Starting phenix.real_space_refine on Thu May 29 19:14:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rms_19369/05_2025/8rms_19369.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rms_19369/05_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_19369/05_2025/8rms_19369.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rms_19369/05_2025/8rms_19369.map" model { file = "/net/cci-nas-00/data/ceres_data/8rms_19369/05_2025/8rms_19369.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rms_19369/05_2025/8rms_19369.cif" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mg 1 5.21 5 S 119 5.16 5 C 10191 2.51 5 N 2837 2.21 5 O 3041 1.98 5 H 16245 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 32434 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 11437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 708, 11437 Classifications: {'peptide': 708} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 32, 'TRANS': 675} Chain breaks: 1 Chain: "B" Number of atoms: 11376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 714, 11376 Classifications: {'peptide': 714} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 683} Chain breaks: 4 Chain: "C" Number of atoms: 9620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 9620 Classifications: {'peptide': 597} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 20, 'TRANS': 576} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 16.41, per 1000 atoms: 0.51 Number of scatterers: 32434 At special positions: 0 Unit cell: (115.08, 148.68, 99.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 119 16.00 Mg 1 11.99 O 3041 8.00 N 2837 7.00 C 10191 6.00 H 16245 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.74 Conformation dependent library (CDL) restraints added in 2.6 seconds 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3808 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 24 sheets defined 49.2% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.05 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: 12.69 Time building geometry restraints manager: 10.43 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: 6.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.530 Extract box with map and model: 1.310 Check model and map are aligned: 0.270 Set scattering table: 0.290 Process input model: 69.660 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 16487 Z= 0.110 Angle : 0.510 6.357 22214 Z= 0.279 Chirality : 0.038 0.154 2452 Planarity : 0.004 0.075 2867 Dihedral : 17.535 89.945 6332 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.22 % Allowed : 23.03 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.19), residues: 2001 helix: 1.50 (0.18), residues: 889 sheet: -0.00 (0.36), residues: 236 loop : -1.42 (0.19), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 131 HIS 0.006 0.001 HIS A 74 PHE 0.010 0.001 PHE B 730 TYR 0.010 0.001 TYR B 555 ARG 0.006 0.000 ARG B 706 Details of bonding type rmsd hydrogen bonds : bond 0.14584 ( 806) hydrogen bonds : angle 5.92118 ( 2244) covalent geometry : bond 0.00241 (16487) covalent geometry : angle 0.50998 (22214) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 268 time to evaluate : 2.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 301 ASN cc_start: 0.2769 (t0) cc_final: 0.2476 (m-40) REVERT: C 476 ARG cc_start: 0.6357 (ttm170) cc_final: 0.4832 (ttm170) outliers start: 4 outliers final: 3 residues processed: 270 average time/residue: 0.7071 time to fit residues: 271.4060 Evaluate side-chains 246 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 243 time to evaluate : 2.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain C residue 357 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 4.9990 chunk 151 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 102 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 156 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 181 optimal weight: 6.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN B 247 GLN B 306 ASN B 312 ASN B 694 ASN C 425 ASN C 728 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.167431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.136173 restraints weight = 82897.797| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 2.97 r_work: 0.3778 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16487 Z= 0.150 Angle : 0.521 5.642 22214 Z= 0.282 Chirality : 0.039 0.147 2452 Planarity : 0.004 0.047 2867 Dihedral : 4.198 57.151 2212 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.12 % Allowed : 23.15 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.19), residues: 2001 helix: 1.34 (0.17), residues: 916 sheet: -0.26 (0.35), residues: 243 loop : -1.38 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 666 HIS 0.005 0.001 HIS A 74 PHE 0.012 0.001 PHE B 730 TYR 0.011 0.001 TYR A 564 ARG 0.005 0.000 ARG B 706 Details of bonding type rmsd hydrogen bonds : bond 0.04718 ( 806) hydrogen bonds : angle 5.02637 ( 2244) covalent geometry : bond 0.00337 (16487) covalent geometry : angle 0.52079 (22214) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 247 time to evaluate : 2.