Starting phenix.real_space_refine on Tue Aug 26 01:55:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rms_19369/08_2025/8rms_19369.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rms_19369/08_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_19369/08_2025/8rms_19369.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rms_19369/08_2025/8rms_19369.map" model { file = "/net/cci-nas-00/data/ceres_data/8rms_19369/08_2025/8rms_19369.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rms_19369/08_2025/8rms_19369.cif" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 5.69, per 1000 atoms: 0.18 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: 3.05 Conformation dependent library (CDL) restraints added in 967.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.04 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: 8.66 Time building geometry restraints manager: 4.16 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: 4.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.180 Extract box with map and model: 0.480 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 31.840 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.250 ------------------------------------------------------------------------------- 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 : 8.69 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 ARG 0.006 0.000 ARG B 706 TYR 0.010 0.001 TYR B 555 PHE 0.010 0.001 PHE B 730 TRP 0.009 0.001 TRP B 131 HIS 0.006 0.001 HIS A 74 Details of bonding type rmsd covalent geometry : bond 0.00241 (16487) covalent geometry : angle 0.50998 (22214) hydrogen bonds : bond 0.14584 ( 806) hydrogen bonds : angle 5.92118 ( 2244) *********************** 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 : 0.920 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: C 301 ASN cc_start: 0.2769 (t0) cc_final: 0.2475 (m-40) REVERT: C 476 ARG cc_start: 0.6357 (ttm170) cc_final: 0.4831 (ttm170) outliers start: 4 outliers final: 3 residues processed: 270 average time/residue: 0.3735 time to fit residues: 143.2001 Evaluate side-chains 243 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 240 time to evaluate : 0.825 ------------------------------------------------------------------------------- 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 98 optimal weight: 5.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 690 GLN B 694 ASN C 425 ASN C 728 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.166111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.134859 restraints weight = 83639.758| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 2.95 r_work: 0.3767 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16487 Z= 0.188 Angle : 0.543 5.617 22214 Z= 0.296 Chirality : 0.040 0.150 2452 Planarity : 0.004 0.050 2867 Dihedral : 4.312 57.715 2212 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.45 % Allowed : 23.26 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.19), residues: 2001 helix: 1.16 (0.17), residues: 915 sheet: -0.33 (0.35), residues: 243 loop : -1.50 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 706 TYR 0.013 0.002 TYR A 564 PHE 0.012 0.001 PHE B 22 TRP 0.009 0.001 TRP A 577 HIS 0.005 0.001 HIS A 74 Details of bonding type rmsd covalent geometry : bond 0.00421 (16487) covalent geometry : angle 0.54284 (22214) hydrogen bonds : bond 0.05059 ( 806) hydrogen bonds : angle 5.14887 ( 2244) *********************** 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: 26 poor density : 241 time to evaluate : 0.886 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: A 334 TYR cc_start: 0.7063 (m-10) cc_final: 0.6813 (m-10) REVERT: A 581 MET cc_start: 0.5573 (OUTLIER) cc_final: 0.5147 (ttm) REVERT: B 305 ASP cc_start: 0.7608 (OUTLIER) cc_final: 0.7286 (m-30) REVERT: B 475 ILE cc_start: 0.7571 (mt) cc_final: 0.7254 (mt) REVERT: C 476 ARG cc_start: 0.6425 (ttm170) cc_final: 0.4840 (ttm170) outliers start: 26 outliers final: 18 residues processed: 257 average time/residue: 0.3372 time to fit residues: 126.3890 Evaluate side-chains 253 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 233 time to evaluate : 0.902 ------------------------------------------------------------------------------- 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 308 ILE Chi-restraints excluded: chain A residue 341 VAL 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 245 THR 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 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 135 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 37 optimal weight: 0.3980 chunk 142 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 159 optimal weight: 0.9990 chunk 151 optimal weight: 8.9990 chunk 58 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 192 optimal weight: 9.