Starting phenix.real_space_refine on Sat Jun 28 02:11:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rms_19369/06_2025/8rms_19369.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rms_19369/06_2025/8rms_19369.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rms_19369/06_2025/8rms_19369.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rms_19369/06_2025/8rms_19369.map" model { file = "/net/cci-nas-00/data/ceres_data/8rms_19369/06_2025/8rms_19369.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rms_19369/06_2025/8rms_19369.cif" } resolution = 3.21 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= 0.002 sd= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mg 1 5.21 5 S 119 5.16 5 C 10191 2.51 5 N 2837 2.21 5 O 3041 1.98 5 H 16245 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 32434 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 11437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 708, 11437 Classifications: {'peptide': 708} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 32, 'TRANS': 675} Chain breaks: 1 Chain: "B" Number of atoms: 11376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 714, 11376 Classifications: {'peptide': 714} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 683} Chain breaks: 4 Chain: "C" Number of atoms: 9620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 9620 Classifications: {'peptide': 597} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 20, 'TRANS': 576} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 15.97, per 1000 atoms: 0.49 Number of scatterers: 32434 At special positions: 0 Unit cell: (115.08, 148.68, 99.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 119 16.00 Mg 1 11.99 O 3041 8.00 N 2837 7.00 C 10191 6.00 H 16245 1.00 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: 8.87 Conformation dependent library (CDL) restraints added in 2.3 seconds 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3808 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 24 sheets defined 49.2% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.99 Creating SS restraints... Processing helix chain 'A' and resid 1 through 9 Processing helix chain 'A' and resid 10 through 23 Processing helix chain 'A' and resid 32 through 49 Processing helix chain 'A' and resid 83 through 99 Processing helix chain 'A' and resid 126 through 139 removed outlier: 3.694A pdb=" N TYR A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 164 through 185 Processing helix chain 'A' and resid 187 through 194 Processing helix chain 'A' and resid 209 through 217 Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 240 through 249 Processing helix chain 'A' and resid 302 through 313 Processing helix chain 'A' and resid 330 through 352 removed outlier: 3.678A pdb=" N GLU A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 405 through 415 Processing helix chain 'A' and resid 433 through 451 Processing helix chain 'A' and resid 453 through 476 Processing helix chain 'A' and resid 529 through 538 Proline residue: A 534 - end of helix removed outlier: 3.986A pdb=" N GLU A 538 " --> pdb=" O HIS A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 580 Processing helix chain 'A' and resid 582 through 604 removed outlier: 4.282A pdb=" N LEU A 586 " --> pdb=" O ARG A 582 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N MET A 595 " --> pdb=" O GLN A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 613 Processing helix chain 'A' and resid 632 through 650 Processing helix chain 'A' and resid 652 through 674 removed outlier: 3.561A pdb=" N GLU A 656 " --> pdb=" O SER A 652 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYS A 664 " --> pdb=" O ALA A 660 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 692 Processing helix chain 'A' and resid 697 through 716 removed outlier: 3.752A pdb=" N ARG A 716 " --> pdb=" O THR A 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 17 through 22 Processing helix chain 'B' and resid 35 through 50 Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 117 Processing helix chain 'B' and resid 118 through 125 removed outlier: 3.513A pdb=" N LYS B 121 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY B 125 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 153 Processing helix chain 'B' and resid 156 through 161 Processing helix chain 'B' and resid 162 through 175 removed outlier: 3.519A pdb=" N ASP B 175 " --> pdb=" O MET B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 246 through 248 No H-bonds generated for 'chain 'B' and resid 246 through 248' Processing helix chain 'B' and resid 249 through 265 removed outlier: 3.760A pdb=" N LYS B 265 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 292 removed outlier: 3.818A pdb=" N LYS B 279 " --> pdb=" O GLY B 275 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA B 280 " --> pdb=" O ASN B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 removed outlier: 3.571A pdb=" N PHE B 318 " --> pdb=" O ASN B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 346 removed outlier: 4.499A pdb=" N ALA B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix removed outlier: 3.879A pdb=" N ASN B 346 " --> pdb=" O ILE B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 376 removed outlier: 3.817A pdb=" N ALA B 374 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE B 376 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 412 through 426 Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 455 through 474 Processing helix chain 'B' and resid 518 through 536 Processing helix chain 'B' and resid 540 through 559 Processing helix chain 'B' and resid 572 through 583 Processing helix chain 'B' and resid 590 through 594 Processing helix chain 'B' and resid 607 through 612 Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 636 through 640 