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 TYR cc_start: 0.7009 (m-10) cc_final: 0.6777 (m-10) REVERT: A 581 MET cc_start: 0.5506 (OUTLIER) cc_final: 0.5082 (ttm) REVERT: B 305 ASP cc_start: 0.7581 (OUTLIER) cc_final: 0.7281 (m-30) REVERT: C 476 ARG cc_start: 0.6373 (ttm170) cc_final: 0.4811 (ttm170) outliers start: 20 outliers final: 13 residues processed: 260 average time/residue: 0.6820 time to fit residues: 257.5708 Evaluate side-chains 251 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 236 time to evaluate : 2.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 247 GLN Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 662 THR Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 357 HIS Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 751 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 145 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 62 optimal weight: 0.1980 chunk 53 optimal weight: 5.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 690 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.168171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.136868 restraints weight = 82955.788| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 2.97 r_work: 0.3791 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 16487 Z= 0.119 Angle : 0.487 6.682 22214 Z= 0.259 Chirality : 0.038 0.143 2452 Planarity : 0.004 0.042 2867 Dihedral : 4.002 56.552 2207 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.67 % Allowed : 22.42 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.19), residues: 2001 helix: 1.49 (0.17), residues: 918 sheet: -0.23 (0.34), residues: 246 loop : -1.40 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 368 HIS 0.004 0.001 HIS A 74 PHE 0.008 0.001 PHE B 505 TYR 0.010 0.001 TYR B 555 ARG 0.004 0.000 ARG B 706 Details of bonding type rmsd hydrogen bonds : bond 0.04034 ( 806) hydrogen bonds : angle 4.74556 ( 2244) covalent geometry : bond 0.00270 (16487) covalent geometry : angle 0.48656 (22214) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 253 time to evaluate : 2.519 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: 0.6614 (tmtt) cc_final: 0.6363 (tmtt) REVERT: A 581 MET cc_start: 0.5568 (OUTLIER) cc_final: 0.5095 (ttm) REVERT: A 599 GLU cc_start: 0.7571 (tp30) cc_final: 0.7108 (tp30) REVERT: B 247 GLN cc_start: 0.7112 (mp10) cc_final: 0.6787 (mt0) REVERT: B 305 ASP cc_start: 0.7454 (OUTLIER) cc_final: 0.7161 (m-30) REVERT: B 317 MET cc_start: 0.6405 (mmp) cc_final: 0.6163 (mmp) REVERT: B 634 HIS cc_start: 0.5209 (OUTLIER) cc_final: 0.4351 (m-70) REVERT: C 476 ARG cc_start: 0.6398 (ttm170) cc_final: 0.4798 (ttm170) outliers start: 30 outliers final: 19 residues processed: 274 average time/residue: 0.7349 time to fit residues: 288.8713 Evaluate side-chains 260 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 238 time to evaluate : 2.577 ------------------------------------------------------------------------------- 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 157 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 590 GLN Chi-restraints excluded: chain A residue 609 LYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 634 HIS Chi-restraints excluded: chain B residue 662 THR Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain C residue 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 52 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 174 optimal weight: 9.9990 chunk 145 optimal weight: 0.5980 chunk 137 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 600 ASN B 642 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.165311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.134056 restraints weight = 84103.516| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 2.90 r_work: 0.3754 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.1683 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= 0.187 Angle : 0.549 10.087 22214 Z= 0.296 Chirality : 0.040 0.153 2452 Planarity : 0.004 0.055 2867 Dihedral : 4.094 19.560 2205 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.40 % Allowed : 23.20 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.18), residues: 2001 helix: 1.09 (0.17), residues: 916 sheet: -0.39 (0.34), residues: 241 loop : -1.63 (0.19), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 422 HIS 0.008 0.001 HIS A 74 PHE 0.021 0.002 PHE A 53 TYR 0.013 0.002 TYR A 564 ARG 0.004 0.000 ARG A 124 Details of bonding type rmsd hydrogen bonds : bond 0.04419 ( 806) hydrogen bonds : angle 4.86983 ( 2244) covalent geometry : bond 0.00419 (16487) covalent geometry : angle 0.54855 (22214) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 243 time to evaluate : 2.498 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 423 VAL cc_start: 0.7502 (OUTLIER) cc_final: 0.7252 (p) REVERT: A 581 MET cc_start: 0.5627 (OUTLIER) cc_final: 0.5199 (ttm) REVERT: B 305 ASP cc_start: 0.7534 (OUTLIER) cc_final: 0.7197 (m-30) REVERT: B 317 MET cc_start: 0.6644 (mmp) cc_final: 0.6149 (mmt) REVERT: B 634 HIS cc_start: 0.5351 (OUTLIER) cc_final: 0.4287 (m-70) REVERT: C 283 MET cc_start: 0.7168 (OUTLIER) cc_final: 0.6886 (mmt) REVERT: C 476 ARG cc_start: 0.6448 (ttm170) cc_final: 0.4794 (ttp80) outliers start: 43 outliers final: 31 residues processed: 266 average time/residue: 0.7096 time to fit residues: 274.7437 Evaluate side-chains 270 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 234 time to evaluate : 2.