Starting phenix.real_space_refine on Tue Nov 18 21:31:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6cm9_7457/11_2025/6cm9_7457.cif Found real_map, /net/cci-nas-00/data/ceres_data/6cm9_7457/11_2025/6cm9_7457.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6cm9_7457/11_2025/6cm9_7457.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6cm9_7457/11_2025/6cm9_7457.map" model { file = "/net/cci-nas-00/data/ceres_data/6cm9_7457/11_2025/6cm9_7457.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6cm9_7457/11_2025/6cm9_7457.cif" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 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 6 5.49 5 Mg 2 5.21 5 S 102 5.16 5 C 11256 2.51 5 N 3014 2.21 5 O 3303 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17683 Number of models: 1 Model: "" Number of chains: 11 Chain: "L" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 76 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "T" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Link IDs: {'PTRANS': 1, 'TRANS': 11} Chain: "B" Number of atoms: 4513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4513 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 25, 'TRANS': 544} Chain: "C" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1330 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 3, 'TRANS': 161} Chain: "G" Number of atoms: 4633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4633 Classifications: {'peptide': 585} Link IDs: {'PTRANS': 13, 'TRANS': 571} Chain: "H" Number of atoms: 1312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1312 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 3, 'TRANS': 159} Chain: "M" Number of atoms: 3362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3362 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 20, 'TRANS': 394} Chain breaks: 1 Chain: "S" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1197 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 1, 'TRANS': 140} Chain: "N" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1089 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 118} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" 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} Chain: "H" 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} Time building chain proxies: 3.66, per 1000 atoms: 0.21 Number of scatterers: 17683 At special positions: 0 Unit cell: (139.777, 152.581, 130.174, 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 102 16.00 P 6 15.00 Mg 2 11.99 O 3303 8.00 N 3014 7.00 C 11256 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.33 Conformation dependent library (CDL) restraints added in 667.3 milliseconds 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4198 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 18 sheets defined 52.7% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'B' and resid 15 through 22 Processing helix chain 'B' and resid 26 through 41 removed outlier: 3.728A pdb=" N LYS B 30 " --> pdb=" O LYS B 26 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLU B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 50 through 55 removed outlier: 3.599A pdb=" N VAL B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL B 55 " --> pdb=" O PHE B 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 50 through 55' Processing helix chain 'B' and resid 65 through 76 Processing helix chain 'B' and resid 82 through 86 removed outlier: 3.959A pdb=" N ILE B 85 " --> pdb=" O ASP B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 95 Processing helix chain 'B' and resid 99 through 111 removed outlier: 3.553A pdb=" N ARG B 103 " --> pdb=" O ASN B 99 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY B 111 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 131 removed outlier: 3.576A pdb=" N LEU B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LYS B 131 " --> pdb=" O ARG B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 152 removed outlier: 3.698A pdb=" N ARG B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE B 151 " --> pdb=" O LYS B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 160 removed outlier: 4.085A pdb=" N VAL B 156 " --> pdb=" O ASN B 152 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 167 Processing helix chain 'B' and resid 174 through 191 removed outlier: 3.853A pdb=" N SER B 190 " --> pdb=" O GLU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 209 Processing helix chain 'B' and resid 217 through 222 removed outlier: 3.680A pdb=" N PHE B 221 " --> pdb=" O TRP B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 245 removed outlier: 4.030A pdb=" N ARG B 243 " --> pdb=" O SER B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 250 removed outlier: 3.701A pdb=" N SER B 249 " --> pdb=" O PRO B 246 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS B 250 " --> pdb=" O ARG B 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 246 through 250' Processing helix chain 'B' and resid 254 through 267 Processing helix chain 'B' and resid 275 through 282 removed outlier: 3.527A pdb=" N THR B 279 " --> pdb=" O ASP B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 291 removed outlier: 3.645A pdb=" N LEU B 288 " --> pdb=" O LEU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 294 No H-bonds generated for 'chain 'B' and resid 292 through 294' Processing helix chain 'B' and resid 297 through 310 removed outlier: 4.120A pdb=" N VAL B 301 " --> pdb=" O GLU B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 320 removed outlier: 4.592A pdb=" N HIS B 319 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU B 320 " --> pdb=" O LEU B 317 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 316 through 320' Processing helix chain 'B' and resid 321 through 325 Processing helix chain 'B' and resid 331 through 345 removed outlier: 4.315A pdb=" N GLU B 337 " --> pdb=" O TYR B 333 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU B 339 " --> pdb=" O LYS B 335 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 349 No H-bonds generated for 'chain 'B' and resid 347 through 349' Processing helix chain 'B' and resid 350 through 359 removed outlier: 3.521A pdb=" N VAL B 354 " --> pdb=" O ASN B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 384 Processing helix chain 'B' and resid 387 through 400 Processing helix chain 'B' and resid 403 through 419 removed outlier: 4.364A pdb=" N VAL B 412 " --> pdb=" O GLN B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 441 through 455 removed outlier: 3.920A pdb=" N ALA B 446 " --> pdb=" O PRO B 442 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA B 447 " --> pdb=" O GLU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 466 removed outlier: 3.678A pdb=" N LEU B 465 " --> pdb=" O ASN B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 470 Processing helix chain 'B' and resid 472 through 476 removed outlier: 3.544A pdb=" N ASP B 475 " --> pdb=" O GLY B 472 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS B 476 " --> pdb=" O PHE B 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 472 through 476' Processing helix chain 'B' and resid 477 through 495 removed outlier: 3.976A pdb=" N GLN B 481 " --> pdb=" O SER B 477 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 511 removed outlier: 3.765A pdb=" N GLN B 504 " --> pdb=" O GLN B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 533 Processing helix chain 'B' and resid 536 through 541 Processing helix chain 'B' and resid 559 through 564 Processing helix chain 'B' and resid 569 through 574 removed outlier: 3.529A pdb=" N TYR B 574 " --> pdb=" O LEU B 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 39 Processing helix chain 'C' and resid 75 through 79 removed outlier: 3.833A pdb=" N TRP C 78 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG C 79 " --> pdb=" O PRO C 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 75 through 79' Processing helix chain 'C' and resid 96 through 111 removed outlier: 4.018A pdb=" N ASN C 101 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N GLU C 102 " --> pdb=" O GLU C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 144 Processing helix chain 'C' and resid 165 through 178 Processing helix chain 'G' and resid 6 through 16 removed outlier: 3.614A pdb=" N THR G 16 " --> pdb=" O ARG G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 40 removed outlier: 4.155A pdb=" N GLU G 25 " --> pdb=" O ALA G 21 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU G 30 " --> pdb=" O MET G 26 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU