Starting phenix.real_space_refine on Mon May 12 11:26:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fuq_50774/05_2025/9fuq_50774.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fuq_50774/05_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_50774/05_2025/9fuq_50774.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fuq_50774/05_2025/9fuq_50774.map" model { file = "/net/cci-nas-00/data/ceres_data/9fuq_50774/05_2025/9fuq_50774.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fuq_50774/05_2025/9fuq_50774.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.027 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 6.36, per 1000 atoms: 0.71 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: 2.22 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.90 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: 2.38 Time building geometry restraints manager: 2.54 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: 0.04 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: 4.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.440 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.970 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.280 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.009 0.001 TRP B 66 HIS 0.002 0.001 HIS A 405 PHE 0.007 0.001 PHE B 157 TYR 0.007 0.001 TYR B 393 ARG 0.002 0.000 ARG A 530 Details of bonding type rmsd hydrogen bonds : bond 0.28287 ( 272) hydrogen bonds : angle 9.70235 ( 786) covalent geometry : bond 0.00450 ( 9050) covalent geometry : angle 0.74786 (12202) *********************** 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 : 0.920 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: 0.2051 time to fit residues: 45.3378 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 : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 chunk 65 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.3897 r_free = 0.3897 target = 0.167372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.127862 restraints weight = 11455.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.129689 restraints weight = 24548.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.129194 restraints weight = 15083.799| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9050 Z= 0.173 Angle : 0.648 7.046 12202 Z= 0.340 Chirality : 0.045 0.184 1442 Planarity : 0.005 0.044 1536 Dihedral : 8.477 122.444 1336 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 3.10 % Allowed : 12.50 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.63 (0.23), residues: 1134 helix: -2.60 (0.17), residues: 676 sheet: -1.64 (0.72), residues: 44 loop : -1.80 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 17 HIS 0.003 0.001 HIS A 537 PHE 0.023 0.001 PHE B 56 TYR 0.013 0.001 TYR A 410 ARG 0.005 0.000 ARG A 229 Details of bonding type rmsd hydrogen bonds : bond 0.03616 ( 272) hydrogen bonds : angle 5.66814 ( 786) covalent geometry : bond 0.00407 ( 9050) covalent geometry : angle 0.64824 (12202) *********************** 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 154 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 MET cc_start: 0.7762 (tpt) cc_final: 0.6822 (tmm) REVERT: B 240 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.7486 (tm-30) REVERT: B 322 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8341 (tt) REVERT: B 370 LYS cc_start: 0.8164 (mmtm) cc_final: 0.7627 (mmmm) outliers start: 30 outliers final: 16 residues processed: 146 average time/residue: 0.1960 time to fit residues: 40.3730 Evaluate side-chains 120 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 147 VAL 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 46 optimal weight: 0.0070 chunk 78 optimal weight: 0.9990 chunk 95 optimal weight: 8.9990 chunk 3 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 58 optimal weight: 0.4980 chunk 88 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 64 optimal weight: 0.4980 overall best weight: 0.4598 ------------------------------------------------------------------------------- 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 240 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.171850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.131732 restraints weight = 11429.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.125394 restraints weight = 18883.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.126829 restraints weight = 15668.634| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9050 Z= 0.102 Angle : 0.572 10.637 12202 Z= 0.298 Chirality : 0.041 0.180 1442 Planarity : 0.004 0.042 1536 Dihedral : 7.975 116.919 1336 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 2.48 % Allowed : 14.77 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.24), residues: 1134 helix: -2.20 (0.18), residues: 682 sheet: -2.00 (0.55), residues: 80 loop : -1.56 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 17 HIS 0.002 0.001 HIS A 537 PHE 0.017 0.001 PHE B 56 TYR 0.010 0.001 TYR A 410 ARG 0.004 0.000 ARG B 455 Details of bonding type rmsd hydrogen bonds : bond 0.02809 ( 272) hydrogen bonds : angle 4.95925 ( 786) covalent geometry : bond 0.00226 ( 9050) covalent geometry : angle 0.57176 (12202) *********************** 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 144 