Processing helix chain 'B' and resid 687 through 694 Processing helix chain 'B' and resid 695 through 700 removed outlier: 4.006A pdb=" N PHE B 699 " --> pdb=" O LEU B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 706 removed outlier: 4.011A pdb=" N TYR B 705 " --> pdb=" O PRO B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 733 Processing helix chain 'B' and resid 736 through 756 Processing helix chain 'C' and resid 2 through 13 removed outlier: 3.748A pdb=" N GLN C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 23 Processing helix chain 'C' and resid 24 through 31 removed outlier: 4.543A pdb=" N ALA C 29 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 52 removed outlier: 3.925A pdb=" N ALA C 52 " --> pdb=" O LYS C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 67 removed outlier: 3.926A pdb=" N MET C 66 " --> pdb=" O ARG C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 103 removed outlier: 3.660A pdb=" N VAL C 96 " --> pdb=" O SER C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 115 removed outlier: 4.442A pdb=" N LYS C 113 " --> pdb=" O VAL C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 127 Processing helix chain 'C' and resid 155 through 168 Processing helix chain 'C' and resid 169 through 172 removed outlier: 4.295A pdb=" N VAL C 172 " --> pdb=" O PRO C 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 169 through 172' Processing helix chain 'C' and resid 173 through 178 removed outlier: 3.763A pdb=" N LEU C 177 " --> pdb=" O GLY C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 193 removed outlier: 3.525A pdb=" N LYS C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 212 Processing helix chain 'C' and resid 225 through 229 Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 254 through 272 removed outlier: 4.337A pdb=" N VAL C 272 " --> pdb=" O ARG C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 286 Processing helix chain 'C' and resid 294 through 301 Processing helix chain 'C' and resid 305 through 316 Processing helix chain 'C' and resid 390 through 406 Processing helix chain 'C' and resid 407 through 412 removed outlier: 3.877A pdb=" N ILE C 411 " --> pdb=" O GLU C 407 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS C 412 " --> pdb=" O ASP C 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 407 through 412' Processing helix chain 'C' and resid 429 through 441 Processing helix chain 'C' and resid 442 through 448 Processing helix chain 'C' and resid 514 through 518 Processing helix chain 'C' and resid 709 through 716 removed outlier: 4.397A pdb=" N SER C 714 " --> pdb=" O ASN C 711 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN C 715 " --> pdb=" O GLU C 712 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 759 Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 62 removed outlier: 4.320A pdb=" N LYS A 73 " --> pdb=" O ILE A 54 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 Processing sheet with id=AA3, first strand: chain 'A' and resid 195 through 196 Processing sheet with id=AA4, first strand: chain 'A' and resid 258 through 259 removed outlier: 4.679A pdb=" N ASP B 305 " --> pdb=" O SER B 478 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N LYS B 480 " --> pdb=" O THR B 303 " (cutoff:3.500A) removed outlier: 9.733A pdb=" N THR B 303 " --> pdb=" O LYS B 480 " (cutoff:3.500A) removed outlier: 9.743A pdb=" N SER B 482 " --> pdb=" O THR B 301 " (cutoff:3.500A) removed outlier: 10.841A pdb=" N THR B 301 " --> pdb=" O SER B 482 " (cutoff:3.500A) removed outlier: 10.248A pdb=" N ILE B 484 " --> pdb=" O SER B 299 " (cutoff:3.500A) removed outlier: 11.221A pdb=" N SER B 299 " --> pdb=" O ILE B 484 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA B 448 " --> pdb=" O LEU B 441 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 290 through 292 removed outlier: 7.362A pdb=" N TYR A 501 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLY A 555 " --> pdb=" O ARG A 551 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ARG A 551 " --> pdb=" O GLY A 555 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N VAL A 557 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU A 549 " --> pdb=" O VAL A 557 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ARG A 559 " --> pdb=" O ASP A 547 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ASP A 547 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N MET A 561 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL A 542 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 290 through 292 removed outlier: 5.358A pdb=" N THR A 498 " --> pdb=" O CYS A 489 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N CYS A 489 " --> pdb=" O THR A 498 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU A 500 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N SER A 487 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY A 502 " --> pdb=" O MET A 485 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN A 481 " --> pdb=" O LYS A 506 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N PHE A 480 " --> pdb=" O MET A 360 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 377 through 380 removed outlier: 4.079A pdb=" N GLN B 367 " --> pdb=" O VAL A 379 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 627 through 631 removed outlier: 6.954A pdb=" N GLY A 627 " --> pdb=" O GLU A 623 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N GLU A 623 " --> pdb=" O GLY A 627 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLU A 629 " --> pdb=" O ILE A 621 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AB1, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AB2, first strand: chain 'B' and resid 178 through 185 removed outlier: 3.752A pdb=" N PHE B 185 " --> pdb=" O GLY B 206 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY B 206 " --> pdb=" O PHE B 185 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 243 through 244 removed outlier: 6.597A pdb=" N LEU B 224 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 489 through 492 Processing sheet with id=AB5, first strand: chain 'B' and resid 642 through 643 Processing sheet with id=AB6, first strand: chain 'C' and resid 57 through 58 removed outlier: 3.828A pdb=" N MET C 90 " --> pdb=" O SER C 79 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 129 through 135 removed outlier: 4.116A pdb=" N MET C 243 " --> pdb=" O GLY C 131 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL C 133 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLU C 241 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 141 through 146 Processing sheet with id=AB9, first strand: chain 'C' and resid 288 through 289 Processing sheet with id=AC1, first strand: chain 'C' and resid 319 through 320 removed outlier: 4.729A pdb=" N ILE C 319 " --> pdb=" O VAL C 494 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL C 494 " --> pdb=" O ILE C 319 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 324 through 325 removed outlier: 6.856A pdb=" N GLU C 362 " --> pdb=" O THR C 333 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA C 370 " --> pdb=" O GLY C 367 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR C 371 " --> pdb=" O VAL C 386 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N VAL C 386 " --> pdb=" O THR C 371 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE C 373 " --> pdb=" O LEU C 384 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LEU C 384 " --> pdb=" O ILE C 373 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ARG C 375 " --> pdb=" O ILE C 382 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N GLY C 388 " --> pdb=" O SER C 481 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N VAL C 478 " --> pdb=" O ILE C 463 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ILE C 463 " --> pdb=" O VAL C 478 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 337 through 345 Processing sheet with id=AC4, first strand: chain 'C' and resid 451 through 453 Processing sheet with id=AC5, first strand: chain 'C' and resid 496 through 498 removed outlier: 6.293A pdb=" N VAL C 504 " --> pdb=" O LEU C 512 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 694 through 699 removed outlier: 5.012A pdb=" N LEU C 733 " --> pdb=" O LEU C 697 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N LYS C 699 " --> pdb=" O VAL C 731 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N VAL C 731 " --> pdb=" O LYS C 699 " (cutoff:3.500A) 810 hydrogen bonds defined for protein. 2244 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: 13.57 Time building geometry restraints manager: 10.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 16213 1.03 - 1.23: 40 1.23 - 1.42: 6743 1.42 - 1.62: 9530 1.62 - 1.81: 206 Bond restraints: 32732 Sorted by residual: bond pdb=" N SER B 404 " pdb=" CA SER B 404 " ideal model delta sigma weight residual 1.463 1.456 0.008 6.90e-03 2.10e+04 1.20e+00 bond pdb=" CB MET A 374 " pdb=" CG MET A 374 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.44e-01 bond pdb=" CB PRO C 465 " pdb=" CG PRO C 465 " ideal model delta sigma weight residual 1.492 1.535 -0.043 5.00e-02 4.00e+02 7.54e-01 bond pdb=" CG MET B 718 " pdb=" SD MET B 718 " ideal model delta sigma weight residual 1.803 1.782 0.021 2.50e-02 1.60e+03 6.96e-01 bond pdb=" C ILE B 667 " pdb=" O ILE B 667 " ideal model delta sigma weight residual 1.232 1.239 -0.007 8.90e-03 1.26e+04 6.45e-01 ... (remaining 32727 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 57155 1.27 - 2.54: 1877 2.54 - 3.81: 129 3.81 - 5.09: 18 5.09 - 6.36: 2 Bond angle restraints: 59181 Sorted by residual: angle pdb=" N ILE A 79 " pdb=" CA ILE A 79 " pdb=" C ILE A 79 " ideal model delta sigma weight residual 113.53 109.93 3.60 9.80e-01 1.04e+00 1.35e+01 angle pdb=" N ILE A 30 " pdb=" CA ILE A 30 " pdb=" C ILE A 30 " ideal model delta sigma weight residual 111.81 108.91 2.90 8.60e-01 1.35e+00 1.14e+01 angle pdb=" CA MET B 718 " pdb=" CB MET B 718 " pdb=" CG MET B 718 " ideal model delta sigma weight residual 114.10 120.46 -6.36 2.00e+00 2.50e-01 1.01e+01 angle pdb=" N THR C 178 " pdb=" CA THR C 178 " pdb=" C THR C 178 " ideal model delta sigma weight residual 111.30 106.93 4.37 1.43e+00 4.89e-01 9.32e+00 angle pdb=" N LYS C 738 " pdb=" CA LYS C 738 " pdb=" C LYS C 738 " ideal model delta sigma weight residual 114.04 110.38 3.66 1.24e+00 6.50e-01 8.70e+00 ... (remaining 59176 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 13333 17.99 - 35.98: 1396 35.98 - 53.97: 460 53.97 - 71.96: 82 71.96 - 89.94: 28 Dihedral angle restraints: 15299 sinusoidal: 8522 harmonic: 6777 Sorted by residual: dihedral pdb=" CA LEU A 261 " pdb=" C LEU A 261 " pdb=" N ARG A 262 " pdb=" CA ARG A 262 " ideal model delta harmonic sigma weight residual 180.00 158.14 21.86 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA LEU B 695 " pdb=" C LEU B 695 " pdb=" N PHE B 696 " pdb=" CA PHE B 696 " ideal model delta harmonic sigma weight residual 180.00 161.63 18.37 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA SER A 291 " pdb=" C SER A 291 " pdb=" N ILE A 292 " pdb=" CA ILE A 292 " ideal model delta harmonic sigma weight residual 180.00 163.30 16.70 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 15296 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1649 0.031 - 0.062: 561 0.062 - 0.092: 140 0.092 - 0.123: 89 0.123 - 0.154: 13 Chirality restraints: 2452 Sorted by residual: chirality pdb=" CA ILE B 735 " pdb=" N ILE B 735 " pdb=" C ILE B 735 " pdb=" CB ILE B 735 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.94e-01 chirality pdb=" CA ILE C 385 " pdb=" N ILE C 385 " pdb=" C ILE C 385 " pdb=" CB ILE C 385 