G 40 " --> pdb=" O SER G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 59 Processing helix chain 'G' and resid 67 through 75 removed outlier: 4.090A pdb=" N LEU G 73 " --> pdb=" O GLU G 69 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA G 75 " --> pdb=" O LEU G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 93 removed outlier: 3.661A pdb=" N LYS G 82 " --> pdb=" O LYS G 78 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU G 93 " --> pdb=" O ALA G 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 102 removed outlier: 3.588A pdb=" N LEU G 102 " --> pdb=" O VAL G 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 99 through 102' Processing helix chain 'G' and resid 103 through 111 Processing helix chain 'G' and resid 117 through 130 removed outlier: 3.734A pdb=" N LEU G 126 " --> pdb=" O ALA G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 143 removed outlier: 5.793A pdb=" N GLY G 140 " --> pdb=" O ARG G 136 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N GLU G 141 " --> pdb=" O ASP G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 150 through 168 removed outlier: 3.552A pdb=" N LYS G 155 " --> pdb=" O SER G 151 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS G 156 " --> pdb=" O TYR G 152 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU G 159 " --> pdb=" O LYS G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 175 Processing helix chain 'G' and resid 187 through 205 removed outlier: 3.667A pdb=" N LEU G 191 " --> pdb=" O ASN G 187 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER G 205 " --> pdb=" O MET G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 213 Processing helix chain 'G' and resid 215 through 229 removed outlier: 3.573A pdb=" N LEU G 219 " --> pdb=" O LEU G 215 " (cutoff:3.500A) Processing helix chain 'G' and resid 242 through 256 removed outlier: 3.626A pdb=" N ARG G 248 " --> pdb=" O PHE G 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 261 through 267 Processing helix chain 'G' and resid 267 through 275 removed outlier: 3.632A pdb=" N LEU G 271 " --> pdb=" O MET G 267 " (cutoff:3.500A) Processing helix chain 'G' and resid 282 through 299 removed outlier: 3.713A pdb=" N ASN G 286 " --> pdb=" O LYS G 282 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP G 298 " --> pdb=" O LEU G 294 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE G 299 " --> pdb=" O THR G 295 " (cutoff:3.500A) Processing helix chain 'G' and resid 302 through 318 removed outlier: 3.699A pdb=" N ARG G 306 " --> pdb=" O GLU G 302 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL G 307 " --> pdb=" O SER G 303 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU G 308 " --> pdb=" O GLY G 304 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU G 318 " --> pdb=" O GLY G 314 " (cutoff:3.500A) Processing helix chain 'G' and resid 321 through 335 Processing helix chain 'G' and resid 343 through 345 No H-bonds generated for 'chain 'G' and resid 343 through 345' Processing helix chain 'G' and resid 346 through 353 removed outlier: 3.534A pdb=" N CYS G 353 " --> pdb=" O THR G 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 354 through 356 No H-bonds generated for 'chain 'G' and resid 354 through 356' Processing helix chain 'G' and resid 358 through 373 Processing helix chain 'G' and resid 377 through 391 removed outlier: 3.624A pdb=" N MET G 382 " --> pdb=" O ILE G 378 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LYS G 383 " --> pdb=" O ARG G 379 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU G 384 " --> pdb=" O GLY G 380 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP G 390 " --> pdb=" O LEU G 386 " (cutoff:3.500A) Processing helix chain 'G' and resid 396 through 411 removed outlier: 3.886A pdb=" N PHE G 405 " --> pdb=" O ALA G 401 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS G 410 " --> pdb=" O LEU G 406 " (cutoff:3.500A) Processing helix chain 'G' and resid 415 through 429 Processing helix chain 'G' and resid 436 through 448 removed outlier: 4.279A pdb=" N ASN G 440 " --> pdb=" O ASP G 436 " (cutoff:3.500A) Processing helix chain 'G' and resid 452 through 464 removed outlier: 3.925A pdb=" N ARG G 458 " --> pdb=" O TYR G 454 " (cutoff:3.500A) Processing helix chain 'G' and resid 469 through 488 removed outlier: 3.536A pdb=" N VAL G 473 " --> pdb=" O GLN G 469 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TRP G 478 " --> pdb=" O GLN G 474 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ASP G 485 " --> pdb=" O GLY G 481 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU G 486 " --> pdb=" O GLU G 482 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU G 487 " --> pdb=" O TYR G 483 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL G 488 " --> pdb=" O GLY G 484 " (cutoff:3.500A) Processing helix chain 'G' and resid 503 through 515 removed outlier: 3.715A pdb=" N LEU G 509 " --> pdb=" O VAL G 505 " (cutoff:3.500A) Processing helix chain 'G' and resid 521 through 533 Processing helix chain 'G' and resid 543 through 551 removed outlier: 3.732A pdb=" N VAL G 547 " --> pdb=" O ARG G 543 " (cutoff:3.500A) Processing helix chain 'G' and resid 556 through 573 removed outlier: 3.727A pdb=" N VAL G 564 " --> pdb=" O GLN G 560 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU G 569 " --> pdb=" O GLU G 565 " (cutoff:3.500A) Processing helix chain 'G' and resid 577 through 581 removed outlier: 3.543A pdb=" N LEU G 580 " --> pdb=" O ARG G 577 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU G 581 " --> pdb=" O SER G 578 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 577 through 581' Processing helix chain 'H' and resid 29 through 38 Processing helix chain 'H' and resid 74 through 81 removed outlier: 3.823A pdb=" N TRP H 78 " --> pdb=" O ARG H 75 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG H 79 " --> pdb=" O PRO H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 111 Processing helix chain 'H' and resid 135 through 144 removed outlier: 3.638A pdb=" N ILE H 139 " --> pdb=" O ASN H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 148 Processing helix chain 'H' and resid 165 through 176 Processing helix chain 'M' and resid 26 through 31 removed outlier: 3.819A pdb=" N VAL M 30 " --> pdb=" O MET M 27 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU M 31 " --> pdb=" O SER M 28 " (cutoff:3.500A) Processing helix chain 'M' and resid 32 through 42 removed outlier: 3.695A pdb=" N ILE M 36 " --> pdb=" O HIS M 32 " (cutoff:3.500A) Processing helix chain 'M' and resid 76 through 95 Processing helix chain 'M' and resid 99 through 104 removed outlier: 3.815A pdb=" N ILE M 103 " --> pdb=" O GLU M 99 " (cutoff:3.500A) Processing helix chain 'M' and resid 106 through 117 removed outlier: 3.848A pdb=" N TYR M 111 " --> pdb=" O PHE M 107 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLU M 112 " --> pdb=" O VAL M 108 " (cutoff:3.500A) Processing helix chain 'M' and resid 127 through 132 Processing helix chain 'M' and resid 150 through 155 removed outlier: 3.811A pdb=" N THR M 154 " --> pdb=" O PRO M 150 " (cutoff:3.500A) Processing helix chain 'M' and resid 216 through 224 Processing helix chain 'M' and resid 243 through 251 removed outlier: 3.570A pdb=" N ASP M 250 " --> pdb=" O ARG M 246 " (cutoff:3.500A) Processing helix chain 'S' and resid 24 through 40 removed outlier: 3.833A pdb=" N LYS S 29 " --> pdb=" O ASP S 25 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG S 33 " --> pdb=" O LYS S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 77 through 96 removed outlier: 3.702A pdb=" N LEU S 81 " --> pdb=" O GLU S 77 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE S 95 " --> pdb=" O LEU S 91 " (cutoff:3.500A) Processing helix chain 'S' and resid 100 through 105 Processing helix chain 'S' and resid 106 through 116 removed outlier: 3.568A pdb=" N PHE S 112 " --> pdb=" O GLU S 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 128 through 141 removed outlier: 4.102A pdb=" N VAL S 132 " --> pdb=" O LYS S 128 " (cutoff:3.500A) Processing helix chain 'N' and resid 14 through 23 Processing helix chain 'N' and resid 80 through 95 removed outlier: 3.593A pdb=" N GLY N 95 " --> pdb=" O LEU N 91 " (cutoff:3.500A) Processing helix chain 'N' and resid 103 through 119 removed outlier: 3.709A pdb=" N GLN N 107 " --> pdb=" O SER N 103 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY N 119 " --> pdb=" O TYR N 115 " (cutoff:3.500A) Processing helix chain 'N' and resid 193 through 199 Processing sheet with id=AA1, first