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 609 LYS Chi-restraints excluded: chain A residue 682 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 602 ARG Chi-restraints excluded: chain B residue 634 HIS Chi-restraints excluded: chain B residue 662 THR Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 734 ARG Chi-restraints excluded: chain B residue 755 ARG Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 751 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 188 optimal weight: 10.0000 chunk 157 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 165 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 172 optimal weight: 6.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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 = 0.4268 r_free = 0.4268 target = 0.165100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.134200 restraints weight = 83002.165| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 2.89 r_work: 0.3757 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16487 Z= 0.162 Angle : 0.521 8.106 22214 Z= 0.280 Chirality : 0.039 0.151 2452 Planarity : 0.004 0.046 2867 Dihedral : 4.082 21.728 2205 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.79 % Allowed : 23.70 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.18), residues: 2001 helix: 1.17 (0.17), residues: 918 sheet: -0.47 (0.34), residues: 246 loop : -1.72 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 422 HIS 0.006 0.001 HIS A 74 PHE 0.012 0.001 PHE B 505 TYR 0.012 0.001 TYR A 564 ARG 0.003 0.000 ARG B 706 Details of bonding type rmsd hydrogen bonds : bond 0.04106 ( 806) hydrogen bonds : angle 4.75119 ( 2244) covalent geometry : bond 0.00368 (16487) covalent geometry : angle 0.52120 (22214) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 237 time to evaluate : 2.778 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 581 MET cc_start: 0.5595 (OUTLIER) cc_final: 0.5176 (ttm) REVERT: B 7 LEU cc_start: 0.8411 (mp) cc_final: 0.7885 (mp) REVERT: B 8 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7693 (tt) REVERT: B 127 GLN cc_start: 0.7036 (mm-40) cc_final: 0.6736 (mm-40) REVERT: B 305 ASP cc_start: 0.7476 (OUTLIER) cc_final: 0.7158 (m-30) REVERT: B 634 HIS cc_start: 0.5333 (OUTLIER) cc_final: 0.4243 (m-70) REVERT: B 697 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7448 (mt-10) REVERT: C 476 ARG cc_start: 0.6470 (ttm170) cc_final: 0.4826 (ttp80) REVERT: C 746 ASP cc_start: 0.2996 (OUTLIER) cc_final: 0.1935 (p0) outliers start: 50 outliers final: 36 residues processed: 270 average time/residue: 0.7452 time to fit residues: 291.1463 Evaluate side-chains 273 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 231 time to evaluate : 2.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 590 GLN Chi-restraints excluded: chain A residue 609 LYS Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 247 GLN 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 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 342 GLU Chi-restraints excluded: chain C residue 379 ARG Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 746 ASP Chi-restraints excluded: chain C residue 751 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 118 optimal weight: 5.9990 chunk 195 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 181 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 184 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 600 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.167364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.136912 restraints weight = 85472.737| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 2.76 r_work: 0.3844 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3727 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16487 Z= 0.203 Angle : 0.557 7.462 22214 Z= 0.302 Chirality : 0.040 0.156 2452 Planarity : 0.005 0.081 2867 Dihedral : 4.256 21.823 2205 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.18 % Allowed : 23.65 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.18), residues: 2001 helix: 0.96 (0.17), residues: 914 sheet: -0.49 (0.34), residues: 231 loop : -1.86 (0.19), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 