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- 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 600 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.165552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.134363 restraints weight = 83785.676| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 2.90 r_work: 0.3758 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 16487 Z= 0.188 Angle : 0.540 6.676 22214 Z= 0.293 Chirality : 0.040 0.147 2452 Planarity : 0.004 0.050 2867 Dihedral : 4.348 58.139 2207 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.29 % Allowed : 23.15 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.18), residues: 2001 helix: 0.99 (0.17), residues: 918 sheet: -0.37 (0.35), residues: 241 loop : -1.66 (0.19), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 706 TYR 0.013 0.002 TYR A 564 PHE 0.013 0.001 PHE B 505 TRP 0.009 0.001 TRP B 131 HIS 0.006 0.001 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00430 (16487) covalent geometry : angle 0.54018 (22214) hydrogen bonds : bond 0.04602 ( 806) hydrogen bonds : angle 5.02233 ( 2244) *********************** 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 291 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 250 time to evaluate : 0.889 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 391 LYS cc_start: 0.6747 (tmtt) cc_final: 0.6493 (tmtt) REVERT: A 423 VAL cc_start: 0.7438 (OUTLIER) cc_final: 0.7216 (p) REVERT: A 581 MET cc_start: 0.5676 (OUTLIER) cc_final: 0.5265 (ttm) REVERT: B 305 ASP cc_start: 0.7556 (OUTLIER) cc_final: 0.7230 (m-30) REVERT: B 634 HIS cc_start: 0.5264 (OUTLIER) cc_final: 0.4325 (m-70) REVERT: C 476 ARG cc_start: 0.6444 (ttm170) cc_final: 0.4843 (ttm110) outliers start: 41 outliers final: 27 residues processed: 272 average time/residue: 0.3671 time to fit residues: 142.9362 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 : 0.875 ------------------------------------------------------------------------------- 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 261 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 308 ILE 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 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 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 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 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 84 optimal weight: 4.9990 chunk 152 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 112 optimal weight: 0.2980 chunk 195 optimal weight: 0.9980 chunk 127 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.168590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.137454 restraints weight = 82775.043| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 2.93 r_work: 0.3799 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16487 Z= 0.099 Angle : 0.480 7.946 22214 Z= 0.254 Chirality : 0.038 0.145 2452 Planarity : 0.004 0.050 2867 Dihedral : 3.764 22.271 2205 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.67 % Allowed : 23.54 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.19), residues: 2001 helix: 1.52 (0.17), residues: 917 sheet: -0.28 (0.34), residues: 246 loop : -1.50 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 706 TYR 0.010 0.001 TYR B 555 PHE 0.007 0.001 PHE C 217 TRP 0.009 0.001 TRP A 368 HIS 0.004 0.001 HIS A 74 Details of bonding type rmsd covalent geometry : bond 0.00220 (16487) covalent geometry : angle 0.47962 (22214) hydrogen bonds : bond 0.03676 ( 806) hydrogen bonds : angle 4.61398 ( 2244) *********************** 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 282 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 252 time to evaluate : 0.911 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 581 MET cc_start: 0.5514 (OUTLIER) cc_final: 0.5087 (ttm) REVERT: A 599 GLU cc_start: 0.7580 (tp30) cc_final: 0.7157 (tp30) REVERT: B 305 ASP cc_start: 0.7463 (OUTLIER) cc_final: 0.7177 (m-30) REVERT: B 634 HIS cc_start: 0.5154 (OUTLIER) cc_final: 0.4224 (m-70) REVERT: C 476 ARG cc_start: 0.6396 (ttm170) cc_final: 0.4762 (ttm110) outliers start: 30 outliers final: 19 residues processed: 274 average time/residue: 0.3426 time to fit residues: 133.8150 Evaluate side-chains 261 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 239 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 261 LEU 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 