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.04e-01 chirality pdb=" CA VAL C 386 " pdb=" N VAL C 386 " pdb=" C VAL C 386 " pdb=" CB VAL C 386 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.75e-01 ... (remaining 2449 not shown) Planarity restraints: 4794 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 464 " -0.050 5.00e-02 4.00e+02 7.50e-02 8.99e+00 pdb=" N PRO C 465 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO C 465 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 465 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 624 " -0.033 5.00e-02 4.00e+02 5.01e-02 4.01e+00 pdb=" N PRO A 625 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 625 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 625 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 78 " 0.024 5.00e-02 4.00e+02 3.72e-02 2.21e+00 pdb=" N PRO B 79 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 79 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 79 " 0.021 5.00e-02 4.00e+02 ... (remaining 4791 not shown) Histogram of nonbonded interaction distances: 1.14 - 1.83: 103 1.83 - 2.53: 27723 2.53 - 3.22: 100305 3.22 - 3.91: 127059 3.91 - 4.60: 201884 Nonbonded interactions: 457074 Sorted by model distance: nonbonded pdb=" HB3 GLU B 636 " pdb=" HZ1 LYS C 32 " model vdw 1.142 2.270 nonbonded pdb=" HB3 SER C 225 " pdb=" HD2 TYR C 228 " model vdw 1.241 2.270 nonbonded pdb=" HG2 GLU C 341 " pdb=" HD2 ARG C 355 " model vdw 1.517 2.440 nonbonded pdb=" HE ARG A 75 " pdb=" OD1 ASP A 111 " model vdw 1.559 2.450 nonbonded pdb=" OD1 ASN A 647 " pdb=" HE1 TRP A 699 " model vdw 1.563 2.450 ... (remaining 457069 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.520 Extract box with map and model: 1.350 Check model and map are aligned: 0.240 Set scattering table: 0.320 Process input model: 69.980 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 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 : 0.002 0.043 16487 Z= 0.110 Angle : 0.510 6.357 22214 Z= 0.279 Chirality : 0.038 0.154 2452 Planarity : 0.004 0.075 2867 Dihedral : 17.535 89.945 6332 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.22 % Allowed : 23.03 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.19), residues: 2001 helix: 1.50 (0.18), residues: 889 sheet: -0.00 (0.36), residues: 236 loop : -1.42 (0.19), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 131 HIS 0.006 0.001 HIS A 74 PHE 0.010 0.001 PHE B 730 TYR 0.010 0.001 TYR B 555 ARG 0.006 0.000 ARG B 706 Details of bonding type rmsd hydrogen bonds : bond 0.14584 ( 806) hydrogen bonds : angle 5.92118 ( 2244) covalent geometry : bond 0.00241 (16487) covalent geometry : angle 0.50998 (22214) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 268 time to evaluate : 2.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 301 ASN cc_start: 0.2769 (t0) cc_final: 0.2476 (m-40) REVERT: C 476 ARG cc_start: 0.6357 (ttm170) cc_final: 0.4832 (ttm170) outliers start: 4 outliers final: 3 residues processed: 270 average time/residue: 0.7266 time to fit residues: 281.1713 Evaluate side-chains 246 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 243 time to evaluate : 2.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain C residue 357 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 4.9990 chunk 151 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 102 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 156 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 181 optimal weight: 6.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN B 247 GLN B 306 ASN B 312 ASN B 694 ASN C 425 ASN C 728 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.167431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.136187 restraints weight = 82897.808| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 2.96 r_work: 0.3777 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16487 Z= 0.150 Angle : 0.521 5.642 22214 Z= 0.282 Chirality : 0.039 0.147 2452 Planarity : 0.004 0.047 2867 Dihedral : 4.198 57.151 2212 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.12 % Allowed : 23.15 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.19), residues: 2001 helix: 1.34 (0.17), residues: 916 sheet: -0.26 (0.35), residues: 243 loop : -1.38 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 666 HIS 0.005 0.001 HIS A 74 PHE 0.012 0.001 PHE B 730 TYR 0.011 0.001 TYR A 564 ARG 0.005 0.000 ARG B 706 Details of bonding type rmsd hydrogen bonds : bond 0.04718 ( 806) hydrogen bonds : angle 5.02637 ( 2244) covalent geometry : bond 0.00337 (16487) covalent geometry : angle 0.52079 (22214) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 247 time to evaluate : 3.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 TYR cc_start: 0.7006 (m-10) cc_final: 0.6775 (m-10) REVERT: A 581 MET cc_start: 0.5507 (OUTLIER) cc_final: 0.5082 (ttm) REVERT: B 305 ASP cc_start: 0.7581 (OUTLIER) cc_final: 0.7281 (m-30) REVERT: C 476 ARG cc_start: 0.6376 (ttm170) cc_final: 0.4813 (ttm170) outliers start: 20 outliers final: 13 residues processed: 260 average time/residue: 0.8154 time to fit residues: 312.8747 Evaluate side-chains 251 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 236 time to evaluate : 2.