Starting phenix.real_space_refine on Wed Sep 17 13:47:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fuq_50774/09_2025/9fuq_50774.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fuq_50774/09_2025/9fuq_50774.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fuq_50774/09_2025/9fuq_50774.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fuq_50774/09_2025/9fuq_50774.map" model { file = "/net/cci-nas-00/data/ceres_data/9fuq_50774/09_2025/9fuq_50774.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fuq_50774/09_2025/9fuq_50774.cif" } resolution = 3.8 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= 0.000 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 54 5.16 5 C 5672 2.51 5 N 1538 2.21 5 O 1658 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8924 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4411 Classifications: {'peptide': 569} Link IDs: {'PTRANS': 13, 'TRANS': 555} Chain: "B" Number of atoms: 4411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4411 Classifications: {'peptide': 569} Link IDs: {'PTRANS': 13, 'TRANS': 555} Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.49, per 1000 atoms: 0.28 Number of scatterers: 8924 At special positions: 0 Unit cell: (115.6, 104.72, 138.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 54 16.00 P 2 15.00 O 1658 8.00 N 1538 7.00 C 5672 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: 0.99 Conformation dependent library (CDL) restraints added in 432.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2128 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 7 sheets defined 51.6% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 16 through 21 removed outlier: 3.502A pdb=" N ILE A 20 " --> pdb=" O LEU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 24 No H-bonds generated for 'chain 'A' and resid 22 through 24' Processing helix chain 'A' and resid 31 through 36 removed outlier: 3.504A pdb=" N ILE A 35 " --> pdb=" O GLY A 31 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU A 36 " --> pdb=" O VAL A 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 31 through 36' Processing helix chain 'A' and resid 41 through 46 removed outlier: 3.768A pdb=" N SER A 46 " --> pdb=" O THR A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 53 Processing helix chain 'A' and resid 67 through 84 removed outlier: 3.539A pdb=" N LEU A 77 " --> pdb=" O GLY A 73 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER A 82 " --> pdb=" O ARG A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 106 through 111 removed outlier: 5.154A pdb=" N MET A 109 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N MET A 111 " --> pdb=" O MET A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 117 removed outlier: 4.162A pdb=" N PHE A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP A 117 " --> pdb=" O VAL A 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 112 through 117' Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 133 through 138 removed outlier: 3.564A pdb=" N SER A 138 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 164 removed outlier: 3.627A pdb=" N TYR A 163 " --> pdb=" O MET A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 169 Processing helix chain 'A' and resid 170 through 172 No H-bonds generated for 'chain 'A' and resid 170 through 172' Processing helix chain 'A' and resid 173 through 182 removed outlier: 4.015A pdb=" N ILE A 177 " --> pdb=" O VAL A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 189 removed outlier: 3.732A pdb=" N ARG A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 212 removed outlier: 3.665A pdb=" N GLN A 197 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN A 198 " --> pdb=" O LYS A 194 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR A 199 " --> pdb=" O ASN A 195 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN A 202 " --> pdb=" O ASN A 198 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL A 203 " --> pdb=" O THR A 199 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SER A 206 " --> pdb=" O GLN A 202 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N MET A 210 " --> pdb=" O SER A 206 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS A 212 " --> pdb=" O GLU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 220 removed outlier: 3.705A pdb=" N PHE A 220 " --> pdb=" O GLU A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 234 removed outlier: 3.577A pdb=" N PHE A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LYS A 232 " --> pdb=" O LYS A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 240 removed outlier: 3.605A pdb=" N LEU A 239 " --> pdb=" O ASN A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 263 removed outlier: 4.468A pdb=" N ILE A 258 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA A 259 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A 262 " --> pdb=" O ILE A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 270 Processing helix chain 'A' and resid 288 through 294 Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 320 through 324 removed outlier: 3.638A pdb=" N SER A 324 " --> pdb=" O ILE A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 386 removed outlier: 3.726A pdb=" N ILE A 385 " --> pdb=" O LYS A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 411 through 417 Processing helix chain 'A' and resid 432 through 437 Processing helix chain 'A' and resid 446 through 457 Processing helix chain 'A' and resid 459 through 466 removed outlier: 3.589A