (tt) cc_final: 0.8553 (mt) REVERT: A 175 PRO cc_start: 0.9022 (Cg_exo) cc_final: 0.8722 (Cg_endo) REVERT: A 176 GLN cc_start: 0.8907 (mm110) cc_final: 0.8463 (mm110) REVERT: A 211 ASP cc_start: 0.8071 (m-30) cc_final: 0.7638 (m-30) REVERT: A 230 LEU cc_start: 0.9212 (mm) cc_final: 0.8901 (tm) REVERT: A 293 ASN cc_start: 0.8345 (m-40) cc_final: 0.6874 (m-40) REVERT: A 301 GLN cc_start: 0.7772 (tp-100) cc_final: 0.6954 (mm110) REVERT: A 302 MET cc_start: 0.7107 (tmm) cc_final: 0.6245 (ttm) REVERT: A 311 LYS cc_start: 0.6869 (tptt) cc_final: 0.6412 (tptp) REVERT: A 392 ASP cc_start: 0.7990 (m-30) cc_final: 0.7506 (m-30) outliers start: 29 outliers final: 14 residues processed: 260 average time/residue: 0.9165 time to fit residues: 260.5398 Evaluate side-chains 235 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 218 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 229 HIS Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 385 GLN Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 300 ILE Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 431 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 3 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 8 optimal weight: 0.0050 chunk 70 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 chunk 115 optimal weight: 0.9990 chunk 106 optimal weight: 9.9990 chunk 86 optimal weight: 4.9990 overall best weight: 2.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 HIS ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 ASN B 350 ASN B 380 ASN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 GLN ** K 198 ASN ** 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 = 0.3705 r_free = 0.3705 target = 0.111522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.095481 restraints weight = 21552.134| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 3.87 r_work: 0.3305 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3313 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3313 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 1.6716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.221 9741 Z= 0.429 Angle : 1.100 59.150 13221 Z= 0.594 Chirality : 0.064 1.432 1458 Planarity : 0.005 0.051 1708 Dihedral : 10.083 138.500 1460 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 22.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.42 % Allowed : 37.46 % Favored : 60.12 % Cbeta Deviations : 0.09 % 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: -0.33 (0.23), residues: 1184 helix: 0.39 (0.22), residues: 501 sheet: 0.17 (0.36), residues: 191 loop : -0.91 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 21 HIS 0.013 0.002 HIS B 28 PHE 0.024 0.002 PHE K 82 TYR 0.018 0.002 TYR B 185 ARG 0.005 0.001 ARG B 284 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6357.33 seconds wall clock time: 113 minutes 21.89 seconds (6801.89 seconds total)