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 TRP cc_start: 0.8115 (t60) cc_final: 0.5672 (m-10) REVERT: A 67 MET cc_start: 0.8295 (ttm) cc_final: 0.8017 (tpp) REVERT: A 240 GLN cc_start: 0.8858 (tp40) cc_final: 0.7807 (tm-30) REVERT: A 439 TYR cc_start: 0.8935 (t80) cc_final: 0.8680 (t80) REVERT: B 54 ASP cc_start: 0.7468 (t0) cc_final: 0.7196 (t0) REVERT: B 240 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.7526 (tm-30) REVERT: B 280 THR cc_start: 0.8680 (p) cc_final: 0.8455 (p) REVERT: B 322 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8273 (tt) REVERT: B 410 TYR cc_start: 0.6882 (m-80) cc_final: 0.6653 (m-80) outliers start: 24 outliers final: 15 residues processed: 136 average time/residue: 0.1929 time to fit residues: 37.0759 Evaluate side-chains 126 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 98 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 88 optimal weight: 20.0000 chunk 92 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.3895 r_free = 0.3895 target = 0.167605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.127470 restraints weight = 11451.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.126373 restraints weight = 26939.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.127926 restraints weight = 20300.294| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9050 Z= 0.170 Angle : 0.620 10.250 12202 Z= 0.319 Chirality : 0.044 0.178 1442 Planarity : 0.004 0.041 1536 Dihedral : 8.197 115.167 1336 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 3.72 % Allowed : 15.50 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.24), residues: 1134 helix: -2.09 (0.19), residues: 680 sheet: -1.83 (0.55), residues: 80 loop : -1.45 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 17 HIS 0.004 0.001 HIS A 405 PHE 0.013 0.001 PHE A 115 TYR 0.019 0.001 TYR B 268 ARG 0.007 0.000 ARG A 488 Details of bonding type rmsd hydrogen bonds : bond 0.02900 ( 272) hydrogen bonds : angle 4.84585 ( 786) covalent geometry : bond 0.00408 ( 9050) covalent geometry : angle 0.62025 (12202) *********************** 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 148 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 112 time to evaluate : 0.917 Fit side-chains revert: symmetry clash REVERT: A 66 TRP cc_start: 0.8103 (t60) cc_final: 0.5632 (m-10) REVERT: A 67 MET cc_start: 0.8448 (ttm) cc_final: 0.8212 (tpp) REVERT: A 439 TYR cc_start: 0.8976 (t80) cc_final: 0.8702 (t80) REVERT: B 54 ASP cc_start: 0.7637 (t0) cc_final: 0.7215 (t0) REVERT: B 61 ARG cc_start: 0.6486 (mtm180) cc_final: 0.6070 (mtm110) REVERT: B 280 THR cc_start: 0.8809 (p) cc_final: 0.8566 (p) REVERT: B 312 MET cc_start: 0.7435 (OUTLIER) cc_final: 0.7064 (ttt) REVERT: B 322 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8274 (tt) outliers start: 36 outliers final: 20 residues processed: 137 average time/residue: 0.1980 time to fit residues: 38.1358 Evaluate side-chains 126 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.910 ------------------------------------------------------------------------------- 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 242 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 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 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 312 MET Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 407 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 39 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 18 optimal weight: 0.0770 chunk 48 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 overall best weight: 0.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.170265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.130977 restraints weight = 11265.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.133232 restraints weight = 21211.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.132505 restraints weight = 12788.957| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9050 Z= 0.117 Angle : 0.577 10.722 12202 Z= 0.300 Chirality : 0.042 0.188 1442 Planarity : 0.004 0.041 1536 Dihedral : 7.898 112.188 1336 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 3.62 % Allowed : 16.84 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.24), residues: 1134 helix: -1.93 (0.19), residues: 684 sheet: -1.84 (0.55), residues: 82 loop : -1.43 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 17 HIS 0.002 0.000 HIS A 405 PHE 0.011 0.001 PHE B 56 TYR 0.012 0.001 TYR A 130 ARG 0.007 0.000 ARG A 488 Details of bonding type rmsd hydrogen bonds : bond 0.02543 ( 272) hydrogen bonds : angle 4.65639 ( 786) covalent geometry : bond 0.00273 ( 9050) covalent geometry : angle 0.57723 (12202) *********************** 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 145 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 110 time to evaluate : 0.898 Fit side-chains revert: symmetry clash REVERT: A 66 TRP cc_start: 0.7976 (t60) cc_final: 0.5614 (m-10) REVERT: A 267 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8724 (mp) REVERT: A 360 ARG cc_start: 0.6916 (OUTLIER) cc_final: 0.6429 (mtt90) REVERT: B 12 THR cc_start: 0.6934 (OUTLIER) cc_final: 0.5640 (t) REVERT: B 54 ASP cc_start: 0.7521 (t0) cc_final: 0.7043 (t0) REVERT: B 61 ARG cc_start: 0.6383 (mtm180) cc_final: 0.6019 (mtm110) REVERT: B 115 PHE cc_start: 0.8259 (t80) cc_final: 0.7951 (t80) REVERT: B 280 THR cc_start: 0.8693 (p) cc_final: 0.8433 (p) REVERT: B 322 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8248 (tt) outliers start: 35 outliers final: 19 residues processed: 134 average time/residue: 0.1866 time to fit residues: 35.8099 Evaluate side-chains 126 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.902 ------------------------------------------------------------------------------- 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 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 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 89 ILE 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 Chi-restraints excluded: chain B residue 407 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 88 optimal weight: 30.0000 chunk 82 optimal weight: 8.9990 chunk 50 optimal weight: 9.9990 chunk 92 optimal weight: 20.0000 chunk 109 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 74 optimal weight: 0.0980 chunk 70 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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 = 0.3872 r_free = 0.3872 target = 0.165128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.124889 restraints weight = 11288.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.125067 restraints weight = 25399.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.125908 restraints weight = 18657.706| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3049 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= 0.216 Angle : 0.657 11.015 12202 Z= 0.339 Chirality : 0.046 0.159 1442 Planarity : 0.004 0.040 1536 Dihedral : 8.562 113.721 1336 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.50 % Favored : 92.42 % Rotamer: Outliers : 3.51 % Allowed : 18.60 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.24), residues: 1134 helix: -1.97 (0.19), residues: 684 sheet: -2.05 (0.53), residues: 80 loop : -1.39 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 66 HIS 0.003 0.001 HIS B 427 PHE 0.012 0.002 PHE B 56 TYR 0.020 0.002 TYR B 268 ARG 0.008 0.000 ARG A 488 Details of bonding type rmsd hydrogen bonds : bond 0.03101 ( 272) hydrogen bonds : angle 4.85330 ( 786) covalent geometry : bond 0.00519 ( 9050) covalent geometry : angle 0.65737 (12202) *********************** 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 136 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 102 time to evaluate : 0.915 Fit side-chains revert: symmetry clash REVERT: A 267 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8857 (mp) REVERT: A 360 ARG cc_start: 0.6999 (OUTLIER) cc_final: 0.6428 (mtt90) REVERT: A 370 LYS cc_start: 0.7731 (mmmm) cc_final: 0.7522 (mmmm) REVERT: A 439 TYR cc_start: 0.8996 (t80) cc_final: 0.8783 (t80) REVERT: B 12 THR cc_start: 0.7242 (OUTLIER) cc_final: 0.5834 (t) REVERT: B 54 ASP cc_start: 0.7616 (t0) cc_final: 0.7108 (t0) REVERT: B 61 ARG cc_start: 0.6617 (mtm180) cc_final: 0.6281 (mtm110) REVERT: B 280 THR cc_start: 0.8859 (p) cc_final: 0.8610 (p) REVERT: B 312 MET cc_start: 0.7404 (OUTLIER) cc_final: 0.7156 (ttt) REVERT: B 322 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8353 (tt) outliers start: 34 outliers final: 23 residues processed: 128 average time/residue: 0.1877 time to fit residues: 34.7193 Evaluate side-chains 126 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 184 VAL 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 28 ILE Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 89 ILE 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 227 THR Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 407 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 48 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 90 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 100 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 12 optimal weight: 0.0770 chunk 108 optimal weight: 9.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 = 0.3920 r_free = 0.3920 target = 0.170087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 103)---------------| | r_work = 0.3461 r_free = 0.3461 target = 0.129736 restraints weight = 11312.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.123617 restraints weight = 21554.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.126373 restraints weight = 19747.817| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9050 Z= 0.111 Angle : 0.604 14.245 12202 Z= 0.304 Chirality : 0.042 0.163 1442 Planarity : 0.004 0.040 1536 Dihedral : 7.951 109.685 1336 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.70 % Favored : 93.21 % Rotamer: Outliers : 2.79 % Allowed : 19.63 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.25), residues: 1134 helix: -1.75 (0.20), residues: 682 sheet: -1.92 (0.54), residues: 80 loop : -1.33 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 66 HIS 0.003 0.001 HIS A 214 PHE 0.012 0.001 PHE B 56 TYR 0.016 0.001 TYR B 268 ARG 0.008 0.000 ARG A 488 Details of bonding type rmsd hydrogen bonds : bond 0.02487 ( 272) hydrogen bonds : angle 4.65142 ( 786) covalent geometry : bond 0.00259 ( 9050) covalent geometry : angle 0.60441 (12202) *********************** 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 133 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 