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 247 GLN Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 662 THR Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 357 HIS Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 751 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 145 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 53 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 690 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.168019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.136838 restraints weight = 82888.196| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 2.96 r_work: 0.3789 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16487 Z= 0.119 Angle : 0.487 6.116 22214 Z= 0.260 Chirality : 0.038 0.144 2452 Planarity : 0.004 0.043 2867 Dihedral : 4.011 56.671 2207 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.39 % Allowed : 22.81 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.19), residues: 2001 helix: 1.46 (0.17), residues: 918 sheet: -0.24 (0.34), residues: 246 loop : -1.40 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 368 HIS 0.004 0.001 HIS A 74 PHE 0.008 0.001 PHE B 505 TYR 0.010 0.001 TYR B 555 ARG 0.004 0.000 ARG B 706 Details of bonding type rmsd hydrogen bonds : bond 0.04137 ( 806) hydrogen bonds : angle 4.79127 ( 2244) covalent geometry : bond 0.00268 (16487) covalent geometry : angle 0.48742 (22214) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 252 time to evaluate : 3.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 581 MET cc_start: 0.5623 (OUTLIER) cc_final: 0.5184 (ttm) REVERT: A 599 GLU cc_start: 0.7520 (tp30) cc_final: 0.7056 (tp30) REVERT: B 305 ASP cc_start: 0.7498 (OUTLIER) cc_final: 0.7202 (m-30) REVERT: B 634 HIS cc_start: 0.5215 (OUTLIER) cc_final: 0.4363 (m-70) REVERT: B 718 MET cc_start: 0.8580 (mpt) cc_final: 0.8357 (mpt) REVERT: C 476 ARG cc_start: 0.6399 (ttm170) cc_final: 0.4799 (ttm170) outliers start: 25 outliers final: 19 residues processed: 269 average time/residue: 1.2030 time to fit residues: 491.0747 Evaluate side-chains 258 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 236 time to evaluate : 2.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 590 GLN Chi-restraints excluded: chain A residue 609 LYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 634 HIS Chi-restraints excluded: chain B residue 662 THR Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 379 ARG Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 751 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 52 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 174 optimal weight: 10.0000 chunk 145 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 162 optimal weight: 0.0060 chunk 16 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.167120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.135918 restraints weight = 83513.511| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 2.92 r_work: 0.3777 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16487 Z= 0.141 Angle : 0.498 4.521 22214 Z= 0.266 Chirality : 0.038 0.145 2452 Planarity : 0.004 0.048 2867 Dihedral : 3.841 20.376 2205 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.23 % Allowed : 22.76 % Favored : 75.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.19), residues: 2001 helix: 1.39 (0.17), residues: 918 sheet: -0.31 (0.34), residues: 246 loop : -1.50 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 368 HIS 0.007 0.001 HIS A 74 PHE 0.011 0.001 PHE B 505 TYR 0.011 0.001 TYR A 564 ARG 0.004 0.000 ARG A 256 Details of bonding type rmsd hydrogen bonds : bond 0.03943 ( 806) hydrogen bonds : angle 4.69947 ( 2244) covalent geometry : bond 0.00320 (16487) covalent geometry : angle 0.49770 (22214) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 241 time to evaluate : 3.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 391 LYS cc_start: 0.6620 (tmtt) cc_final: 0.6352 (tmtt) REVERT: A 423 VAL cc_start: 0.7442 (OUTLIER) cc_final: 0.7198 (p) REVERT: A 581 MET cc_start: 0.5563 (OUTLIER) cc_final: 0.5137 (ttm) REVERT: A 599 GLU cc_start: 0.7607 (tp30) cc_final: 0.7163 (tp30) REVERT: B 305 ASP cc_start: 0.7486 (OUTLIER) cc_final: 0.7157 (m-30) REVERT: B 317 MET cc_start: 0.6460 (mmp) cc_final: 0.5998 (mmt) REVERT: B 634 HIS cc_start: 0.5250 (OUTLIER) cc_final: 0.4312 (m-70) REVERT: C 283 MET cc_start: 0.7159 (OUTLIER) cc_final: 0.6936 (mmt) REVERT: C 476 ARG cc_start: 0.6413 (ttm170) cc_final: 0.4785 (ttm110) outliers start: 40 outliers final: 27 residues processed: 266 average time/residue: 0.7278 time to fit residues: 279.1787 Evaluate side-chains 263 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 231 time to evaluate : 2.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 590 GLN Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 602 ARG Chi-restraints excluded: chain B residue 634 HIS Chi-restraints excluded: chain B residue 662 THR Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 755 ARG Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain C residue 379 ARG Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 751 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 188 optimal weight: 7.9990 chunk 157 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 155 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 165 optimal weight: 0.0670 chunk 113 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 overall best weight: 2.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 600 ASN B 642 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.165324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.134097 restraints weight = 83668.776| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 2.89 r_work: 0.3754 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16487 Z= 0.185 Angle : 0.530 4.814 22214 Z= 0.287 Chirality : 0.039 0.152 2452 Planarity : 0.004 0.046 2867 Dihedral : 4.052 20.957 2205 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.96 % Allowed : 23.26 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.18), residues: 2001 helix: 1.17 (0.17), residues: 916 sheet: -0.38 (0.34), residues: 241 loop : -1.63 (0.19), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 422 HIS 0.006 0.001 HIS A 74 PHE 0.014 0.002 PHE B 505 TYR 0.013 0.002 TYR A 564 ARG 0.003 0.000 ARG A 116 Details of bonding type rmsd hydrogen bonds : bond 0.04236 ( 806) hydrogen bonds : angle 4.77280 ( 2244) covalent geometry : bond 0.00422 (16487) covalent geometry : angle 0.53022 (22214) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 238 time to evaluate : 3.