314 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 662 THR Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain C residue 260 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 130 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 96 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 74 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 166 optimal weight: 0.6980 chunk 147 optimal weight: 3.9990 chunk 11 optimal weight: 0.3980 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 = 0.4299 r_free = 0.4299 target = 0.167859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.136639 restraints weight = 83127.694| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 2.92 r_work: 0.3786 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.1744 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= 0.115 Angle : 0.479 6.262 22214 Z= 0.254 Chirality : 0.038 0.149 2452 Planarity : 0.004 0.041 2867 Dihedral : 3.752 21.399 2205 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.84 % Allowed : 23.37 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.19), residues: 2001 helix: 1.54 (0.17), residues: 918 sheet: -0.26 (0.34), residues: 246 loop : -1.46 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 318 TYR 0.011 0.001 TYR A 564 PHE 0.012 0.001 PHE A 53 TRP 0.008 0.001 TRP A 368 HIS 0.006 0.001 HIS A 74 Details of bonding type rmsd covalent geometry : bond 0.00263 (16487) covalent geometry : angle 0.47910 (22214) hydrogen bonds : bond 0.03663 ( 806) hydrogen bonds : angle 4.54284 ( 2244) *********************** 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 275 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 242 time to evaluate : 0.935 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: 0.7420 (OUTLIER) cc_final: 0.7182 (p) REVERT: A 581 MET cc_start: 0.5560 (OUTLIER) cc_final: 0.5137 (ttm) REVERT: A 599 GLU cc_start: 0.7601 (tp30) cc_final: 0.7196 (tp30) REVERT: B 305 ASP cc_start: 0.7406 (OUTLIER) cc_final: 0.7098 (m-30) REVERT: B 634 HIS cc_start: 0.5188 (OUTLIER) cc_final: 0.4197 (m-70) REVERT: C 476 ARG cc_start: 0.6446 (ttm170) cc_final: 0.4833 (ttm110) REVERT: C 746 ASP cc_start: 0.2835 (OUTLIER) cc_final: 0.1925 (p0) outliers start: 33 outliers final: 21 residues processed: 266 average time/residue: 0.3242 time to fit residues: 125.1714 Evaluate side-chains 262 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 236 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 157 THR 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 288 LYS Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 314 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 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 280 LEU Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 379 ARG 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 102 optimal weight: 8.9990 chunk 156 optimal weight: 7.9990 chunk 154 optimal weight: 0.7980 chunk 145 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 127 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 = 0.4290 r_free = 0.4290 target = 0.167109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.136047 restraints weight = 83186.707| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 2.89 r_work: 0.3780 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.1896 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= 0.132 Angle : 0.491 7.149 22214 Z= 0.262 Chirality : 0.038 0.146 2452 Planarity : 0.004 0.056 2867 Dihedral : 3.805 21.736 2205 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.34 % Allowed : 23.54 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.19), residues: 2001 helix: 1.48 (0.17), residues: 921 sheet: -0.18 (0.34), residues: 236 loop : -1.52 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 706 TYR 0.011 0.001 TYR A 564 PHE 0.010 0.001 PHE B 505 TRP 0.012 0.001 TRP A 422 HIS 0.005 0.001 HIS A 74 Details of bonding type rmsd covalent geometry : bond 0.00302 (16487) covalent geometry : angle 0.49137 (22214) hydrogen bonds : bond 0.03729 ( 806) hydrogen bonds : angle 4.53742 ( 2244) *********************** 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 277 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 235 time to evaluate : 0.810 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 581 MET cc_start: 0.5595 (OUTLIER) cc_final: 0.5171 (ttm) REVERT: A 599 GLU cc_start: 0.7679 (tp30) cc_final: 0.7272 (tp30) REVERT: B 7 LEU cc_start: 0.8301 (mp) cc_final: 0.7712 (mp) REVERT: B 127 GLN cc_start: 0.7010 (mm-40) cc_final: 0.6741 (mm-40) REVERT: B 305 ASP cc_start: 0.7409 (OUTLIER) cc_final: 0.7084 (m-30) REVERT: B 634 HIS cc_start: 0.5264 (OUTLIER) cc_final: 0.4175 (m-70) REVERT: B 697 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7261 (mt-10) REVERT: C 283 MET cc_start: 0.7008 (OUTLIER) cc_final: 0.6749 (mmt) REVERT: C 476 ARG cc_start: 0.6398 (ttm170) cc_final: 0.4798 (ttm110) REVERT: C 746 ASP cc_start: 0.3069 (OUTLIER) cc_final: 0.2090 (p0) outliers start: 42 outliers final: 27 residues processed: 265 average time/residue: 0.3356 time to fit residues: 128.6101 Evaluate side-chains 264 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 231 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET 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 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 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 6 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 192 optimal weight: 10.0000 chunk 151 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 247 GLN B 642 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.164732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.133671 restraints weight = 83994.060| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 2.89 r_work: 0.3750 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16487 Z= 0.190 Angle : 0.544 8.964 22214 Z= 0.294 Chirality : 0.040 0.153 2452 Planarity : 0.004 0.051 2867 Dihedral : 4.060 20.752 2205 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.79 % Allowed : 23.48 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.18), residues: 2001 helix: 1.17 (0.17), residues: 920 sheet: -0.36 (0.34), residues: 236 loop : -1.68 (0.20), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 706 TYR 0.012 0.002 TYR A 564 PHE 0.015 0.002 PHE B 505 TRP 0.014 0.001 TRP A 422 HIS 0.005 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00433 (16487) covalent geometry : angle 0.54381 (22214) hydrogen bonds : bond 0.04213 ( 806) hydrogen bonds : angle 4.74630 ( 2244) *********************** 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 290 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 240 time to evaluate : 0.919 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: 0.7466 (OUTLIER) cc_final: 0.7230 (p) REVERT: A 581 MET cc_start: 0.5701 (OUTLIER) cc_final: 0.5281 (ttm) REVERT: B 7 LEU cc_start: 0.8457 (mp) cc_final: 0.7937 (mp) REVERT: B 127 GLN cc_start: 0.7015 (mm-40) cc_final: 0.6664 (mm-40) REVERT: B 305 ASP cc_start: 0.7429 (OUTLIER) cc_final: 0.7111 (m-30) REVERT: B 634 HIS cc_start: 0.5407 (OUTLIER) cc_final: 0.4171 (m-70) REVERT: B 697 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7490 (mt-10) REVERT: C 476 ARG cc_start: 0.6451 (ttm170) cc_final: 0.4778 (ttp80) REVERT: C 746 ASP cc_start: 0.3501 (OUTLIER) cc_final: 0.2402 (p0) outliers start: 50 outliers final: 35 residues processed: 272 average time/residue: 0.3529 time to fit residues: 137.9922 Evaluate side-chains 281 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 240 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET 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 308 ILE 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 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 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 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 724 VAL Chi-restraints excluded: chain C residue 746 ASP Chi-restraints excluded: chain C residue 751 THR Chi-restraints excluded: chain C residue 755 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 84 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 75 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 190 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.4274 r_free = 0.4274 target = 0.165475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.134512 restraints weight = 82865.649| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 2.92 r_work: 0.3763 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.2240 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= 0.146 Angle : 0.513 6.981 22214 Z= 0.273 Chirality : 0.039 0.148 2452 Planarity : 0.004 0.045 2867 Dihedral : 4.007 21.860 2205 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.34 % Allowed : 24.