106 time to evaluate : 1.012 Fit side-chains revert: symmetry clash REVERT: A 97 VAL cc_start: 0.9305 (t) cc_final: 0.9087 (m) REVERT: A 100 MET cc_start: 0.8404 (ttm) cc_final: 0.8164 (ttm) REVERT: A 360 ARG cc_start: 0.7196 (OUTLIER) cc_final: 0.6606 (mtt90) REVERT: B 54 ASP cc_start: 0.7470 (t0) cc_final: 0.6971 (t0) REVERT: B 61 ARG cc_start: 0.6599 (mtm180) cc_final: 0.6371 (mtm110) REVERT: B 115 PHE cc_start: 0.8187 (t80) cc_final: 0.7843 (t80) REVERT: B 280 THR cc_start: 0.8726 (p) cc_final: 0.8477 (p) REVERT: B 322 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8200 (tt) REVERT: B 410 TYR cc_start: 0.6800 (m-80) cc_final: 0.6510 (m-80) outliers start: 27 outliers final: 19 residues processed: 127 average time/residue: 0.1965 time to fit residues: 35.6319 Evaluate side-chains 123 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL 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 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 46 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 89 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 14 optimal weight: 0.5980 chunk 98 optimal weight: 3.9990 chunk 77 optimal weight: 0.4980 chunk 49 optimal weight: 7.9990 chunk 28 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 67 optimal weight: 0.0870 chunk 108 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 55 optimal weight: 7.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 = 0.4000 r_free = 0.4000 target = 0.176368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.133577 restraints weight = 11409.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.125491 restraints weight = 18224.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.128390 restraints weight = 16913.403| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9050 Z= 0.106 Angle : 0.607 12.117 12202 Z= 0.305 Chirality : 0.041 0.158 1442 Planarity : 0.004 0.039 1536 Dihedral : 7.786 108.758 1336 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.61 % Favored : 93.30 % Rotamer: Outliers : 2.69 % Allowed : 20.04 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.25), residues: 1134 helix: -1.64 (0.20), residues: 682 sheet: -1.85 (0.54), residues: 80 loop : -1.30 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 66 HIS 0.002 0.001 HIS A 214 PHE 0.010 0.001 PHE A 429 TYR 0.015 0.001 TYR B 268 ARG 0.009 0.000 ARG A 488 Details of bonding type rmsd hydrogen bonds : bond 0.02453 ( 272) hydrogen bonds : angle 4.58579 ( 786) covalent geometry : bond 0.00246 ( 9050) covalent geometry : angle 0.60657 (12202) *********************** 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 138 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 0.948 Fit side-chains revert: symmetry clash REVERT: A 100 MET cc_start: 0.8336 (ttm) cc_final: 0.8100 (ttm) REVERT: A 267 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8742 (mp) REVERT: A 360 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.6734 (mtt90) REVERT: B 54 ASP cc_start: 0.7377 (t0) cc_final: 0.6889 (t0) REVERT: B 61 ARG cc_start: 0.6658 (mtm180) cc_final: 0.6391 (mtm110) REVERT: B 115 PHE cc_start: 0.8089 (t80) cc_final: 0.7629 (t80) REVERT: B 280 THR cc_start: 0.8669 (p) cc_final: 0.8395 (p) REVERT: B 322 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8233 (tt) outliers start: 26 outliers final: 19 residues processed: 131 average time/residue: 0.2023 time to fit residues: 37.6026 Evaluate side-chains 128 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL 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 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 89 ILE 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 78 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 111 optimal weight: 20.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3919 r_free = 0.3919 target = 0.169955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.129630 restraints weight = 11294.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.131341 restraints weight = 22302.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.131607 restraints weight = 15882.960| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3462 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= 0.128 Angle : 0.633 15.923 12202 Z= 0.314 Chirality : 0.042 0.149 1442 Planarity : 0.004 0.039 1536 Dihedral : 7.888 108.657 1336 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.32 % Favored : 92.59 % Rotamer: Outliers : 2.89 % Allowed : 20.25 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.25), residues: 1134 helix: -1.53 (0.20), residues: 678 sheet: -1.58 (0.55), residues: 82 loop : -1.34 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 66 HIS 0.003 0.001 HIS B 405 PHE 0.012 0.001 PHE A 272 TYR 0.015 0.001 TYR B 268 ARG 0.010 0.000 ARG A 488 Details of bonding type rmsd hydrogen bonds : bond 0.02558 ( 272) hydrogen bonds : angle 4.56326 ( 786) covalent geometry : bond 0.00305 ( 9050) covalent geometry : angle 0.63347 (12202) *********************** 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 128 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 0.901 Fit side-chains revert: symmetry clash REVERT: A 240 GLN cc_start: 0.8778 (tp40) cc_final: 0.8520 (tp40) REVERT: A 267 