strand: chain 'C' and resid 19 through 22 removed outlier: 3.895A pdb=" N TYR C 58 " --> pdb=" O ILE C 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 90 through 91 removed outlier: 6.997A pdb=" N PHE C 90 " --> pdb=" O PHE C 124 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 236 through 237 Processing sheet with id=AA4, first strand: chain 'H' and resid 18 through 22 removed outlier: 5.998A pdb=" N MET H 18 " --> pdb=" O THR H 64 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N TRP H 66 " --> pdb=" O MET H 18 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE H 20 " --> pdb=" O TRP H 66 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N VAL H 68 " --> pdb=" O ILE H 20 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N MET H 22 " --> pdb=" O VAL H 68 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL H 65 " --> pdb=" O GLU H 54 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU H 54 " --> pdb=" O VAL H 65 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 91 through 93 Processing sheet with id=AA6, first strand: chain 'M' and resid 17 through 20 removed outlier: 3.574A pdb=" N ILE M 17 " --> pdb=" O VAL M 8 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA M 5 " --> pdb=" O THR M 70 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET M 58 " --> pdb=" O ALA M 69 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'M' and resid 193 through 194 removed outlier: 6.843A pdb=" N ILE M 198 " --> pdb=" O LEU M 264 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE M 176 " --> pdb=" O SER M 197 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VAL M 175 " --> pdb=" O ILE M 412 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'M' and resid 235 through 238 removed outlier: 3.614A pdb=" N LYS M 237 " --> pdb=" O SER M 266 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE M 198 " --> pdb=" O LEU M 264 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL M 171 " --> pdb=" O TRP M 408 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'M' and resid 179 through 183 removed outlier: 7.081A pdb=" N VAL M 179 " --> pdb=" O GLY M 416 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TYR M 418 " --> pdb=" O VAL M 179 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU M 181 " --> pdb=" O TYR M 418 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N LEU M 420 " --> pdb=" O LEU M 181 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N VAL M 183 " --> pdb=" O LEU M 420 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'M' and resid 253 through 255 removed outlier: 3.710A pdb=" N ILE M 253 " --> pdb=" O LEU M 212 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY M 213 " --> pdb=" O TYR M 394 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR M 394 " --> pdb=" O GLY M 213 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 277 through 280 removed outlier: 3.621A pdb=" N ILE M 291 " --> pdb=" O PHE M 360 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ARG M 357 " --> pdb=" O PHE M 325 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N PHE M 325 " --> pdb=" O ARG M 357 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N HIS M 359 " --> pdb=" O PRO M 323 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP M 321 " --> pdb=" O GLY M 361 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 306 through 312 removed outlier: 6.969A pdb=" N THR M 306 " --> pdb=" O PRO M 349 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ASN M 308 " --> pdb=" O SER M 347 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N SER M 347 " --> pdb=" O ASN M 308 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS M 333 " --> pdb=" O VAL M 342 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 385 through 386 Processing sheet with id=AB6, first strand: chain 'S' and resid 4 through 5 Processing sheet with id=AB7, first strand: chain 'S' and resid 49 through 51 removed outlier: 3.827A pdb=" N ILE S 71 " --> pdb=" O LYS S 56 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'S' and resid 118 through 119 Processing sheet with id=AB9, first strand: chain 'N' and resid 101 through 102 removed outlier: 3.501A pdb=" N LEU N 181 " --> pdb=" O HIS N 102 " (cutoff:3.500A) 738 hydrogen bonds defined for protein. 2127 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.31 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 5201 1.33 - 1.45: 2779 1.45 - 1.57: 9851 1.57 - 1.69: 10 1.69 - 1.81: 166 Bond restraints: 18007 Sorted by residual: bond pdb=" C LEU G 176 " pdb=" N PRO G 177 " ideal model delta sigma weight residual 1.334 1.374 -0.040 8.40e-03 1.42e+04 2.26e+01 bond pdb=" CG1 ILE S 35 " pdb=" CD1 ILE S 35 " ideal model delta sigma weight residual 1.513 1.426 0.087 3.90e-02 6.57e+02 4.98e+00 bond pdb=" CB VAL M 77 " pdb=" CG2 VAL M 77 " ideal model delta sigma weight residual 1.521 1.449 0.072 3.30e-02 9.18e+02 4.71e+00 bond pdb=" CB VAL B 262 " pdb=" CG2 VAL B 262 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 4.06e+00 bond pdb=" CB VAL M 332 " pdb=" CG2 VAL M 332 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 3.96e+00 ... (remaining 18002 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 23253 2.19 - 4.38: 954 4.38 - 6.57: 116 6.57 - 8.76: 34 8.76 - 10.94: 11 Bond angle restraints: 24368 Sorted by residual: angle pdb=" N VAL B 47 " pdb=" CA VAL B 47 " pdb=" C VAL B 47 " ideal model delta sigma weight residual 111.91 106.87 5.04 8.90e-01 1.26e+00 3.20e+01 angle pdb=" C LYS H 59 " pdb=" N ASN H 60 " pdb=" CA ASN H 60 " ideal model delta sigma weight residual 121.54 130.83 -9.29 1.91e+00 2.74e-01 2.36e+01 angle pdb=" C ASN M 308 " pdb=" N ASN M 309 " pdb=" CA ASN M 309 " ideal model delta sigma weight residual 121.54 130.49 -8.95 1.91e+00 2.74e-01 2.20e+01 angle pdb=" N GLY N 130 " pdb=" CA GLY N 130 " pdb=" C GLY N 130 " ideal model delta sigma weight residual 112.34 121.54 -9.20 2.04e+00 2.40e-01 2.03e+01 angle pdb=" CA HIS L 166 " pdb=" C HIS L 166 " pdb=" N PRO L 167 " ideal model delta sigma weight residual 118.16 121.24 -3.08 7.00e-01 2.04e+00 1.94e+01 ... (remaining 24363 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.58: 10916 34.58 - 69.16: 70 69.16 - 103.74: 16 103.74 - 138.32: 3 138.32 - 172.91: 3 Dihedral angle restraints: 11008 sinusoidal: 4546 harmonic: 6462 Sorted by residual: dihedral pdb=" O5' GTP H1001 " pdb=" O3A GTP H1001 " pdb=" PA GTP H1001 " pdb=" PB GTP H1001 " ideal model delta sinusoidal sigma weight residual -85.88 87.03 -172.91 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O5' GTP C1001 " pdb=" O3A GTP C1001 " pdb=" PA GTP C1001 " pdb=" PB GTP C1001 " ideal model delta sinusoidal sigma weight residual 274.12 109.86 164.26 1 2.00e+01 2.50e-03 4.71e+01 dihedral pdb=" C8 GTP H1001 " pdb=" C1' GTP H1001 " pdb=" N9 GTP H1001 " pdb=" O4' GTP H1001 " ideal model delta sinusoidal sigma weight residual 104.59 -38.21 142.80 1 2.00e+01 2.50e-03 4.31e+01 ... (remaining 11005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1923 0.057 - 0.114: 716 0.114 - 0.171: 128 0.171 - 0.228: 17 0.228 - 0.285: 6 Chirality restraints: 2790 Sorted by residual: chirality pdb=" CA ASN M 309 " pdb=" N ASN M 309 " pdb=" C ASN M 309 " pdb=" CB ASN M 309 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CB VAL B 47 " pdb=" CA VAL B 47 " pdb=" CG1 VAL B 47 " pdb=" CG2 VAL B 47 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CG LEU B 197 " pdb=" CB LEU B 197 " pdb=" CD1 LEU B 197 " pdb=" CD2 LEU B 197 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 2787 not shown) Planarity restraints: 3085 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS L 166 " 0.057 5.00e-02 4.00e+02 8.59e-02 1.18e+01 pdb=" N PRO L 167 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO L 167 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO L 167 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG H 75 " 0.043 5.00e-02 4.00e+02 6.41e-02 6.58e+00 pdb=" N PRO H 76 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO H 76 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO H 76 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP M 343 " 0.018 2.00e-02 2.50e+03 1.60e-02 6.44e+00 pdb=" CG TRP M 343 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP M 343 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP M 343 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP M 343 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP M 343 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP M 343 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 343 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 343 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP M 343 " 0.002 2.00e-02 2.50e+03 ... (remaining 3082 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 85 2.51 - 3.10: 12070 3.10 - 3.70: 26825 3.70 - 4.30: 38369 4.30 - 4.90: 63750 Nonbonded interactions: 141099 Sorted by model distance: nonbonded pdb=" O2G GTP H1001 " pdb="MG MG H1002 " model vdw 1.906 2.170 nonbonded pdb=" O1G GTP C1001 " pdb="MG MG C1002 " model vdw 1.933 2.170 nonbonded pdb=" CG2 THR H 31 " pdb="MG MG H1002 " model vdw 2.015 2.590 nonbonded pdb=" O1B GTP C1001 " pdb="MG MG C1002 " model vdw 2.195 2.170 nonbonded pdb=" O2B GTP H1001 " pdb="MG MG H1002 " model vdw 2.209 2.170 ... (remaining 141094 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 17 through 179 or resid 1001 through 1002)) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 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: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.570 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.087 18007 Z= 0.358 Angle : 1.022 10.944 24368 Z= 0.539 Chirality : 0.059 0.285 2790 Planarity : 0.007 0.086 3085 Dihedral : 11.579 172.905 6810 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 0.26 % Allowed : 2.81 % Favored : 96.