pdb=" N ILE A 463 " --> pdb=" O ALA A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 498 removed outlier: 3.703A pdb=" N GLN A 487 " --> pdb=" O GLY A 483 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG A 488 " --> pdb=" O GLY A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 527 Processing helix chain 'A' and resid 539 through 544 removed outlier: 3.920A pdb=" N GLU A 543 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LYS A 544 " --> pdb=" O SER A 540 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 539 through 544' Processing helix chain 'A' and resid 561 through 568 removed outlier: 4.081A pdb=" N HIS A 568 " --> pdb=" O ASP A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 580 Processing helix chain 'B' and resid 16 through 21 removed outlier: 3.719A pdb=" N ILE B 20 " --> pdb=" O LEU B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 24 No H-bonds generated for 'chain 'B' and resid 22 through 24' Processing helix chain 'B' and resid 31 through 39 removed outlier: 3.559A pdb=" N ILE B 35 " --> pdb=" O GLY B 31 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU B 36 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASN B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 46 removed outlier: 4.001A pdb=" N LEU B 45 " --> pdb=" O ASP B 41 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER B 46 " --> pdb=" O THR B 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 41 through 46' Processing helix chain 'B' and resid 47 through 54 removed outlier: 3.863A pdb=" N LEU B 51 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 88 removed outlier: 3.855A pdb=" N LEU B 77 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER B 85 " --> pdb=" O THR B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 107 removed outlier: 3.591A pdb=" N HIS B 107 " --> pdb=" O LEU B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 118 removed outlier: 4.209A pdb=" N PHE B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LYS B 118 " --> pdb=" O SER B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 124 No H-bonds generated for 'chain 'B' and resid 122 through 124' Processing helix chain 'B' and resid 125 through 130 Processing helix chain 'B' and resid 151 through 164 removed outlier: 4.169A pdb=" N PHE B 157 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET B 160 " --> pdb=" O LEU B 156 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER B 164 " --> pdb=" O MET B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 191 removed outlier: 3.640A pdb=" N ARG B 188 " --> pdb=" O VAL B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 212 removed outlier: 3.990A pdb=" N MET B 200 " --> pdb=" O MET B 196 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER B 206 " --> pdb=" O GLN B 202 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N MET B 210 " --> pdb=" O SER B 206 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS B 212 " --> pdb=" O GLU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 220 Processing helix chain 'B' and resid 224 through 247 removed outlier: 3.520A pdb=" N ASP B 231 " --> pdb=" O THR B 227 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LYS B 232 " --> pdb=" O LYS B 228 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN B 235 " --> pdb=" O ASP B 231 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET B 237 " --> pdb=" O VAL B 233 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU B 239 " --> pdb=" O ASN B 235 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS B 243 " --> pdb=" O LEU B 239 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N MET B 244 " --> pdb=" O GLN B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 272 removed outlier: 3.632A pdb=" N ALA B 259 " --> pdb=" O ILE B 255 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA B 262 " --> pdb=" O ILE B 258 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER B 271 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N PHE B 272 " --> pdb=" O TYR B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 291 removed outlier: 4.254A pdb=" N PHE B 288 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET B 291 " --> pdb=" O VAL B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 300 Processing helix chain 'B' and resid 313 through 322 removed outlier: 3.684A pdb=" N THR B 317 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU B 318 " --> pdb=" O ALA B 314 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE B 321 " --> pdb=" O THR B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 removed outlier: 4.390A pdb=" N SER B 387 " --> pdb=" O SER B 383 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU B 388 " --> pdb=" O THR B 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 383 through 388' Processing helix chain 'B' and resid 411 through 417 removed outlier: 3.610A pdb=" N ASN B 417 " --> pdb=" O ALA B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 438 removed outlier: 3.656A pdb=" N ASN B 436 " --> pdb=" O THR B 432 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 457 Processing helix chain 'B' and resid 459 through 466 Processing helix chain 'B' and resid 482 through 498 Processing helix chain 'B' and resid 515 through 527 Processing helix chain 'B' and resid 538 through 544 removed outlier: 3.810A pdb=" N ILE B 542 " --> pdb=" O ARG B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 568 removed outlier: 3.656A pdb=" N GLU B 567 " --> pdb=" O ASN B 563 