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 VAL cc_start: 0.7464 (OUTLIER) cc_final: 0.7243 (p) REVERT: A 581 MET cc_start: 0.5598 (OUTLIER) cc_final: 0.5179 (ttm) REVERT: B 7 LEU cc_start: 0.8379 (mp) cc_final: 0.7835 (mp) REVERT: B 8 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7684 (tt) REVERT: B 305 ASP cc_start: 0.7471 (OUTLIER) cc_final: 0.7152 (m-30) REVERT: B 634 HIS cc_start: 0.5355 (OUTLIER) cc_final: 0.4307 (m-70) REVERT: B 697 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7404 (mt-10) REVERT: C 476 ARG cc_start: 0.6470 (ttm170) cc_final: 0.4809 (ttp80) REVERT: C 746 ASP cc_start: 0.3211 (OUTLIER) cc_final: 0.2163 (p0) outliers start: 53 outliers final: 38 residues processed: 272 average time/residue: 1.1238 time to fit residues: 461.2088 Evaluate side-chains 278 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 233 time to evaluate : 3.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 590 GLN Chi-restraints excluded: chain A residue 609 LYS Chi-restraints excluded: chain A residue 682 ASP Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 602 ARG Chi-restraints excluded: chain B residue 634 HIS Chi-restraints excluded: chain B residue 662 THR Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 755 ARG Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain C residue 357 HIS Chi-restraints excluded: chain C residue 379 ARG Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 746 ASP Chi-restraints excluded: chain C residue 751 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 118 optimal weight: 5.9990 chunk 195 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 181 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 184 optimal weight: 7.9990 chunk 134 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 133 optimal weight: 0.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.166141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.135100 restraints weight = 83660.785| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 2.90 r_work: 0.3767 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16487 Z= 0.136 Angle : 0.500 4.639 22214 Z= 0.267 Chirality : 0.039 0.149 2452 Planarity : 0.004 0.056 2867 Dihedral : 3.938 20.858 2205 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.51 % Allowed : 23.93 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.19), residues: 2001 helix: 1.36 (0.17), residues: 919 sheet: -0.38 (0.34), residues: 246 loop : -1.63 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 368 HIS 0.005 0.001 HIS A 74 PHE 0.012 0.001 PHE B 740 TYR 0.011 0.001 TYR A 564 ARG 0.003 0.000 ARG B 706 Details of bonding type rmsd hydrogen bonds : bond 0.03879 ( 806) hydrogen bonds : angle 4.60789 ( 2244) covalent geometry : bond 0.00312 (16487) covalent geometry : angle 0.49967 (22214) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 244 time to evaluate : 2.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 VAL cc_start: 0.7448 (OUTLIER) cc_final: 0.7221 (p) REVERT: A 581 MET cc_start: 0.5658 (OUTLIER) cc_final: 0.5256 (ttm) REVERT: A 599 GLU cc_start: 0.7732 (tp30) cc_final: 0.7258 (tp30) REVERT: B 7 LEU cc_start: 0.8393 (mp) cc_final: 0.7839 (mp) REVERT: B 305 ASP cc_start: 0.7439 (OUTLIER) cc_final: 0.7139 (m-30) REVERT: B 634 HIS cc_start: 0.5270 (OUTLIER) cc_final: 0.4193 (m-70) REVERT: C 241 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7839 (tm-30) REVERT: C 476 ARG cc_start: 0.6421 (ttm170) cc_final: 0.4821 (ttm110) REVERT: C 746 ASP cc_start: 0.3013 (m-30) cc_final: 0.1964 (p0) outliers start: 45 outliers final: 33 residues processed: 271 average time/residue: 0.7152 time to fit residues: 282.1174 Evaluate side-chains 277 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 240 time to evaluate : 2.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 609 LYS Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 602 ARG Chi-restraints excluded: chain B residue 634 HIS Chi-restraints excluded: chain B residue 662 THR Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 755 ARG Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain C residue 323 PHE Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 751 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 145 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 chunk 190 optimal weight: 8.9990 chunk 24 optimal weight: 0.9980 chunk 194 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.164690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.133757 restraints weight = 83407.349| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 2.91 r_work: 0.3752 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16487 Z= 0.172 Angle : 0.526 5.002 22214 Z= 0.284 Chirality : 0.039 0.151 2452 Planarity : 0.005 0.095 2867 Dihedral : 4.081 20.730 2205 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.68 % Allowed : 24.21 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.19), residues: 2001 helix: 1.19 (0.17), residues: 920 sheet: -0.47 (0.34), residues: 246 loop : -1.74 (0.20), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 422 HIS 0.005 0.001 HIS A 452 PHE 0.013 0.001 PHE B 505 TYR 0.012 0.002 TYR A 564 ARG 0.013 0.000 ARG C 379 Details of bonding type rmsd hydrogen bonds : bond 0.04077 ( 806) hydrogen bonds : angle 4.68301 ( 2244) covalent geometry : bond 0.00394 (16487) covalent geometry : angle 0.52628 (22214) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 241 time to evaluate : 2.