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8785 (mp) REVERT: A 360 ARG cc_start: 0.6882 (OUTLIER) cc_final: 0.6329 (mtt90) REVERT: B 54 ASP cc_start: 0.7406 (t0) cc_final: 0.6896 (t0) REVERT: B 61 ARG cc_start: 0.6531 (mtm180) cc_final: 0.6291 (mtm110) REVERT: B 115 PHE cc_start: 0.8070 (t80) cc_final: 0.7671 (t80) REVERT: B 280 THR cc_start: 0.8656 (p) cc_final: 0.8407 (p) REVERT: B 322 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8233 (tt) outliers start: 28 outliers final: 20 residues processed: 122 average time/residue: 0.1885 time to fit residues: 33.0111 Evaluate side-chains 123 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.992 ------------------------------------------------------------------------------- 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 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 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 89 ILE 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 104 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 84 optimal weight: 0.4980 chunk 24 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 80 optimal weight: 0.3980 chunk 72 optimal weight: 0.5980 chunk 95 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3939 r_free = 0.3939 target = 0.172078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.131569 restraints weight = 11154.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.126213 restraints weight = 23212.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.128815 restraints weight = 21163.157| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9050 Z= 0.105 Angle : 0.615 13.456 12202 Z= 0.305 Chirality : 0.041 0.153 1442 Planarity : 0.004 0.040 1536 Dihedral : 7.733 106.558 1336 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.79 % Favored : 93.12 % Rotamer: Outliers : 2.79 % Allowed : 20.45 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.25), residues: 1134 helix: -1.31 (0.20), residues: 670 sheet: -1.49 (0.55), residues: 82 loop : -1.33 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 66 HIS 0.002 0.001 HIS A 214 PHE 0.011 0.001 PHE A 43 TYR 0.018 0.001 TYR A 130 ARG 0.011 0.000 ARG A 488 Details of bonding type rmsd hydrogen bonds : bond 0.02372 ( 272) hydrogen bonds : angle 4.51122 ( 786) covalent geometry : bond 0.00243 ( 9050) covalent geometry : angle 0.61544 (12202) ********************** 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 131 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.910 Fit side-chains revert: symmetry clash REVERT: A 240 GLN cc_start: 0.8778 (tp40) cc_final: 0.8522 (tp40) REVERT: A 267 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8748 (mp) REVERT: A 360 ARG cc_start: 0.7095 (OUTLIER) cc_final: 0.6496 (mtt90) REVERT: B 48 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8329 (mp) REVERT: B 54 ASP cc_start: 0.7426 (t0) cc_final: 0.6899 (t0) REVERT: B 115 PHE cc_start: 0.7930 (t80) cc_final: 0.7480 (t80) REVERT: B 280 THR cc_start: 0.8551 (p) cc_final: 0.8276 (p) REVERT: B 322 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8192 (tt) REVERT: B 439 TYR cc_start: 0.8777 (t80) cc_final: 0.8462 (t80) outliers start: 27 outliers final: 21 residues processed: 124 average time/residue: 0.1847 time to fit residues: 33.0292 Evaluate side-chains 129 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 0.957 ------------------------------------------------------------------------------- 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 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 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 48 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 89 ILE 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 75 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 99 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 88 optimal weight: 0.0770 chunk 82 optimal weight: 7.9990 chunk 84 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 109 optimal weight: 8.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- 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 = 0.170381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.130105 restraints weight = 11180.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.131969 restraints weight = 23608.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.131871 restraints weight = 14455.793| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9050 Z= 0.133 Angle : 0.627 13.132 12202 Z= 0.312 Chirality : 0.043 0.147 1442 Planarity : 0.004 0.039 1536 Dihedral : 7.894 106.751 1336 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.97 % Favored : 92.95 % Rotamer: Outliers : 2.69 % Allowed : 20.66 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.25), residues: 1134 helix: -1.35 (0.20), residues: 680 sheet: -0.99 (0.65), residues: 68 loop : -1.34 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 66 HIS 0.002 0.001 HIS B 107 PHE 0.018 0.001 PHE A 43 TYR 0.017 0.001 TYR A 130 ARG 0.010 0.000 ARG A 488 Details of bonding type rmsd hydrogen bonds : bond 0.02558 ( 272) hydrogen bonds : angle 4.50007 ( 786) covalent geometry : bond 0.00317 ( 9050) covalent geometry : angle 0.62711 (12202) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2633.43 seconds wall clock time: 46 minutes 57.69 seconds (2817.69 seconds total)