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.19), residues: 2001 helix: 1.31 (0.17), residues: 913 sheet: -0.48 (0.34), residues: 246 loop : -1.69 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 706 TYR 0.012 0.001 TYR A 564 PHE 0.011 0.001 PHE B 505 TRP 0.008 0.001 TRP A 368 HIS 0.005 0.001 HIS A 452 Details of bonding type rmsd covalent geometry : bond 0.00336 (16487) covalent geometry : angle 0.51271 (22214) hydrogen bonds : bond 0.03862 ( 806) hydrogen bonds : angle 4.62751 ( 2244) *********************** 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 286 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 244 time to evaluate : 0.737 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: 0.7469 (OUTLIER) cc_final: 0.7248 (p) REVERT: A 457 GLU cc_start: 0.7889 (tp30) cc_final: 0.7670 (tp30) REVERT: A 581 MET cc_start: 0.5628 (OUTLIER) cc_final: 0.5225 (ttm) REVERT: A 599 GLU cc_start: 0.7824 (tp30) cc_final: 0.7321 (tp30) REVERT: B 7 LEU cc_start: 0.8441 (mp) cc_final: 0.7915 (mp) REVERT: B 305 ASP cc_start: 0.7422 (OUTLIER) cc_final: 0.7109 (m-30) REVERT: B 634 HIS cc_start: 0.5428 (OUTLIER) cc_final: 0.4188 (m-70) REVERT: B 697 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7477 (mt-10) REVERT: C 476 ARG cc_start: 0.6401 (ttm170) cc_final: 0.4752 (ttp80) REVERT: C 746 ASP cc_start: 0.3303 (OUTLIER) cc_final: 0.2363 (p0) outliers start: 42 outliers final: 32 residues processed: 269 average time/residue: 0.3234 time to fit residues: 125.3177 Evaluate side-chains 275 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 237 time to evaluate : 0.729 ------------------------------------------------------------------------------- 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 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 308 ILE 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 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 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 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 Chi-restraints excluded: chain C residue 755 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 74 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 194 optimal weight: 7.9990 chunk 184 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 162 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 600 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.169433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.138663 restraints weight = 85463.436| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 2.80 r_work: 0.3842 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16487 Z= 0.191 Angle : 0.552 7.806 22214 Z= 0.298 Chirality : 0.040 0.154 2452 Planarity : 0.005 0.082 2867 Dihedral : 4.190 20.693 2205 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.57 % Allowed : 24.04 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.18), residues: 2001 helix: 1.05 (0.17), residues: 914 sheet: -0.35 (0.35), residues: 225 loop : -1.85 (0.19), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 379 TYR 0.013 0.002 TYR C 55 PHE 0.016 0.002 PHE B 505 TRP 0.012 0.001 TRP A 422 HIS 0.005 0.001 HIS A 452 Details of bonding type rmsd covalent geometry : bond 0.00437 (16487) covalent geometry : angle 0.55198 (22214) hydrogen bonds : bond 0.04228 ( 806) hydrogen bonds : angle 4.78220 ( 2244) *********************** 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 283 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 237 time to evaluate : 0.788 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: A 423 VAL cc_start: 0.7560 (OUTLIER) cc_final: 0.7343 (p) REVERT: A 581 MET cc_start: 0.5568 (OUTLIER) cc_final: 0.5116 (ttm) REVERT: B 7 LEU cc_start: 0.8481 (mp) cc_final: 0.8026 (mp) REVERT: B 305 ASP cc_start: 0.7439 (OUTLIER) cc_final: 0.7121 (m-30) REVERT: B 634 HIS cc_start: 0.5370 (OUTLIER) cc_final: 0.4072 (m-70) REVERT: B 697 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7650 (mt-10) REVERT: C 476 ARG cc_start: 0.6452 (ttm170) cc_final: 0.4794 (ttp80) REVERT: C 746 ASP cc_start: 0.3423 (OUTLIER) cc_final: 0.2300 (p0) outliers start: 46 outliers final: 38 residues processed: 264 average time/residue: 0.3029 time to fit residues: 115.5725 Evaluate side-chains 276 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 232 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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 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 288 LEU Chi-restraints excluded: chain A residue 308 ILE 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 594 SER 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 223 THR Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 298 LEU 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 600 ASN 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 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 Chi-restraints excluded: chain C residue 755 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 104 optimal weight: 0.0070 chunk 26 optimal weight: 0.7980 chunk 183 optimal