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N HIS B 568 " --> pdb=" O ASP B 564 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 563 through 568' Processing helix chain 'B' and resid 571 through 580 removed outlier: 3.538A pdb=" N HIS B 576 " --> pdb=" O TYR B 572 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS B 577 " --> pdb=" O ALA B 573 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN B 579 " --> pdb=" O LEU B 575 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 359 through 366 removed outlier: 7.024A pdb=" N ARG A 360 " --> pdb=" O THR A 348 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N THR A 348 " --> pdb=" O ARG A 360 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ILE A 362 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU A 399 " --> pdb=" O ARG A 345 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N VAL A 347 " --> pdb=" O GLU A 397 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N GLU A 397 " --> pdb=" O VAL A 347 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 532 through 534 removed outlier: 6.787A pdb=" N THR A 371 " --> pdb=" O GLU A 547 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N VAL A 549 " --> pdb=" O THR A 371 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ALA A 373 " --> pdb=" O VAL A 549 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL A 551 " --> pdb=" O ALA A 373 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ILE A 548 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N ARG A 559 " --> pdb=" O ILE A 548 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N VAL A 550 " --> pdb=" O VAL A 557 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL A 557 " --> pdb=" O VAL A 550 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 419 through 420 removed outlier: 3.722A pdb=" N ALA A 420 " --> pdb=" O ILE A 501 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 359 through 362 removed outlier: 3.720A pdb=" N ASN B 361 " --> pdb=" O VAL B 347 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N VAL B 347 " --> pdb=" O ASN B 361 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL B 342 " --> pdb=" O ILE B 366 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 359 through 362 removed outlier: 3.720A pdb=" N ASN B 361 " --> pdb=" O VAL B 347 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N VAL B 347 " --> pdb=" O ASN B 361 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG B 345 " --> pdb=" O GLU B 399 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU B 399 " --> pdb=" O ARG B 345 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL B 347 " --> pdb=" O GLU B 397 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLU B 397 " --> pdb=" O VAL B 347 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 532 through 534 removed outlier: 6.347A pdb=" N VAL B 372 " --> pdb=" O VAL B 534 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N THR B 371 " --> pdb=" O GLU B 547 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N VAL B 549 " --> pdb=" O THR B 371 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N ALA B 373 " --> pdb=" O VAL B 549 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL B 551 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL B 375 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU B 558 " --> pdb=" O VAL B 550 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N GLU B 552 " --> pdb=" O ILE B 556 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ILE B 556 " --> pdb=" O GLU B 552 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 421 through 422 274 hydrogen bonds defined for protein. 786 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: 1.56 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1493 1.32 - 1.44: 2205 1.44 - 1.57: 5244 1.57 - 1.69: 4 1.69 - 1.81: 104 Bond restraints: 9050 Sorted by residual: bond pdb=" C PHE B 272 " pdb=" N PRO B 273 " ideal model delta sigma weight residual 1.331 1.358 -0.027 7.90e-03 1.60e+04 1.14e+01 bond pdb=" N LYS A 49 " pdb=" CA LYS A 49 " ideal model delta sigma weight residual 1.463 1.486 -0.023 6.90e-03 2.10e+04 1.14e+01 bond pdb=" N LYS B 49 " pdb=" CA LYS B 49 " ideal model delta sigma weight residual 1.461 1.490 -0.029 9.20e-03 1.18e+04 1.02e+01 bond pdb=" N SER A 120 " pdb=" CA SER A 120 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.29e-02 6.01e+03 8.45e+00 bond pdb=" N MET A 67 " pdb=" CA MET A 67 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.41e-02 5.03e+03 7.75e+00 ... (remaining 9045 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 11242 1.28 - 2.57: 796 2.57 - 3.85: 128 3.85 - 5.14: 29 5.14 - 6.42: 7 Bond angle restraints: 12202 Sorted by residual: angle pdb=" N ILE B 154 " pdb=" CA ILE B 154 " pdb=" C ILE B 154 " ideal model delta sigma weight residual 111.90 106.31 5.59 8.10e-01 1.52e+00 4.76e+01 angle pdb=" N VAL A 173 " pdb=" CA VAL A 173 " pdb=" C VAL A 173 " ideal model delta sigma weight residual 112.96 108.15 4.81 1.00e+00 1.00e+00 2.31e+01 angle pdb=" N VAL B 147 " pdb=" CA VAL B 147 " pdb=" C VAL B 147 " ideal model delta sigma weight residual 113.53 109.55 3.98 9.80e-01 1.04e+00 1.65e+01 angle pdb=" N SER B 515 " pdb=" CA SER B 515 " pdb=" C SER B 515 " ideal model delta sigma weight residual 112.72 108.28 4.44 1.28e+00 6.10e-01 1.21e+01 angle pdb=" N VAL A 571 " pdb=" CA VAL A 571 " pdb=" C VAL A 571 " ideal model delta sigma weight residual 113.71 110.45 3.26 9.50e-01 1.11e+00 1.18e+01 ... (remaining 12197 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.15: 