422 HIS 0.006 0.001 HIS A 74 PHE 0.015 0.002 PHE B 505 TYR 0.014 0.002 TYR A 564 ARG 0.010 0.000 ARG C 318 Details of bonding type rmsd hydrogen bonds : bond 0.04397 ( 806) hydrogen bonds : angle 4.86208 ( 2244) covalent geometry : bond 0.00464 (16487) covalent geometry : angle 0.55717 (22214) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 235 time to evaluate : 2.434 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: 0.7527 (OUTLIER) cc_final: 0.7308 (p) REVERT: A 581 MET cc_start: 0.5674 (OUTLIER) cc_final: 0.5216 (ttm) REVERT: B 7 LEU cc_start: 0.8525 (mp) cc_final: 0.8067 (mp) REVERT: B 8 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7851 (tt) REVERT: B 305 ASP cc_start: 0.7532 (OUTLIER) cc_final: 0.7237 (m-30) REVERT: B 634 HIS cc_start: 0.5494 (OUTLIER) cc_final: 0.4332 (m-70) REVERT: B 697 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.7801 (mt-10) REVERT: C 476 ARG cc_start: 0.6556 (ttm170) cc_final: 0.4901 (ttp80) REVERT: C 746 ASP cc_start: 0.3106 (OUTLIER) cc_final: 0.2006 (p0) REVERT: C 752 LYS cc_start: 0.6967 (mmmt) cc_final: 0.6627 (pttp) outliers start: 57 outliers final: 40 residues processed: 272 average time/residue: 0.6881 time to fit residues: 268.3888 Evaluate side-chains 279 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 232 time to evaluate : 2.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 609 LYS Chi-restraints excluded: chain A residue 682 ASP Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 247 GLN Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 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 662 THR Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 755 ARG Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 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 342 GLU Chi-restraints excluded: chain C residue 357 HIS Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 746 ASP Chi-restraints excluded: chain C residue 751 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 145 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 chunk 190 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 194 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 110 optimal weight: 0.5980 chunk 134 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 = 0.4270 r_free = 0.4270 target = 0.165175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.134000 restraints weight = 83513.013| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 2.93 r_work: 0.3757 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16487 Z= 0.135 Angle : 0.513 6.155 22214 Z= 0.274 Chirality : 0.039 0.148 2452 Planarity : 0.004 0.072 2867 Dihedral : 4.111 21.921 2205 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.84 % Allowed : 24.04 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.19), residues: 2001 helix: 1.21 (0.17), residues: 914 sheet: -0.45 (0.34), residues: 236 loop : -1.79 (0.19), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 368 HIS 0.005 0.001 HIS A 452 PHE 0.012 0.001 PHE B 740 TYR 0.011 0.001 TYR A 564 ARG 0.005 0.000 ARG B 706 Details of bonding type rmsd hydrogen bonds : bond 0.03972 ( 806) hydrogen bonds : angle 4.67031 ( 2244) covalent geometry : bond 0.00307 (16487) covalent geometry : angle 0.51314 (22214) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 237 time to evaluate : 2.481 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: symmetry clash REVERT: A 423 VAL cc_start: 0.7495 (OUTLIER) cc_final: 0.7272 (p) REVERT: A 581 MET cc_start: 0.5649 (OUTLIER) cc_final: 0.5239 (ttm) REVERT: B 7 LEU cc_start: 0.8448 (mp) cc_final: 0.7940 (mp) REVERT: B 8 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7718 (tt) REVERT: B 305 ASP cc_start: 0.7456 (OUTLIER) cc_final: 0.7155 (m-30) REVERT: B 634 HIS cc_start: 0.5391 (OUTLIER) cc_final: 0.4212 (m-70) REVERT: B 697 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7484 (mt-10) REVERT: C 241 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7804 (tm-30) REVERT: C 333 THR cc_start: 0.5011 (OUTLIER) cc_final: 0.4661 (m) REVERT: C 365 MET cc_start: 0.4983 (mpp) cc_final: 0.4690 (mpp) REVERT: C 476 ARG cc_start: 0.6398 (ttm170) cc_final: 0.4786 (ttp80) REVERT: C 746 ASP cc_start: 0.3112 (OUTLIER) cc_final: 0.2236 (p0) REVERT: C 752 LYS cc_start: 0.7214 (mmmt) cc_final: 0.6752 (pttp) outliers start: 51 outliers final: 37 residues processed: 272 average time/residue: 0.6961 time to fit residues: 276.9276 Evaluate side-chains 280 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 235 time to evaluate : 2.675 ------------------------------------------------------------------------------- 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 21 MET Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 346 GLN 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 8 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 247 GLN 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 