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.83 (0.14), residues: 2170 helix: -3.18 (0.10), residues: 1090 sheet: -4.03 (0.27), residues: 242 loop : -2.66 (0.19), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 251 TYR 0.034 0.003 TYR G 290 PHE 0.029 0.004 PHE M 95 TRP 0.043 0.004 TRP M 343 HIS 0.016 0.003 HIS G 235 Details of bonding type rmsd covalent geometry : bond 0.00880 (18007) covalent geometry : angle 1.02245 (24368) hydrogen bonds : bond 0.17489 ( 733) hydrogen bonds : angle 7.30258 ( 2127) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 561 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 155 LEU cc_start: 0.8426 (tp) cc_final: 0.8129 (tp) REVERT: B 204 ILE cc_start: 0.8980 (mt) cc_final: 0.8745 (mm) REVERT: B 212 ASN cc_start: 0.7890 (m-40) cc_final: 0.7624 (t0) REVERT: G 29 LYS cc_start: 0.8157 (ttmp) cc_final: 0.7900 (tttt) REVERT: G 183 LEU cc_start: 0.7994 (mm) cc_final: 0.7717 (mt) REVERT: G 201 MET cc_start: 0.7703 (mmm) cc_final: 0.7435 (mtp) REVERT: H 114 ASP cc_start: 0.7740 (t70) cc_final: 0.7384 (t0) REVERT: M 28 SER cc_start: 0.7237 (m) cc_final: 0.6634 (p) REVERT: M 58 MET cc_start: 0.8690 (mpp) cc_final: 0.8229 (mtt) REVERT: M 86 LYS cc_start: 0.8346 (tppp) cc_final: 0.7946 (mptt) REVERT: M 264 LEU cc_start: 0.8739 (tp) cc_final: 0.8532 (tp) REVERT: M 298 LYS cc_start: 0.8496 (ptpp) cc_final: 0.8216 (tttm) REVERT: M 324 LYS cc_start: 0.8430 (mttp) cc_final: 0.7761 (tttt) outliers start: 5 outliers final: 4 residues processed: 566 average time/residue: 0.1566 time to fit residues: 127.8687 Evaluate side-chains 328 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 324 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain G residue 527 LEU Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 378 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 1.9990 chunk 212 optimal weight: 9.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 GLN ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 ASN B 386 GLN C 86 GLN C 150 HIS C 180 GLN G 184 ASN G 218 GLN G 273 GLN G 452 HIS G 474 GLN H 101 ASN H 128 GLN M 63 ASN M 169 ASN M 239 HIS M 300 GLN M 313 HIS M 359 HIS M 414 GLN ** M 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 HIS S 74 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.166493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.139287 restraints weight = 23167.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.136937 restraints weight = 41495.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.138180 restraints weight = 37843.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.138829 restraints weight = 24885.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.139017 restraints weight = 20979.373| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18007 Z= 0.164 Angle : 0.666 9.661 24368 Z= 0.341 Chirality : 0.045 0.177 2790 Planarity : 0.005 0.067 3085 Dihedral : 9.920 168.783 2423 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.30 % Allowed : 10.98 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.20 (0.16), residues: 2170 helix: -1.60 (0.14), residues: 1097 sheet: -3.86 (0.28), residues: 235 loop : -2.07 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 211 TYR 0.016 0.002 TYR G 290 PHE 0.015 0.002 PHE N 68 TRP 0.022 0.002 TRP B 450 HIS 0.010 0.001 HIS N 116 Details of bonding type rmsd covalent geometry : bond 0.00380 (18007) covalent geometry : angle 0.66641 (24368) hydrogen bonds : bond 0.04072 ( 733) hydrogen bonds : angle 5.10820 ( 2127) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 375 time to evaluate : 0.735 Fit side-chains REVERT: B 58 MET cc_start: 0.8530 (ttp) cc_final: 0.8070 (ttp) REVERT: B 212 ASN cc_start: 0.8076 (m-40) cc_final: 0.7403 (t0) REVERT: C 79 ARG cc_start: 0.7529 (ptt-90) cc_final: 0.7324 (tmm-80) REVERT: G 123 LEU cc_start: 0.9077 (mt) cc_final: 0.8512 (mt) REVERT: G 183 LEU cc_start: 0.7997 (mm) cc_final: 0.7610 (mt) REVERT: G 201 MET cc_start: 0.7800 (mmm) cc_final: 0.7173 (mtp) REVERT: G 212 PHE cc_start: 0.7970 (m-10) cc_final: 0.7314 (m-10) REVERT: G 313 LEU cc_start: 0.8151 (mt) cc_final: 0.7879 (mt) REVERT: G 474 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8586 (mt0) REVERT: G 587 MET cc_start: 0.6076 (ptm) cc_final: 0.5806 (ptm) REVERT: M 10 ASP cc_start: 0.7132 (p0) cc_final: 0.6926 (p0) REVERT: M 58 MET cc_start: 0.8786 (mpp) cc_final: 0.8287 (mtt) REVERT: M 86 LYS cc_start: 0.8574 (tppp) cc_final: 0.7994 (mptt) REVERT: M 264 LEU cc_start: 0.9041 (tp) cc_final: 0.8787 (tp) REVERT: M 298 LYS cc_start: 0.8341 (ptpp) cc_final: 0.7992 (tttm) REVERT: M 324 LYS cc_start: 0.8451 (mttp) cc_final: 0.7649 (tttt) REVERT: S 13 LYS cc_start: 0.8607 (mmtm) cc_final: 0.8230 (tttt) REVERT: S 142 GLN cc_start: 0.6591 (pm20) cc_final: 0.5675 (pm20) REVERT: N 77 ARG cc_start: 0.6322 (ptt180) cc_final: 0.5247 (mtt90) outliers start: 45 outliers final: 27 residues processed: 405 average time/residue: 0.1517 time to fit residues: 91.2629 Evaluate side-chains 344 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 316 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 321 ASP Chi-restraints excluded: chain G residue 474 GLN Chi-restraints excluded: chain G residue 527 LEU Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 175 ASN Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 161 SER Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 310 VAL Chi-restraints excluded: chain M residue 322 SER Chi-restraints excluded: chain M residue 362 LEU Chi-restraints excluded: chain M residue 378 VAL Chi-restraints excluded: chain S residue 99 CYS Chi-restraints excluded: chain S residue 119 ILE Chi-restraints excluded: chain S residue 127 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 141 optimal weight: 8.9990 chunk 154 optimal weight: 0.7980 chunk 173 optimal weight: 6.9990 chunk 168 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 201 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 187 optimal weight: 0.9990 chunk 177 optimal weight: 3.9990 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 152 ASN B 348 GLN C 80 HIS C 180 GLN G 100 HIS ** G 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 474 GLN G 491 GLN H 128 GLN ** M 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 104 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.167214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.140871 restraints weight = 23266.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.140010 restraints weight = 37555.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.141128 restraints weight = 37491.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.140777 restraints weight = 24937.