5331 26.15 - 52.30: 194 52.30 - 78.45: 22 78.45 - 104.61: 4 104.61 - 130.76: 1 Dihedral angle restraints: 5552 sinusoidal: 2262 harmonic: 3290 Sorted by residual: dihedral pdb=" CA ILE A 254 " pdb=" C ILE A 254 " pdb=" N ILE A 255 " pdb=" CA ILE A 255 " ideal model delta harmonic sigma weight residual 180.00 151.48 28.52 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA VAL B 375 " pdb=" C VAL B 375 " pdb=" N GLY B 376 " pdb=" CA GLY B 376 " ideal model delta harmonic sigma weight residual -180.00 -157.15 -22.85 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA ARG B 101 " pdb=" C ARG B 101 " pdb=" N ARG B 102 " pdb=" CA ARG B 102 " ideal model delta harmonic sigma weight residual 180.00 158.39 21.61 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 5549 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1137 0.045 - 0.090: 233 0.090 - 0.136: 62 0.136 - 0.181: 7 0.181 - 0.226: 3 Chirality restraints: 1442 Sorted by residual: chirality pdb=" CA ILE B 177 " pdb=" N ILE B 177 " pdb=" C ILE B 177 " pdb=" CB ILE B 177 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CB ILE A 503 " pdb=" CA ILE A 503 " pdb=" CG1 ILE A 503 " pdb=" CG2 ILE A 503 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.43e-01 chirality pdb=" CA SER A 120 " pdb=" N SER A 120 " pdb=" C SER A 120 " pdb=" CB SER A 120 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.39e-01 ... (remaining 1439 not shown) Planarity restraints: 1536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 13 " 0.012 2.00e-02 2.50e+03 2.42e-02 5.85e+00 pdb=" C PHE A 13 " -0.042 2.00e-02 2.50e+03 pdb=" O PHE A 13 " 0.016 2.00e-02 2.50e+03 pdb=" N ARG A 14 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 503 " 0.011 2.00e-02 2.50e+03 2.26e-02 5.10e+00 pdb=" C ILE A 503 " -0.039 2.00e-02 2.50e+03 pdb=" O ILE A 503 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU A 504 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP B 17 " 0.031 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO B 18 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 18 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 18 " 0.026 5.00e-02 4.00e+02 ... (remaining 1533 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 812 2.75 - 3.29: 8936 3.29 - 3.82: 13097 3.82 - 4.36: 16789 4.36 - 4.90: 27932 Nonbonded interactions: 67566 Sorted by model distance: nonbonded pdb=" O THR A 285 " pdb=" OG SER A 289 " model vdw 2.209 3.040 nonbonded pdb=" O LEU B 566 " pdb=" NH2 ARG B 569 " model vdw 2.273 3.120 nonbonded pdb=" NH2 ARG A 229 " pdb=" OD2 ASP B 431 " model vdw 2.283 3.120 nonbonded pdb=" OG1 THR A 280 " pdb=" O GLY A 282 " model vdw 2.293 3.040 nonbonded pdb=" NE ARG B 101 " pdb=" O ILE B 128 " model vdw 2.304 3.120 ... (remaining 67561 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 5.260 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: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.850 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9050 Z= 0.253 Angle : 0.748 6.423 12202 Z= 0.460 Chirality : 0.042 0.226 1442 Planarity : 0.004 0.046 1536 Dihedral : 13.917 130.758 3424 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.85 % Favored : 92.06 % Rotamer: Outliers : 0.41 % Allowed : 8.26 % Favored : 91.32 % 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 aren not related in a simple way. whole: -4.19 (0.23), residues: 1134 helix: -3.10 (0.16), residues: 674 sheet: -3.00 (0.54), residues: 70 loop : -1.62 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 530 TYR 0.007 0.001 TYR B 393 PHE 0.007 0.001 PHE B 157 TRP 0.009 0.001 TRP B 66 HIS 0.002 0.001 HIS A 405 Details of bonding type rmsd covalent geometry : bond 0.00450 ( 9050) covalent geometry : angle 0.74786 (12202) hydrogen bonds : bond 0.28287 ( 272) hydrogen bonds : angle 9.70235 ( 786) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 158 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 PHE cc_start: 0.8019 (t80) cc_final: 0.7495 (m-80) REVERT: A 466 MET cc_start: 0.6685 (mmt) cc_final: 0.6448 (mmp) REVERT: B 54 ASP cc_start: 0.7314 (t0) cc_final: 0.6987 (t0) REVERT: B 129 THR cc_start: 0.9058 (m) cc_final: 0.8705 (p) REVERT: B 409 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8224 (mt-10) REVERT: B 574 GLN cc_start: 0.8908 (mp10) cc_final: 0.8655 (mp10) outliers start: 4 outliers final: 0 residues processed: 160 average time/residue: 0.0983 time to fit residues: 22.0148 Evaluate side-chains 111 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 363 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.165233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.125440 restraints weight = 11629.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.125273 restraints weight = 24341.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.126157 restraints weight = 19397.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.125811 restraints weight = 11873.