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 VAL cc_start: 0.7520 (OUTLIER) cc_final: 0.7290 (p) REVERT: A 581 MET cc_start: 0.5622 (OUTLIER) cc_final: 0.5218 (ttm) REVERT: B 7 LEU cc_start: 0.8441 (mp) cc_final: 0.7947 (mp) REVERT: B 8 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7718 (tt) REVERT: B 127 GLN cc_start: 0.7034 (mm-40) cc_final: 0.6752 (mm-40) REVERT: B 305 ASP cc_start: 0.7451 (OUTLIER) cc_final: 0.7127 (m-30) REVERT: B 634 HIS cc_start: 0.5414 (OUTLIER) cc_final: 0.4233 (m-70) REVERT: B 697 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7501 (mt-10) REVERT: C 241 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7822 (tm-30) REVERT: C 476 ARG cc_start: 0.6452 (ttm170) cc_final: 0.4810 (ttp80) REVERT: C 746 ASP cc_start: 0.2994 (OUTLIER) cc_final: 0.2085 (p0) REVERT: C 752 LYS cc_start: 0.6948 (mmmt) cc_final: 0.6618 (pttp) outliers start: 48 outliers final: 34 residues processed: 271 average time/residue: 0.7242 time to fit residues: 286.1759 Evaluate side-chains 280 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 239 time to evaluate : 2.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 590 GLN Chi-restraints excluded: chain A residue 609 LYS Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 602 ARG Chi-restraints excluded: chain B residue 634 HIS Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 755 ARG Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain C residue 323 PHE Chi-restraints excluded: chain C residue 357 HIS Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 746 ASP Chi-restraints excluded: chain C residue 751 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 106 optimal weight: 0.9980 chunk 164 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 188 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 71 optimal weight: 0.5980 chunk 151 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 466 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.166770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.135830 restraints weight = 82946.500| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 2.93 r_work: 0.3779 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16487 Z= 0.109 Angle : 0.486 4.896 22214 Z= 0.256 Chirality : 0.038 0.150 2452 Planarity : 0.004 0.054 2867 Dihedral : 3.852 21.502 2205 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.01 % Allowed : 24.60 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.19), residues: 2001 helix: 1.57 (0.17), residues: 920 sheet: -0.36 (0.34), residues: 247 loop : -1.59 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 368 HIS 0.005 0.001 HIS A 452 PHE 0.012 0.001 PHE B 740 TYR 0.011 0.001 TYR A 564 ARG 0.004 0.000 ARG B 706 Details of bonding type rmsd hydrogen bonds : bond 0.03561 ( 806) hydrogen bonds : angle 4.44140 ( 2244) covalent geometry : bond 0.00250 (16487) covalent geometry : angle 0.48570 (22214) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 246 time to evaluate : 2.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 581 MET cc_start: 0.5641 (OUTLIER) cc_final: 0.5229 (ttm) REVERT: A 599 GLU cc_start: 0.7757 (tp30) cc_final: 0.7303 (tp30) REVERT: B 7 LEU cc_start: 0.8430 (mp) cc_final: 0.7894 (mp) REVERT: B 127 GLN cc_start: 0.7048 (mm-40) cc_final: 0.6740 (mm-40) REVERT: B 305 ASP cc_start: 0.7403 (OUTLIER) cc_final: 0.7113 (m-30) REVERT: B 634 HIS cc_start: 0.5368 (OUTLIER) cc_final: 0.4202 (m-70) REVERT: C 164 MET cc_start: 0.8356 (mmt) cc_final: 0.7441 (mmt) REVERT: C 241 GLU cc_start: 0.8004 (tm-30) cc_final: 0.7781 (tm-30) REVERT: C 476 ARG cc_start: 0.6358 (ttm170) cc_final: 0.4698 (ttp80) REVERT: C 746 ASP cc_start: 0.2805 (m-30) cc_final: 0.1989 (p0) REVERT: C 752 LYS cc_start: 0.7188 (mmmt) cc_final: 0.6699 (pttp) outliers start: 36 outliers final: 28 residues processed: 269 average time/residue: 0.7308 time to fit residues: 287.2823 Evaluate side-chains 269 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 238 time to evaluate : 2.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 590 GLN Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 246 MET Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 602 ARG Chi-restraints excluded: chain B residue 634 HIS Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 755 ARG Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain C residue 323 PHE Chi-restraints excluded: chain C residue 357 HIS Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 751 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 42 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 195 optimal weight: 0.8980 chunk 163 optimal weight: 0.8980 chunk 103 optimal weight: 9.9990 chunk 99 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.166590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.135620 restraints weight = 82930.459| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 2.93 r_work: 0.3773 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16487 Z= 0.118 Angle : 0.490 5.380 22214 Z= 0.259 Chirality : 0.038 0.150 2452 Planarity : 0.004 0.046 2867 Dihedral : 3.820 21.060 2205 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.90 % Allowed : 24.76 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.19), residues: 2001 helix: 1.59 (0.17), residues: 922 sheet: -0.25 (0.35), residues: 237 loop : -1.62 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 368 HIS 0.005 0.001 HIS A 452 PHE 0.011 0.001 PHE B 740 TYR 0.010 0.001 TYR A 564 ARG 0.004 0.000 ARG A 213 Details of bonding type rmsd hydrogen bonds : bond 0.03562 ( 806) hydrogen bonds : angle 4.43587 ( 2244) covalent geometry : bond 0.00270 (16487) covalent geometry : angle 0.49021 (22214) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 239 time to evaluate : 2.