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.141430 restraints weight = 25014.163| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18007 Z= 0.141 Angle : 0.623 11.874 24368 Z= 0.311 Chirality : 0.043 0.189 2790 Planarity : 0.004 0.049 3085 Dihedral : 9.587 169.968 2423 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.40 % Allowed : 12.72 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.39 (0.17), residues: 2170 helix: -0.81 (0.15), residues: 1097 sheet: -3.72 (0.29), residues: 220 loop : -1.83 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 246 TYR 0.017 0.001 TYR M 403 PHE 0.017 0.001 PHE M 83 TRP 0.014 0.001 TRP B 450 HIS 0.005 0.001 HIS N 116 Details of bonding type rmsd covalent geometry : bond 0.00332 (18007) covalent geometry : angle 0.62303 (24368) hydrogen bonds : bond 0.03623 ( 733) hydrogen bonds : angle 4.63020 ( 2127) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 339 time to evaluate : 0.649 Fit side-chains REVERT: B 76 TYR cc_start: 0.7853 (m-80) cc_final: 0.7577 (m-80) REVERT: B 175 MET cc_start: 0.6687 (tpp) cc_final: 0.6429 (tpt) REVERT: B 212 ASN cc_start: 0.8197 (m-40) cc_final: 0.7349 (t0) REVERT: B 458 ARG cc_start: 0.6116 (mtm180) cc_final: 0.5822 (mtm180) REVERT: C 26 ASP cc_start: 0.7412 (p0) cc_final: 0.7104 (p0) REVERT: G 123 LEU cc_start: 0.9010 (mt) cc_final: 0.8734 (mt) REVERT: G 183 LEU cc_start: 0.7944 (mm) cc_final: 0.7588 (mt) REVERT: G 201 MET cc_start: 0.7751 (mmm) cc_final: 0.7401 (mtp) REVERT: G 321 ASP cc_start: 0.6402 (OUTLIER) cc_final: 0.6105 (m-30) REVERT: G 474 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.8559 (mt0) REVERT: H 49 ILE cc_start: 0.9082 (mm) cc_final: 0.8779 (mp) REVERT: M 10 ASP cc_start: 0.7070 (p0) cc_final: 0.6752 (p0) REVERT: M 58 MET cc_start: 0.8642 (mpp) cc_final: 0.8269 (mtt) REVERT: M 86 LYS cc_start: 0.8589 (tppp) cc_final: 0.7940 (mptt) REVERT: M 264 LEU cc_start: 0.9012 (tp) cc_final: 0.8803 (tp) REVERT: M 298 LYS cc_start: 0.8408 (ptpp) cc_final: 0.8005 (tttm) REVERT: M 324 LYS cc_start: 0.8341 (mttp) cc_final: 0.7558 (tttt) REVERT: S 23 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8623 (pt) REVERT: S 30 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8193 (mppt) REVERT: S 77 GLU cc_start: 0.7336 (mt-10) cc_final: 0.6882 (mp0) REVERT: S 142 GLN cc_start: 0.6631 (pm20) cc_final: 0.5639 (pm20) REVERT: N 77 ARG cc_start: 0.6416 (ptt180) cc_final: 0.5332 (mtt90) outliers start: 47 outliers final: 30 residues processed: 372 average time/residue: 0.1492 time to fit residues: 83.1821 Evaluate side-chains 335 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 301 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain G residue 160 CYS Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 321 ASP Chi-restraints excluded: chain G residue 392 CYS Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 474 GLN Chi-restraints excluded: chain G residue 502 GLU Chi-restraints excluded: chain G residue 527 LEU Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 175 ASN Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 127 ASP Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 310 VAL Chi-restraints excluded: chain M residue 362 LEU Chi-restraints excluded: chain M residue 378 VAL Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 30 LYS Chi-restraints excluded: chain S residue 99 CYS Chi-restraints excluded: chain S residue 119 ILE Chi-restraints excluded: chain S residue 127 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 68 optimal weight: 20.0000 chunk 11 optimal weight: 0.9980 chunk 124 optimal weight: 0.0670 chunk 85 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 123 optimal weight: 10.0000 chunk 80 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 186 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 192 optimal weight: 3.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 166 HIS ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 GLN ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 180 GLN ** G 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 474 GLN H 128 GLN M 64 ASN ** M 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 74 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.169176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.142517 restraints weight = 23017.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.140635 restraints weight = 35369.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.141983 restraints weight = 35279.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.142309 restraints weight = 23700.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.142444 restraints weight = 26896.748| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18007 Z= 0.115 Angle : 0.593 13.160 24368 Z= 0.292 Chirality : 0.042 0.165 2790 Planarity : 0.004 0.042 3085 Dihedral : 9.341 169.182 2423 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.55 % Allowed : 13.84 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.18), residues: 2170 helix: -0.29 (0.16), residues: 1078 sheet: -3.55 (0.30), residues: 222 loop : -1.55 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 246 TYR 0.014 0.001 TYR G 61 PHE 0.017 0.001 PHE M 83 TRP 0.011 0.001 TRP B 450 HIS 0.006 0.001 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.00267 (18007) covalent geometry : angle 0.59299 (24368) hydrogen bonds : bond 0.03281 ( 733) hydrogen bonds : angle 4.31610 ( 2127) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 337 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 76 TYR cc_start: 0.7817 (m-80) cc_final: 0.7540 (m-80) REVERT: B 175 MET cc_start: 0.6677 (tpp) cc_final: 0.6446 (tpt) REVERT: B 212 ASN cc_start: 0.8193 (m-40) cc_final: 0.7654 (t0) REVERT: C 26 ASP cc_start: 0.7494 (p0) cc_final: 0.7222 (p0) REVERT: G 201 MET cc_start: 0.7756 (mmm) cc_final: 0.7248 (mtp) REVERT: G 427 THR cc_start: 0.7481 (p) cc_final: 0.7182 (t) REVERT: G 483 TYR cc_start: 0.7772 (m-80) cc_final: 0.7567 (m-80) REVERT: H 46 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7496 (mt) REVERT: H 49 ILE cc_start: 0.9135 (mm) cc_final: 0.8881 (mp) REVERT: M 10 ASP cc_start: 0.6924 (p0) cc_final: 0.6684 (p0) REVERT: M 58 MET cc_start: 0.8598 (mpp) cc_final: 0.8281 (mtt) REVERT: M 86 LYS cc_start: 0.8606 (tppp) cc_final: 0.7895 (mptt) REVERT: M 98 LEU cc_start: 0.8405 (tp) cc_final: 0.8187 (tp) REVERT: M 264 LEU cc_start: 0.9061 (tp) cc_final: 0.8808 (tp) REVERT: M 298 LYS cc_start: 0.8357 (ptpp) cc_final: 0.7898 (ttpp) REVERT: M 324 LYS cc_start: 0.8390 (mttp) cc_final: 0.7577 (tttt) REVERT: S 15 ARG cc_start: 0.8252 (mpt-90) cc_final: 0.7964 (mmt-90) REVERT: S 30 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.8118 (mppt) REVERT: N 77 ARG cc_start: 0.6330 (ptt180) cc_final: 0.5163 (mtt90) outliers start: 50 outliers final: 33 residues processed: 368 average time/residue: 0.1503 time to fit residues: 82.8049 Evaluate side-chains 345 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 310 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 268 GLU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 505 GLN Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain G residue 160 CYS Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain G residue 392 CYS Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 474 GLN Chi-restraints excluded: chain G residue 502 GLU Chi-restraints excluded: chain G residue 527 LEU Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 127 ASP Chi-restraints excluded: chain M residue 161 SER Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 310 VAL Chi-restraints excluded: chain M residue 362 LEU Chi-restraints excluded: chain M residue 378 VAL Chi-restraints excluded: chain S residue 30 LYS Chi-restraints excluded: chain S residue 99 CYS Chi-restraints excluded: chain S residue 119 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 47 optimal weight: 0.9990 chunk 212 optimal weight: 8.9990 chunk 205 optimal weight: 7.9990 chunk 92 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 115 optimal weight: 7.9990 chunk 121 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 114 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 ASN ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 ASN ** G 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 474 GLN M 63 ASN M 64 ASN ** M 415 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 = 0.3870 r_free = 0.3870 target = 0.167013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.139240 restraints weight = 23144.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.138178 restraints weight = 38121.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.139058 restraints weight = 35618.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.139907 restraints weight = 23475.