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.126428 restraints weight = 10483.802| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9050 Z= 0.218 Angle : 0.686 7.290 12202 Z= 0.359 Chirality : 0.047 0.184 1442 Planarity : 0.005 0.044 1536 Dihedral : 8.736 122.671 1336 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 3.41 % Allowed : 12.50 % Favored : 84.09 % 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 aren not related in a simple way. whole: -3.67 (0.23), residues: 1134 helix: -2.66 (0.17), residues: 672 sheet: -1.67 (0.72), residues: 44 loop : -1.77 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 229 TYR 0.012 0.001 TYR A 410 PHE 0.023 0.002 PHE B 56 TRP 0.009 0.001 TRP A 17 HIS 0.003 0.001 HIS A 537 Details of bonding type rmsd covalent geometry : bond 0.00520 ( 9050) covalent geometry : angle 0.68559 (12202) hydrogen bonds : bond 0.03977 ( 272) hydrogen bonds : angle 5.77499 ( 786) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 124 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 THR cc_start: 0.8855 (t) cc_final: 0.8612 (m) REVERT: A 291 MET cc_start: 0.7742 (tpt) cc_final: 0.6898 (tmm) REVERT: A 405 HIS cc_start: 0.8059 (m-70) cc_final: 0.7782 (m-70) REVERT: B 240 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.7537 (tm-30) REVERT: B 322 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8401 (tt) REVERT: B 333 ARG cc_start: 0.6443 (mtp85) cc_final: 0.6143 (mmm-85) REVERT: B 370 LYS cc_start: 0.8224 (mmtm) cc_final: 0.7666 (mmmm) outliers start: 33 outliers final: 21 residues processed: 148 average time/residue: 0.0970 time to fit residues: 20.2602 Evaluate side-chains 127 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 240 GLN Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 543 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 59 optimal weight: 0.5980 chunk 39 optimal weight: 0.0670 chunk 53 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 chunk 74 optimal weight: 0.0670 chunk 69 optimal weight: 0.8980 chunk 23 optimal weight: 0.1980 chunk 11 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN A 487 GLN B 107 HIS B 240 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.171444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.130533 restraints weight = 11298.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.125773 restraints weight = 18871.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.127739 restraints weight = 17502.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.128744 restraints weight = 9634.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.129271 restraints weight = 8561.732| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9050 Z= 0.099 Angle : 0.576 11.064 12202 Z= 0.300 Chirality : 0.041 0.183 1442 Planarity : 0.004 0.042 1536 Dihedral : 8.050 117.215 1336 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 2.69 % Allowed : 14.67 % Favored : 82.64 % 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 aren not related in a simple way. whole: -3.25 (0.24), residues: 1134 helix: -2.23 (0.18), residues: 680 sheet: -2.05 (0.54), residues: 80 loop : -1.58 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 488 TYR 0.010 0.001 TYR A 410 PHE 0.019 0.001 PHE B 56 TRP 0.008 0.001 TRP A 17 HIS 0.003 0.001 HIS A 537 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 9050) covalent geometry : angle 0.57557 (12202) hydrogen bonds : bond 0.02802 ( 272) hydrogen bonds : angle 5.04504 ( 786) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 TRP cc_start: 0.8144 (t60) cc_final: 0.5629 (m-10) REVERT: A 67 MET cc_start: 0.8307 (ttm) cc_final: 0.8024 (tpp) REVERT: A 240 GLN cc_start: 0.8852 (tp40) cc_final: 0.7784 (tm-30) REVERT: B 54 ASP cc_start: 0.7534 (t0) cc_final: 0.7262 (t0) REVERT: B 240 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.7492 (tm-30) REVERT: B 280 THR cc_start: 0.8673 (p) cc_final: 0.8443 (p) REVERT: B 322 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8194 (tt) outliers start: 26 outliers final: 17 residues processed: 142 average time/residue: 0.0951 time to fit residues: 19.0926 Evaluate side-chains 126 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 240 GLN Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 528 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 9.9990 chunk 84 optimal weight: 0.1980 chunk 72 optimal weight: 0.3980 chunk 44 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 7 optimal weight: 0.0570 chunk 15 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 240 GLN B 309 GLN 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 = 0.172131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.132850 restraints weight = 11469.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.126317 restraints weight = 22847.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.128915 restraints weight = 18610.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.130289 restraints weight = 10428.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.130857 restraints weight = 8726.194| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9050 Z= 0.102 Angle : 0.569 10.460 12202 Z= 0.294 Chirality : 0.041 0.182 1442 Planarity : 0.004 0.041 1536 Dihedral : 7.805 114.370 1336 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 3.41 % Allowed : 16.01 % Favored : 80.58 % 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 aren not related in a simple way. whole: -2.97 (0.24), residues: 1134 helix: -1.99 (0.19), residues: 684 sheet: -1.81 (0.55), residues: 80 loop : -1.52 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 455 TYR 0.027 0.001 TYR A 439 PHE 0.016 0.001 PHE A 429 TRP 0.007 0.001 TRP A 17 HIS 0.002 0.001 HIS A 537 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 9050) covalent geometry : angle 0.56910 (12202) hydrogen bonds : bond 0.02521 ( 272) hydrogen bonds : angle 4.70817 ( 786) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: A 66 TRP cc_start: 0.8006 (t60) cc_final: 0.5638 (m-10) REVERT: A 67 MET cc_start: 0.8297 (ttm) cc_final: 0.8042 (tpp) REVERT: A 295 MET cc_start: 0.7471 (OUTLIER) cc_final: 0.7216 (mtt) REVERT: B 54 ASP cc_start: 0.7488 (t0) cc_final: 0.7091 (t0) REVERT: B 115 PHE cc_start: 0.8132 (t80) cc_final: 0.7773 (t80) REVERT: B 280 THR cc_start: 0.8578 (p) cc_final: 0.8309 (p) REVERT: B 322 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8177 (tt) outliers start: 33 outliers final: 18 residues processed: 145 average time/residue: 0.0851 time to fit residues: 18.0967 Evaluate side-chains 135 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 322 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 63 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 97 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 71 optimal weight: 0.2980 chunk 85 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.170491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.128826 restraints weight = 11320.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.132429 restraints weight = 21023.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.131536 restraints weight = 12038.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.131274 restraints weight = 10297.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.131943 restraints weight = 8181.618| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9050 Z= 0.127 Angle : 0.580 10.497 12202 Z= 0.301 Chirality : 0.042 0.182 1442 Planarity : 0.004 0.041 1536 Dihedral : 7.852 112.862 1336 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.20 % Allowed : 17.46 % Favored : 79.34 % 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 aren not related in a simple way. whole: -2.79 (0.24), residues: 1134 helix: -1.85 (0.19), residues: 684 sheet: -1.83 (0.55), residues: 82 loop : -1.42 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 455 TYR 0.020 0.001 TYR A 439 PHE 0.020 0.001 PHE A 43 TRP 0.007 0.001 TRP A 17 HIS 0.005 0.001 HIS A 405 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 9050) covalent geometry : angle 0.58049 (12202) hydrogen bonds : bond 0.02621 ( 272) hydrogen bonds : angle 4.60960 ( 786) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 112 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 TRP cc_start: 0.8003 (t60) cc_final: 0.5658 (m-10) REVERT: A 360 ARG cc_start: 0.6958 (OUTLIER) cc_final: 0.6484 (mtt90) REVERT: B 54 ASP cc_start: 0.7473 (t0) cc_final: 0.6983 (t0) REVERT: B 115 PHE cc_start: 0.8158 (t80) cc_final: 0.7766 (t80) REVERT: B 280 THR cc_start: 0.8578 (p) cc_final: 0.8316 (p) REVERT: B 322 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8248 (tt) outliers start: 31 outliers final: 17 residues processed: 132 average time/residue: 0.0950 time to fit residues: 17.9123 Evaluate side-chains 130 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 322 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 100 optimal weight: 10.0000 chunk 111 optimal weight: 20.0000 chunk 108 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 46 optimal weight: 0.0970 chunk 50 optimal weight: 20.0000 chunk 0 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.176624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.134318 restraints weight = 11341.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.133965 restraints weight = 22695.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.135094 restraints weight = 19247.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.134334 restraints weight = 12105.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.135127 restraints weight = 10708.000| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9050 Z= 0.113 Angle : 0.567 11.085 12202 Z= 0.293 Chirality : 0.042 0.182 1442 Planarity : 0.004 0.040 1536 Dihedral : 7.706 111.350 1336 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.17 % Favored : 93.74 % Rotamer: Outliers : 3.20 % Allowed : 18.18 % Favored : 78.62 % 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 aren not related in a simple way. whole: -2.61 (0.24), residues: 1134 helix: -1.67 (0.19), residues: 682 sheet: -1.97 (0.54), residues: 80 loop : -1.36 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 61 TYR 0.017 0.001 TYR A 439 PHE 0.021 0.001 PHE B 429 TRP 0.010 0.001 TRP A 66 HIS 0.003 0.001 HIS A 405 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 9050) covalent geometry : angle 0.56726 (12202) hydrogen bonds : bond 0.02441 ( 272) hydrogen bonds : angle 4.49636 ( 786) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 110 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8720 (mp) REVERT: A 360 ARG cc_start: 0.6935 (OUTLIER) cc_final: 0.6435 (mtt90) REVERT: B 12 THR cc_start: 0.7157 (OUTLIER) cc_final: 0.5759 (t) REVERT: B 54 ASP cc_start: 0.7448 (t0) cc_final: 0.6971 (t0) REVERT: B 115 PHE cc_start: 0.8073 (t80) cc_final: 0.7722 (t80) REVERT: B 280 THR cc_start: 0.8505 (p) cc_final: 0.8230 (p) REVERT: B 322 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8317 (tt) outliers start: 31 outliers final: 19 residues processed: 136 average time/residue: 0.0895 time to fit residues: 17.5116 Evaluate side-chains 131 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 322 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 69 optimal weight: 0.0000 chunk 106 optimal weight: 20.0000 chunk 66 optimal weight: 0.5980 chunk 49 optimal weight: 0.1980 chunk 65 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 24 optimal weight: 0.0770 chunk 97 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 110 optimal weight: 9.9990 chunk 108 optimal weight: 6.9990 overall best weight: 0.