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 VAL cc_start: 0.7472 (OUTLIER) cc_final: 0.7235 (p) REVERT: A 581 MET cc_start: 0.5675 (OUTLIER) cc_final: 0.5265 (ttm) REVERT: A 599 GLU cc_start: 0.7813 (tp30) cc_final: 0.7388 (tp30) REVERT: A 613 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7618 (mm-30) REVERT: B 7 LEU cc_start: 0.8439 (mp) cc_final: 0.7907 (mp) REVERT: B 127 GLN cc_start: 0.6985 (mm-40) cc_final: 0.6623 (mm-40) REVERT: B 305 ASP cc_start: 0.7379 (OUTLIER) cc_final: 0.7100 (m-30) REVERT: B 634 HIS cc_start: 0.5369 (OUTLIER) cc_final: 0.4143 (m-70) REVERT: C 241 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7851 (tm-30) REVERT: C 476 ARG cc_start: 0.6356 (ttm170) cc_final: 0.4704 (ttp80) REVERT: C 746 ASP cc_start: 0.2844 (OUTLIER) cc_final: 0.2002 (p0) REVERT: C 752 LYS cc_start: 0.6965 (mmmt) cc_final: 0.6611 (pttp) outliers start: 34 outliers final: 26 residues processed: 260 average time/residue: 0.7687 time to fit residues: 292.0752 Evaluate side-chains 270 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 239 time to evaluate : 2.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 590 GLN Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 246 MET Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 602 ARG Chi-restraints excluded: chain B residue 634 HIS Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 755 ARG Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain C residue 323 PHE Chi-restraints excluded: chain C residue 357 HIS Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 746 ASP Chi-restraints excluded: chain C residue 751 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 5 optimal weight: 10.0000 chunk 126 optimal weight: 2.9990 chunk 160 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 163 optimal weight: 0.5980 chunk 30 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 196 optimal weight: 6.9990 chunk 193 optimal weight: 10.0000 chunk 95 optimal weight: 0.8980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.165416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.134495 restraints weight = 83326.900| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 2.93 r_work: 0.3762 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16487 Z= 0.144 Angle : 0.517 6.405 22214 Z= 0.274 Chirality : 0.039 0.151 2452 Planarity : 0.004 0.089 2867 Dihedral : 3.929 20.951 2205 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.84 % Allowed : 24.65 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.19), residues: 2001 helix: 1.45 (0.17), residues: 922 sheet: -0.41 (0.34), residues: 243 loop : -1.67 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 422 HIS 0.005 0.001 HIS A 452 PHE 0.012 0.001 PHE B 505 TYR 0.011 0.001 TYR A 564 ARG 0.004 0.000 ARG A 196 Details of bonding type rmsd hydrogen bonds : bond 0.03781 ( 806) hydrogen bonds : angle 4.53627 ( 2244) covalent geometry : bond 0.00332 (16487) covalent geometry : angle 0.51710 (22214) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 236 time to evaluate : 2.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 VAL cc_start: 0.7481 (OUTLIER) cc_final: 0.7232 (p) REVERT: A 581 MET cc_start: 0.5679 (OUTLIER) cc_final: 0.5267 (ttm) REVERT: A 599 GLU cc_start: 0.7767 (tp30) cc_final: 0.7293 (tp30) REVERT: A 613 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7423 (mm-30) REVERT: B 7 LEU cc_start: 0.8470 (mp) cc_final: 0.7988 (mp) REVERT: B 127 GLN cc_start: 0.7046 (mm-40) cc_final: 0.6714 (mm-40) REVERT: B 305 ASP cc_start: 0.7407 (OUTLIER) cc_final: 0.7098 (m-30) REVERT: B 634 HIS cc_start: 0.5324 (OUTLIER) cc_final: 0.3937 (m-70) REVERT: C 241 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7866 (tm-30) REVERT: C 476 ARG cc_start: 0.6396 (ttm170) cc_final: 0.4744 (ttp80) REVERT: C 746 ASP cc_start: 0.3020 (OUTLIER) cc_final: 0.2156 (p0) REVERT: C 752 LYS cc_start: 0.6971 (mmmt) cc_final: 0.6621 (pttp) outliers start: 33 outliers final: 27 residues processed: 256 average time/residue: 0.7187 time to fit residues: 267.0620 Evaluate side-chains 267 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 235 time to evaluate : 2.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 590 GLN Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 246 MET Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 602 ARG Chi-restraints excluded: chain B residue 634 HIS Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 755 ARG Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain C residue 323 PHE Chi-restraints excluded: chain C residue 357 HIS Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 746 ASP Chi-restraints excluded: chain C residue 751 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 152 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 chunk 87 optimal weight: 5.9990 chunk 194 optimal weight: 6.9990 chunk 192 optimal weight: 4.9990 chunk 127 optimal weight: 0.9980 chunk 142 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 162 optimal weight: 0.6980 chunk 156 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.166581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.135691 restraints weight = 82871.110| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 2.92 r_work: 0.3779 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16487 Z= 0.108 Angle : 0.493 6.045 22214 Z= 0.259 Chirality : 0.038 0.150 2452 Planarity : 0.004 0.082 2867 Dihedral : 3.824 21.410 2205 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.84 % Allowed : 24.82 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.19), residues: 2001 helix: 1.64 (0.17), residues: 922 sheet: -0.35 (0.34), residues: 243 loop : -1.57 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 406 HIS 0.004 0.001 HIS A 452 PHE 0.009 0.001 PHE B 740 TYR 0.010 0.001 TYR B 555 ARG 0.004 0.000 ARG B 706 Details of bonding type rmsd hydrogen bonds : bond 0.03503 ( 806) hydrogen bonds : angle 4.41698 ( 2244) covalent geometry : bond 0.00247 (16487) covalent geometry : angle 0.49252 (22214) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14680.81 seconds wall clock time: 258 minutes 40.21 seconds (15520.21 seconds total)