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.140130 restraints weight = 22346.663| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18007 Z= 0.139 Angle : 0.598 12.987 24368 Z= 0.294 Chirality : 0.043 0.161 2790 Planarity : 0.004 0.043 3085 Dihedral : 9.243 170.252 2423 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.96 % Allowed : 14.25 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.18), residues: 2170 helix: -0.11 (0.16), residues: 1089 sheet: -3.57 (0.29), residues: 236 loop : -1.34 (0.22), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG M 246 TYR 0.015 0.001 TYR M 267 PHE 0.016 0.001 PHE M 83 TRP 0.010 0.001 TRP B 450 HIS 0.005 0.001 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.00332 (18007) covalent geometry : angle 0.59807 (24368) hydrogen bonds : bond 0.03271 ( 733) hydrogen bonds : angle 4.23806 ( 2127) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 319 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 76 TYR cc_start: 0.7843 (m-80) cc_final: 0.7633 (m-80) REVERT: B 175 MET cc_start: 0.6734 (tpp) cc_final: 0.6465 (tpt) REVERT: B 212 ASN cc_start: 0.8184 (m-40) cc_final: 0.7693 (t0) REVERT: G 23 GLU cc_start: 0.8573 (tm-30) cc_final: 0.8262 (tm-30) REVERT: G 94 ASP cc_start: 0.7113 (OUTLIER) cc_final: 0.6485 (p0) REVERT: G 201 MET cc_start: 0.7785 (mmm) cc_final: 0.7352 (mtp) REVERT: G 212 PHE cc_start: 0.7589 (m-80) cc_final: 0.7367 (m-80) REVERT: G 483 TYR cc_start: 0.7795 (m-80) cc_final: 0.7586 (m-80) REVERT: H 46 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7417 (mt) REVERT: M 10 ASP cc_start: 0.6936 (p0) cc_final: 0.6669 (p0) REVERT: M 58 MET cc_start: 0.8582 (mpp) cc_final: 0.8253 (mtt) REVERT: M 86 LYS cc_start: 0.8629 (tppp) cc_final: 0.7931 (mptt) REVERT: M 98 LEU cc_start: 0.8386 (tp) cc_final: 0.8148 (tp) REVERT: M 264 LEU cc_start: 0.9069 (tp) cc_final: 0.8837 (tp) REVERT: M 298 LYS cc_start: 0.8357 (ptpp) cc_final: 0.7897 (ttpp) REVERT: S 30 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8187 (mppt) REVERT: N 77 ARG cc_start: 0.6324 (ptt180) cc_final: 0.5160 (mtt90) outliers start: 58 outliers final: 41 residues processed: 358 average time/residue: 0.1574 time to fit residues: 83.9503 Evaluate side-chains 334 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 290 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 268 GLU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 505 GLN Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 160 CYS Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 321 ASP Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain G residue 381 MET Chi-restraints excluded: chain G residue 392 CYS Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 502 GLU Chi-restraints excluded: chain G residue 506 LEU Chi-restraints excluded: chain G residue 527 LEU Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 175 ASN Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 127 ASP Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 310 VAL Chi-restraints excluded: chain M residue 378 VAL Chi-restraints excluded: chain S residue 30 LYS Chi-restraints excluded: chain S residue 99 CYS Chi-restraints excluded: chain S residue 119 ILE Chi-restraints excluded: chain S residue 127 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 143 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 193 optimal weight: 1.9990 chunk 74 optimal weight: 20.0000 chunk 34 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 ASN G 273 GLN G 443 GLN H 128 GLN M 64 ASN ** M 415 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 = 0.3882 r_free = 0.3882 target = 0.167873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.133847 restraints weight = 23509.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.132506 restraints weight = 25912.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.133782 restraints weight = 29922.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.134426 restraints weight = 17999.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.134712 restraints weight = 16040.066| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 18007 Z= 0.189 Angle : 0.635 13.063 24368 Z= 0.314 Chirality : 0.044 0.165 2790 Planarity : 0.004 0.058 3085 Dihedral : 9.281 173.142 2423 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.83 % Allowed : 14.35 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.18), residues: 2170 helix: -0.12 (0.16), residues: 1099 sheet: -3.55 (0.29), residues: 235 loop : -1.29 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 243 TYR 0.016 0.002 TYR G 290 PHE 0.015 0.002 PHE G 79 TRP 0.011 0.001 TRP B 450 HIS 0.005 0.001 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.00458 (18007) covalent geometry : angle 0.63451 (24368) hydrogen bonds : bond 0.03440 ( 733) hydrogen bonds : angle 4.29914 ( 2127) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 301 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 76 TYR cc_start: 0.7933 (m-80) cc_final: 0.7728 (m-80) REVERT: B 175 MET cc_start: 0.6852 (tpp) cc_final: 0.6612 (tpt) REVERT: B 212 ASN cc_start: 0.8286 (m-40) cc_final: 0.7417 (t0) REVERT: G 94 ASP cc_start: 0.7184 (OUTLIER) cc_final: 0.6521 (p0) REVERT: G 123 LEU cc_start: 0.8920 (mt) cc_final: 0.8689 (mt) REVERT: G 201 MET cc_start: 0.7943 (mmm) cc_final: 0.7630 (mtp) REVERT: G 427 THR cc_start: 0.7470 (p) cc_final: 0.7196 (t) REVERT: G 483 TYR cc_start: 0.7876 (m-80) cc_final: 0.7596 (m-80) REVERT: H 46 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7528 (mt) REVERT: M 10 ASP cc_start: 0.7182 (p0) cc_final: 0.6959 (p0) REVERT: M 58 MET cc_start: 0.8659 (mpp) cc_final: 0.8284 (mtt) REVERT: M 86 LYS cc_start: 0.8668 (tppp) cc_final: 0.8046 (mptt) REVERT: M 298 LYS cc_start: 0.8408 (ptpp) cc_final: 0.7915 (ttpp) REVERT: S 30 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8101 (tptt) REVERT: S 42 ARG cc_start: 0.8066 (ttm-80) cc_final: 0.7859 (ttm-80) REVERT: N 77 ARG cc_start: 0.6212 (ptt180) cc_final: 0.4984 (mtt90) outliers start: 75 outliers final: 55 residues processed: 354 average time/residue: 0.1552 time to fit residues: 82.4275 Evaluate side-chains 346 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 288 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 162 THR Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 268 GLU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 505 GLN Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 160 CYS Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 174 MET Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 321 ASP Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain G residue 381 MET Chi-restraints excluded: chain G residue 392 CYS Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain G residue 443 GLN Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 502 GLU Chi-restraints excluded: chain G residue 506 LEU Chi-restraints excluded: chain G residue 527 LEU Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 175 ASN Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 95 PHE Chi-restraints excluded: chain M residue 127 ASP Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 271 THR Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 310 VAL Chi-restraints excluded: chain M residue 378 VAL Chi-restraints excluded: chain S residue 30 LYS Chi-restraints excluded: chain S residue 71 ILE Chi-restraints excluded: chain S residue 99 CYS Chi-restraints excluded: chain S residue 119 ILE Chi-restraints excluded: chain S residue 127 SER Chi-restraints excluded: chain S residue 138 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 100 optimal weight: 9.9990 chunk 140 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 174 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 204 optimal weight: 6.9990 chunk 1 optimal weight: 0.0770 chunk 128 optimal weight: 0.0870 chunk 139 optimal weight: 0.9980 chunk 207 optimal weight: 1.9990 chunk 190 optimal weight: 0.9990 overall best weight: 0.5916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 105 ASN ** M 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.172180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.138063 restraints weight = 23471.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.136634 restraints weight = 24650.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.138135 restraints weight = 28093.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.138624 restraints weight = 18144.