weight: 1.9990 chunk 169 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 196 optimal weight: 0.7980 chunk 195 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 182 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 600 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.167780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.137542 restraints weight = 84996.474| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 2.76 r_work: 0.3852 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3734 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 16487 Z= 0.175 Angle : 0.741 59.199 22214 Z= 0.427 Chirality : 0.039 0.310 2452 Planarity : 0.005 0.110 2867 Dihedral : 4.187 20.740 2205 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.45 % Allowed : 24.09 % Favored : 73.45 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.18), residues: 2001 helix: 1.07 (0.17), residues: 914 sheet: -0.33 (0.35), residues: 227 loop : -1.84 (0.19), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 379 TYR 0.012 0.001 TYR A 564 PHE 0.014 0.001 PHE B 740 TRP 0.033 0.001 TRP A 406 HIS 0.005 0.001 HIS A 452 Details of bonding type rmsd covalent geometry : bond 0.00380 (16487) covalent geometry : angle 0.74149 (22214) hydrogen bonds : bond 0.04122 ( 806) hydrogen bonds : angle 4.76205 ( 2244) ********************** 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 276 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 232 time to evaluate : 1.108 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: 0.7561 (OUTLIER) cc_final: 0.7332 (p) REVERT: A 581 MET cc_start: 0.5645 (OUTLIER) cc_final: 0.5195 (ttm) REVERT: B 7 LEU cc_start: 0.8549 (mp) cc_final: 0.8106 (mp) REVERT: B 305 ASP cc_start: 0.7453 (OUTLIER) cc_final: 0.7154 (m-30) REVERT: B 634 HIS cc_start: 0.5369 (OUTLIER) cc_final: 0.4010 (m-70) REVERT: B 697 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7795 (mt-10) REVERT: C 333 THR cc_start: 0.5159 (OUTLIER) cc_final: 0.4788 (m) REVERT: C 365 MET cc_start: 0.5036 (mpp) cc_final: 0.4722 (mpp) REVERT: C 476 ARG cc_start: 0.6444 (ttm170) cc_final: 0.4759 (ttp80) REVERT: C 746 ASP cc_start: 0.3436 (OUTLIER) cc_final: 0.2230 (p0) outliers start: 44 outliers final: 36 residues processed: 259 average time/residue: 0.3634 time to fit residues: 135.9586 Evaluate side-chains 275 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 232 time to evaluate : 0.895 ------------------------------------------------------------------------------- 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 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 308 ILE 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 594 SER 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 223 THR Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 298 LEU 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 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 333 THR 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 Chi-restraints excluded: chain C residue 755 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 76 optimal weight: 0.7980 chunk 82 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 134 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 185 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 131 optimal weight: 0.6980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 600 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 = 0.4354 r_free = 0.4354 target = 0.167833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.137610 restraints weight = 85052.355| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 2.76 r_work: 0.3852 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3734 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 16487 Z= 0.175 Angle : 0.741 59.199 22214 Z= 0.427 Chirality : 0.039 0.310 2452 Planarity : 0.005 0.110 2867 Dihedral : 4.187 20.740 2205 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.40 % Allowed : 24.15 % Favored : 73.45 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.18), residues: 2001 helix: 1.07 (0.17), residues: 914 sheet: -0.33 (0.35), residues: 227 loop : -1.84 (0.19), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 379 TYR 0.012 0.001 TYR A 564 PHE 0.014 0.001 PHE B 740 TRP 0.033 0.001 TRP A 406 HIS 0.005 0.001 HIS A 452 Details of bonding type rmsd covalent geometry : bond 0.00380 (16487) covalent geometry : angle 0.74149 (22214) hydrogen bonds : bond 0.04122 ( 806) hydrogen bonds : angle 4.76205 ( 2244) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7236.23 seconds wall clock time: 123 minutes 51.45 seconds (7431.45 seconds total)