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.179276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.137147 restraints weight = 11206.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.133529 restraints weight = 19269.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.135465 restraints weight = 18143.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.135680 restraints weight = 10554.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.136593 restraints weight = 8666.628| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9050 Z= 0.093 Angle : 0.559 11.226 12202 Z= 0.286 Chirality : 0.041 0.170 1442 Planarity : 0.004 0.068 1536 Dihedral : 7.480 109.714 1336 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.53 % Favored : 93.39 % Rotamer: Outliers : 2.58 % Allowed : 19.32 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.36 (0.25), residues: 1134 helix: -1.47 (0.20), residues: 686 sheet: -1.83 (0.54), residues: 80 loop : -1.29 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 488 TYR 0.015 0.001 TYR B 268 PHE 0.012 0.001 PHE B 429 TRP 0.019 0.001 TRP A 66 HIS 0.002 0.001 HIS A 405 Details of bonding type rmsd covalent geometry : bond 0.00201 ( 9050) covalent geometry : angle 0.55915 (12202) hydrogen bonds : bond 0.02195 ( 272) hydrogen bonds : angle 4.33289 ( 786) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8529 (mp) REVERT: A 360 ARG cc_start: 0.7155 (OUTLIER) cc_final: 0.6605 (mtt90) REVERT: B 12 THR cc_start: 0.7206 (OUTLIER) cc_final: 0.5857 (t) REVERT: B 54 ASP cc_start: 0.7277 (t0) cc_final: 0.6798 (t0) REVERT: B 67 MET cc_start: 0.8141 (ttm) cc_final: 0.7731 (tpp) REVERT: B 115 PHE cc_start: 0.7897 (t80) cc_final: 0.7464 (t80) REVERT: B 280 THR cc_start: 0.8428 (p) cc_final: 0.8166 (p) REVERT: B 322 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8222 (tt) outliers start: 25 outliers final: 17 residues processed: 134 average time/residue: 0.0938 time to fit residues: 18.1996 Evaluate side-chains 131 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 322 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 50 optimal weight: 9.9990 chunk 10 optimal weight: 0.2980 chunk 4 optimal weight: 0.0010 chunk 28 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 93 optimal weight: 0.2980 chunk 57 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.177878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.136509 restraints weight = 11193.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.137870 restraints weight = 22005.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.137477 restraints weight = 15667.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.136671 restraints weight = 11713.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.137370 restraints weight = 10101.642| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9050 Z= 0.111 Angle : 0.574 11.035 12202 Z= 0.293 Chirality : 0.041 0.160 1442 Planarity : 0.004 0.051 1536 Dihedral : 7.566 110.023 1336 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.61 % Favored : 93.30 % Rotamer: Outliers : 3.31 % Allowed : 18.60 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.27 (0.25), residues: 1134 helix: -1.42 (0.20), residues: 686 sheet: -1.67 (0.55), residues: 78 loop : -1.23 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 455 TYR 0.014 0.001 TYR A 439 PHE 0.011 0.001 PHE A 272 TRP 0.015 0.001 TRP A 66 HIS 0.002 0.001 HIS A 405 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 9050) covalent geometry : angle 0.57409 (12202) hydrogen bonds : bond 0.02383 ( 272) hydrogen bonds : angle 4.36387 ( 786) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: A 267 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8695 (mp) REVERT: A 360 ARG cc_start: 0.6906 (OUTLIER) cc_final: 0.6398 (mtt90) REVERT: B 12 THR cc_start: 0.7320 (OUTLIER) cc_final: 0.5875 (t) REVERT: B 54 ASP cc_start: 0.7315 (t0) cc_final: 0.6811 (t0) REVERT: B 115 PHE cc_start: 0.7920 (t80) cc_final: 0.7487 (t80) REVERT: B 280 THR cc_start: 0.8459 (p) cc_final: 0.8204 (p) REVERT: B 322 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8247 (tt) REVERT: B 466 MET cc_start: 0.6250 (tpp) cc_final: 0.5633 (mmm) outliers start: 32 outliers final: 19 residues processed: 136 average time/residue: 0.0961 time to fit residues: 18.6636 Evaluate side-chains 131 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 407 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 85 optimal weight: 0.0980 chunk 13 optimal weight: 0.8980 chunk 44 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 83 optimal weight: 0.0470 chunk 21 optimal weight: 0.3980 chunk 18 optimal weight: 4.9990 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.179458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.137388 restraints weight = 11149.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.132848 restraints weight = 19994.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.135252 restraints weight = 17578.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.135082 restraints weight = 10224.