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.138978 restraints weight = 16230.696| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18007 Z= 0.111 Angle : 0.588 13.272 24368 Z= 0.287 Chirality : 0.042 0.153 2790 Planarity : 0.004 0.043 3085 Dihedral : 9.108 172.792 2423 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.91 % Allowed : 15.83 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.18), residues: 2170 helix: 0.19 (0.16), residues: 1096 sheet: -3.42 (0.29), residues: 242 loop : -1.11 (0.23), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 246 TYR 0.023 0.001 TYR M 403 PHE 0.016 0.001 PHE M 83 TRP 0.009 0.001 TRP B 450 HIS 0.004 0.001 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.00257 (18007) covalent geometry : angle 0.58758 (24368) hydrogen bonds : bond 0.03158 ( 733) hydrogen bonds : angle 4.11982 ( 2127) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 318 time to evaluate : 0.739 Fit side-chains REVERT: B 76 TYR cc_start: 0.7746 (m-80) cc_final: 0.7513 (m-80) REVERT: B 83 MET cc_start: 0.7434 (mtp) cc_final: 0.7034 (mtp) REVERT: B 175 MET cc_start: 0.6764 (tpp) cc_final: 0.6516 (tpt) REVERT: B 212 ASN cc_start: 0.8255 (m-40) cc_final: 0.7358 (t0) REVERT: C 18 MET cc_start: 0.4979 (mmt) cc_final: 0.4734 (tpt) REVERT: G 23 GLU cc_start: 0.8610 (tm-30) cc_final: 0.8332 (tm-30) REVERT: G 94 ASP cc_start: 0.7212 (OUTLIER) cc_final: 0.6666 (p0) REVERT: G 201 MET cc_start: 0.7892 (mmm) cc_final: 0.7601 (mtp) REVERT: G 427 THR cc_start: 0.7437 (p) cc_final: 0.7126 (t) REVERT: G 483 TYR cc_start: 0.7854 (m-80) cc_final: 0.7546 (m-80) REVERT: H 97 ARG cc_start: 0.7056 (ttm110) cc_final: 0.6644 (ttm-80) REVERT: M 10 ASP cc_start: 0.6998 (p0) cc_final: 0.6753 (p0) REVERT: M 58 MET cc_start: 0.8486 (mpp) cc_final: 0.8254 (mtt) REVERT: M 86 LYS cc_start: 0.8533 (tppp) cc_final: 0.7895 (mptt) REVERT: M 264 LEU cc_start: 0.9079 (tp) cc_final: 0.8850 (tp) REVERT: M 298 LYS cc_start: 0.8425 (ptpp) cc_final: 0.7903 (ttpp) REVERT: S 30 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8204 (mppt) REVERT: S 133 LYS cc_start: 0.8955 (tmtt) cc_final: 0.8753 (tmtt) REVERT: N 77 ARG cc_start: 0.6236 (ptt180) cc_final: 0.4987 (mtt90) REVERT: N 79 MET cc_start: 0.6063 (tpp) cc_final: 0.5774 (mmm) outliers start: 57 outliers final: 39 residues processed: 354 average time/residue: 0.1525 time to fit residues: 80.3083 Evaluate side-chains 336 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 295 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 268 GLU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 505 GLN Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 160 CYS Chi-restraints excluded: chain G residue 174 MET Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain G residue 381 MET Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 527 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 175 ASN Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 127 ASP Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 310 VAL Chi-restraints excluded: chain M residue 378 VAL Chi-restraints excluded: chain S residue 30 LYS Chi-restraints excluded: chain S residue 99 CYS Chi-restraints excluded: chain S residue 119 ILE Chi-restraints excluded: chain S residue 127 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 120 optimal weight: 5.9990 chunk 215 optimal weight: 10.0000 chunk 106 optimal weight: 0.7980 chunk 201 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 138 optimal weight: 0.1980 chunk 135 optimal weight: 8.9990 chunk 41 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.171651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.137996 restraints weight = 23370.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.136328 restraints weight = 28805.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.138237 restraints weight = 28139.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.138656 restraints weight = 17779.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.139107 restraints weight = 16678.922| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18007 Z= 0.128 Angle : 0.599 11.355 24368 Z= 0.295 Chirality : 0.043 0.187 2790 Planarity : 0.004 0.042 3085 Dihedral : 9.031 171.901 2423 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.32 % Allowed : 16.19 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.18), residues: 2170 helix: 0.29 (0.16), residues: 1094 sheet: -3.39 (0.29), residues: 253 loop : -1.00 (0.23), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 246 TYR 0.018 0.001 TYR M 403 PHE 0.014 0.001 PHE M 83 TRP 0.009 0.001 TRP B 450 HIS 0.003 0.001 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.00306 (18007) covalent geometry : angle 0.59942 (24368) hydrogen bonds : bond 0.03205 ( 733) hydrogen bonds : angle 4.09837 ( 2127) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 313 time to evaluate : 0.704 Fit side-chains REVERT: B 76 TYR cc_start: 0.7729 (m-80) cc_final: 0.7518 (m-80) REVERT: B 175 MET cc_start: 0.6721 (tpp) cc_final: 0.6507 (tpt) REVERT: B 212 ASN cc_start: 0.8274 (m-40) cc_final: 0.7380 (t0) REVERT: G 94 ASP cc_start: 0.7130 (OUTLIER) cc_final: 0.6499 (p0) REVERT: G 427 THR cc_start: 0.7558 (p) cc_final: 0.7304 (t) REVERT: G 483 TYR cc_start: 0.7913 (m-80) cc_final: 0.7606 (m-80) REVERT: G 560 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.7792 (tm130) REVERT: H 97 ARG cc_start: 0.7161 (ttm110) cc_final: 0.6758 (ttm-80) REVERT: M 10 ASP cc_start: 0.6974 (p0) cc_final: 0.6678 (p0) REVERT: M 58 MET cc_start: 0.8413 (mpp) cc_final: 0.8130 (mtt) REVERT: M 86 LYS cc_start: 0.8531 (tppp) cc_final: 0.7844 (mptt) REVERT: M 264 LEU cc_start: 0.9110 (tp) cc_final: 0.8909 (tp) REVERT: M 283 ILE cc_start: 0.8772 (mt) cc_final: 0.7998 (pt) REVERT: M 298 LYS cc_start: 0.8441 (ptpp) cc_final: 0.7920 (ttpp) REVERT: S 30 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8047 (tptt) REVERT: N 77 ARG cc_start: 0.6177 (ptt180) cc_final: 0.4978 (mtt90) outliers start: 65 outliers final: 42 residues processed: 360 average time/residue: 0.1544 time to fit residues: 83.0905 Evaluate side-chains 339 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 294 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 505 GLN Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 160 CYS Chi-restraints excluded: chain G residue 174 MET Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 321 ASP Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain G residue 381 MET Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 506 LEU Chi-restraints excluded: chain G residue 527 LEU Chi-restraints excluded: chain G residue 560 GLN Chi-restraints excluded: chain H residue 18 MET Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 175 ASN Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 127 ASP Chi-restraints excluded: chain M residue 271 THR Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 310 VAL Chi-restraints excluded: chain M residue 378 VAL Chi-restraints excluded: chain S residue 30 LYS Chi-restraints excluded: chain S residue 99 CYS Chi-restraints excluded: chain S residue 119 ILE Chi-restraints excluded: chain S residue 127 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 70 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 138 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 186 optimal weight: 0.5980 chunk 124 optimal weight: 0.0040 chunk 155 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS G 112 ASN ** M 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.173266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.139296 restraints weight = 23352.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.137639 restraints weight = 27823.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.139458 restraints weight = 26477.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.139939 restraints weight = 17747.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.140216 restraints weight = 16469.252| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18007 Z= 0.117 Angle : 0.614 9.976 24368 Z= 0.299 Chirality : 0.043 0.256 2790 Planarity : 0.004 0.043 3085 Dihedral : 8.944 172.463 2423 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.40 % Allowed : 16.45 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.19), residues: 2170 helix: 0.40 (0.16), residues: 1100 sheet: -3.34 (0.29), residues: 254 loop : -0.98 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 246 TYR 0.018 0.001 TYR B 566 PHE 0.013 0.001 PHE M 107 TRP 0.008 0.001 TRP B 450 HIS 0.003 0.000 HIS M 62 Details of bonding type rmsd covalent geometry : bond 0.00277 (18007) covalent geometry : angle 0.61386 (24368) hydrogen bonds : bond 0.03125 ( 733) hydrogen bonds : angle 4.05721 ( 2127) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 307 time to evaluate : 0.751 Fit side-chains REVERT: B 76 TYR cc_start: 0.7642 (m-80) cc_final: 0.7425 (m-80) REVERT: B 175 MET cc_start: 0.6726 (tpp) cc_final: 0.6461 (tpt) REVERT: B 212 ASN cc_start: 0.8276 (m-40) cc_final: 0.7358 (t0) REVERT: G 23 GLU cc_start: 0.8482 (tm-30) cc_final: 0.8217 (tm-30) REVERT: G 24 ARG cc_start: 0.8316 (ttp-110) cc_final: 0.8074 (ttp-110) REVERT: G 94 ASP cc_start: 0.7035 (OUTLIER) cc_final: 0.6504 (p0) REVERT: G 101 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8145 (mt) REVERT: G 427 THR cc_start: 0.7434 (p) cc_final: 0.7077 (t) REVERT: G 483 TYR cc_start: 0.7894 (m-80) cc_final: 0.7600 (m-80) REVERT: G 560 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7788 (tm130) REVERT: H 97 ARG cc_start: 0.7190 (ttm110) cc_final: 0.6802 (ttm-80) REVERT: M 58 MET cc_start: 0.8373 (mpp) cc_final: 0.8154 (mtt) REVERT: M 86 LYS cc_start: 0.8467 (tppp) cc_final: 0.7811 (mptt) REVERT: M 207 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7779 (mmt) REVERT: M 264 LEU cc_start: 0.9098 (tp) cc_final: 0.8881 (tp) REVERT: M 283 ILE cc_start: 0.8679 (mt) cc_final: 0.7892 (pt) REVERT: M 298 LYS cc_start: 0.8412 (ptpp) cc_final: 0.7894 (ttpp) REVERT: S 15 ARG cc_start: 0.8252 (mpt-90) cc_final: 0.7983 (mtt-85) REVERT: S 30 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8001 (tptt) outliers start: 47 outliers final: 37 residues processed: 337 average time/residue: 0.1472 time to fit residues: 74.9708 Evaluate side-chains 328 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 286 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 505 GLN Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 160 CYS Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 321 ASP Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain G residue 381 MET Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 506 LEU Chi-restraints excluded: chain G residue 522 THR Chi-restraints excluded: chain G residue 527 LEU Chi-restraints excluded: chain G residue 560 GLN Chi-restraints excluded: chain H residue 18 MET Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 175 ASN Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 127 ASP Chi-restraints excluded: chain M residue 207 MET Chi-restraints excluded: chain M residue 271 THR Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 310 VAL Chi-restraints excluded: chain M residue 378 VAL Chi-restraints excluded: chain S residue 30 LYS Chi-restraints excluded: chain S residue 99 CYS Chi-restraints excluded: chain S residue 119 ILE Chi-restraints excluded: chain S residue 127 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 210 optimal weight: 9.9990 chunk 48 optimal weight: 0.8980 chunk 189 optimal weight: 0.7980 chunk 181 optimal weight: 2.9990 chunk 184 optimal weight: 0.0570 chunk 35 optimal weight: 0.9990 chunk 157 optimal weight: 0.6980 chunk 204 optimal weight: 10.0000 chunk 127 optimal weight: 3.9990 chunk 118 optimal weight: 0.0370 chunk 14 optimal weight: 0.6980 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN ** M 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 11 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.174973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.140244 restraints weight = 23396.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.138498 restraints weight = 27202.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.140606 restraints weight = 27744.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.140913 restraints weight = 18110.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.141456 restraints weight = 16412.263| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18007 Z= 0.110 Angle : 0.610 12.551 24368 Z= 0.298 Chirality : 0.043 0.253 2790 Planarity : 0.004 0.044 3085 Dihedral : 8.857 173.118 2423 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.30 % Allowed : 17.21 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.19), residues: 2170 helix: 0.51 (0.16), residues: 1108 sheet: -3.23 (0.29), residues: 244 loop : -0.95 (0.23), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 246 TYR 0.019 0.001 TYR G 566 PHE 0.013 0.001 PHE M 107 TRP 0.008 0.001 TRP B 450 HIS 0.002 0.000 HIS B 575 Details of bonding type rmsd covalent geometry : bond 0.00258 (18007) covalent geometry : angle 0.61035 (24368) hydrogen bonds : bond 0.03042 ( 733) hydrogen bonds : angle 4.02170 ( 2127) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 304 time to evaluate : 0.700 Fit side-chains revert: symmetry clash REVERT: L 160 GLU cc_start: 0.6948 (mt-10) cc_final: 0.6727 (tt0) REVERT: B 76 TYR cc_start: 0.7619 (m-80) cc_final: 0.7394 (m-80) REVERT: B 175 MET cc_start: 0.6673 (tpp) cc_final: 0.6444 (tpt) REVERT: B 212 ASN cc_start: 0.8332 (m-40) cc_final: 0.7375 (t0) REVERT: B 329 ASN cc_start: 0.8491 (p0) cc_final: 0.7951 (m-40) REVERT: G 94 ASP cc_start: 0.7005 (OUTLIER) cc_final: 0.6492 (p0) REVERT: G 101 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8093 (mt) REVERT: G 427 THR cc_start: 0.7364 (p) cc_final: 0.6948 (t) REVERT: G 483 TYR cc_start: 0.7905 (m-80) cc_final: 0.7612 (m-80) REVERT: G 560 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.7643 (tm130) REVERT: H 97 ARG cc_start: 0.6982 (ttm110) cc_final: 0.6637 (ttm-80) REVERT: H 162 SER cc_start: 0.8679 (m) cc_final: 0.8280 (t) REVERT: H 172 TRP cc_start: 0.8327 (t60) cc_final: 0.8026 (t-100) REVERT: M 58 MET cc_start: 0.8319 (mpp) cc_final: 0.8114 (mtt) REVERT: M 86 LYS cc_start: 0.8458 (tppp) cc_final: 0.7794 (mptt) REVERT: M 207 MET cc_start: 0.8027 (tpp) cc_final: 0.7694 (mmt) REVERT: M 264 LEU cc_start: 0.9094 (tp) cc_final: 0.8891 (tp) REVERT: M 283 ILE cc_start: 0.8623 (mt) cc_final: 0.7846 (pt) REVERT: M 298 LYS cc_start: 0.8420 (ptpp) cc_final: 0.7913 (ttpp) REVERT: S 15 ARG cc_start: 0.8196 (mpt-90) cc_final: 0.7935 (mtt-85) REVERT: S 30 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.7997 (tptt) outliers start: 45 outliers final: 33 residues processed: 336 average time/residue: 0.1490 time to fit residues: 75.2199 Evaluate side-chains 321 residues out of total 1959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 284 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 505 GLN Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 160 CYS Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 321 ASP Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain G residue 381 MET Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain G residue 522 THR Chi-restraints excluded: chain G residue 527 LEU Chi-restraints excluded: chain G residue 560 GLN Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 271 THR Chi-restraints excluded: chain M residue 286 HIS Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 310 VAL Chi-restraints excluded: chain M residue 378 VAL Chi-restraints excluded: chain S residue 30 LYS Chi-restraints excluded: chain S residue 99 CYS Chi-restraints excluded: chain S residue 119 ILE Chi-restraints excluded: chain S residue 127 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 70 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 211 optimal weight: 8.9990 chunk 148 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 28 optimal weight: 0.6980 chunk 194 optimal weight: 0.9980 chunk 157 optimal weight: 0.7980 chunk 111 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 128 GLN ** M 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 11 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.174236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.140787 restraints weight = 23370.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.139366 restraints weight = 26054.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.140948 restraints weight = 29514.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.141449 restraints weight = 18098.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.141964 restraints weight = 16365.786| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18007 Z= 0.123 Angle : 0.627 11.573 24368 Z= 0.302 Chirality : 0.043 0.202 2790 Planarity : 0.004 0.044 3085 Dihedral : 8.852 174.056 2423 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.04 % Allowed : 17.98 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.19), residues: 2170 helix: 0.55 (0.16), residues: 1101 sheet: -3.16 (0.29), residues: 250 loop : -0.92 (0.23), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 458 TYR 0.028 0.001 TYR G 566 PHE 0.015 0.001 PHE M 107 TRP 0.009 0.001 TRP B 450 HIS 0.003 0.001 HIS G 235 Details of bonding type rmsd covalent geometry : bond 0.00295 (18007) covalent geometry : angle 0.62725 (24368) hydrogen bonds : bond 0.03082 ( 733) hydrogen bonds : angle 4.04488 ( 2127) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3010.16 seconds wall clock time: 52 minutes 53.54 seconds (3173.54 seconds total)