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.135862 restraints weight = 9263.536| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9050 Z= 0.095 Angle : 0.569 11.361 12202 Z= 0.288 Chirality : 0.041 0.160 1442 Planarity : 0.004 0.042 1536 Dihedral : 7.466 108.793 1336 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.61 % Favored : 93.30 % Rotamer: Outliers : 2.79 % Allowed : 19.42 % Favored : 77.79 % 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 aren not related in a simple way. whole: -2.02 (0.25), residues: 1134 helix: -1.19 (0.20), residues: 680 sheet: -1.54 (0.55), residues: 78 loop : -1.21 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 455 TYR 0.014 0.001 TYR A 439 PHE 0.008 0.001 PHE A 115 TRP 0.016 0.001 TRP A 66 HIS 0.002 0.001 HIS A 405 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 9050) covalent geometry : angle 0.56939 (12202) hydrogen bonds : bond 0.02224 ( 272) hydrogen bonds : angle 4.31415 ( 786) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 112 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8508 (mp) REVERT: A 360 ARG cc_start: 0.7092 (OUTLIER) cc_final: 0.6536 (mtt90) REVERT: B 12 THR cc_start: 0.7331 (OUTLIER) cc_final: 0.6078 (t) REVERT: B 54 ASP cc_start: 0.7245 (t0) cc_final: 0.6741 (t0) REVERT: B 67 MET cc_start: 0.8181 (ttm) cc_final: 0.7916 (tpp) REVERT: B 280 THR cc_start: 0.8406 (p) cc_final: 0.8148 (p) REVERT: B 322 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8207 (tt) REVERT: B 466 MET cc_start: 0.6240 (tpp) cc_final: 0.5695 (mmm) outliers start: 27 outliers final: 20 residues processed: 132 average time/residue: 0.0911 time to fit residues: 17.4638 Evaluate side-chains 133 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 407 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 65 optimal weight: 0.6980 chunk 91 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 105 optimal weight: 10.0000 chunk 14 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.175375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.132750 restraints weight = 11193.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.128712 restraints weight = 21730.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.130077 restraints weight = 19874.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.133137 restraints weight = 12167.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.132576 restraints weight = 9168.916| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9050 Z= 0.149 Angle : 0.618 11.506 12202 Z= 0.313 Chirality : 0.043 0.149 1442 Planarity : 0.004 0.042 1536 Dihedral : 7.833 110.508 1336 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.23 % Favored : 92.68 % Rotamer: Outliers : 2.69 % Allowed : 19.52 % Favored : 77.79 % 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 aren not related in a simple way. whole: -2.13 (0.25), residues: 1134 helix: -1.34 (0.20), residues: 690 sheet: -1.41 (0.55), residues: 78 loop : -1.14 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 455 TYR 0.015 0.001 TYR A 439 PHE 0.011 0.001 PHE A 230 TRP 0.009 0.001 TRP A 66 HIS 0.002 0.001 HIS A 405 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 9050) covalent geometry : angle 0.61845 (12202) hydrogen bonds : bond 0.02708 ( 272) hydrogen bonds : angle 4.55054 ( 786) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: A 267 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8765 (mp) REVERT: A 360 ARG cc_start: 0.7194 (OUTLIER) cc_final: 0.6585 (mtt90) REVERT: B 12 THR cc_start: 0.7382 (OUTLIER) cc_final: 0.5991 (t) REVERT: B 54 ASP cc_start: 0.7413 (t0) cc_final: 0.6878 (t0) REVERT: B 280 THR cc_start: 0.8511 (p) cc_final: 0.8247 (p) REVERT: B 322 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8296 (tt) REVERT: B 466 MET cc_start: 0.6329 (tpp) cc_final: 0.5819 (mmm) outliers start: 26 outliers final: 20 residues processed: 122 average time/residue: 0.0960 time to fit residues: 16.7746 Evaluate side-chains 125 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 407 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 48 optimal weight: 0.6980 chunk 10 optimal weight: 0.1980 chunk 82 optimal weight: 6.9990 chunk 108 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 24 optimal weight: 0.0770 chunk 44 optimal weight: 10.0000 chunk 27 optimal weight: 0.5980 chunk 110 optimal weight: 20.0000 chunk 38 optimal weight: 3.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.177229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.135148 restraints weight = 11142.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.131257 restraints weight = 20120.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.133419 restraints weight = 18120.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.133182 restraints weight = 11051.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.134104 restraints weight = 9685.124| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9050 Z= 0.117 Angle : 0.602 11.321 12202 Z= 0.305 Chirality : 0.042 0.156 1442 Planarity : 0.003 0.040 1536 Dihedral : 7.695 108.765 1336 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.88 % Favored : 93.03 % Rotamer: Outliers : 2.69 % Allowed : 19.94 % Favored : 77.38 % 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 aren not related in a simple way. whole: -1.97 (0.25), residues: 1134 helix: -1.16 (0.20), residues: 678 sheet: -1.23 (0.57), residues: 78 loop : -1.26 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 455 TYR 0.019 0.001 TYR B 268 PHE 0.008 0.001 PHE B 429 TRP 0.028 0.001 TRP A 66 HIS 0.005 0.001 HIS B 405 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 9050) covalent geometry : angle 0.60204 (12202) hydrogen bonds : bond 0.02458 ( 272) hydrogen bonds : angle 4.45643 ( 786) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1597.06 seconds wall clock time: 28 minutes 26.14 seconds (1706.14 seconds total)