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 245 THR Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain C residue 323 PHE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 357 HIS Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 746 ASP Chi-restraints excluded: chain C residue 751 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 106 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 142 optimal weight: 0.6980 chunk 188 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 71 optimal weight: 0.7980 chunk 151 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.166135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.134955 restraints weight = 83206.953| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 2.94 r_work: 0.3769 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16487 Z= 0.115 Angle : 0.500 7.976 22214 Z= 0.263 Chirality : 0.038 0.152 2452 Planarity : 0.004 0.066 2867 Dihedral : 3.933 21.464 2205 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.29 % Allowed : 24.43 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.19), residues: 2001 helix: 1.44 (0.17), residues: 921 sheet: -0.38 (0.34), residues: 236 loop : -1.72 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 368 HIS 0.004 0.001 HIS A 452 PHE 0.012 0.001 PHE B 740 TYR 0.011 0.001 TYR A 564 ARG 0.004 0.000 ARG B 706 Details of bonding type rmsd hydrogen bonds : bond 0.03668 ( 806) hydrogen bonds : angle 4.51868 ( 2244) covalent geometry : bond 0.00263 (16487) covalent geometry : angle 0.50002 (22214) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 242 time to evaluate : 2.432 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 423 VAL cc_start: 0.7503 (OUTLIER) cc_final: 0.7280 (p) REVERT: A 581 MET cc_start: 0.5651 (OUTLIER) cc_final: 0.5217 (ttm) REVERT: A 599 GLU cc_start: 0.7841 (tp30) cc_final: 0.7383 (tp30) REVERT: B 7 LEU cc_start: 0.8429 (mp) cc_final: 0.7902 (mp) REVERT: B 305 ASP cc_start: 0.7411 (OUTLIER) cc_final: 0.7131 (m-30) REVERT: B 634 HIS cc_start: 0.5360 (OUTLIER) cc_final: 0.4185 (m-70) REVERT: B 697 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7490 (mt-10) REVERT: C 333 THR cc_start: 0.5073 (OUTLIER) cc_final: 0.4721 (m) REVERT: C 365 MET cc_start: 0.4919 (mpp) cc_final: 0.4614 (mpp) REVERT: C 476 ARG cc_start: 0.6346 (ttm170) cc_final: 0.4716 (ttp80) REVERT: C 746 ASP cc_start: 0.3005 (OUTLIER) cc_final: 0.2139 (p0) REVERT: C 752 LYS cc_start: 0.6933 (mmmt) cc_final: 0.6611 (pttp) outliers start: 41 outliers final: 30 residues processed: 268 average time/residue: 0.7007 time to fit residues: 271.5474 Evaluate side-chains 271 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 234 time to evaluate : 2.433 ------------------------------------------------------------------------------- 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 21 MET Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 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 594 SER Chi-restraints excluded: chain A residue 609 LYS Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 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 742 GLU Chi-restraints excluded: chain B residue 755 ARG 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 402 MET Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 746 ASP Chi-restraints excluded: chain C residue 751 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 42 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 195 optimal weight: 0.7980 chunk 163 optimal weight: 0.6980 chunk 103 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 chunk 54 optimal weight: 0.0970 chunk 49 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN A 466 ASN B 225 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.166643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.135498 restraints weight = 82882.689| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 2.94 r_work: 0.3778 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16487 Z= 0.110 Angle : 0.495 6.949 22214 Z= 0.260 Chirality : 0.038 0.171 2452 Planarity : 0.004 0.062 2867 Dihedral : 3.872 22.116 2205 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.95 % Allowed : 24.82 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.19), residues: 2001 helix: 1.60 (0.17), residues: 921 sheet: -0.29 (0.34), residues: 235 loop : -1.66 (0.20), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 406 HIS 0.004 0.001 HIS A 452 PHE 0.011 0.001 PHE B 740 TYR 0.011 0.001 TYR A 564 ARG 0.003 0.000 ARG A 196 Details of bonding type rmsd hydrogen bonds : bond 0.03538 ( 806) hydrogen bonds : angle 4.44363 ( 2244) covalent geometry : bond 0.00252 (16487) covalent geometry : angle 0.49508 (22214) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 235 time to evaluate : 2.484 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: 0.7480 (OUTLIER) cc_final: 0.7248 (p) REVERT: A 599 GLU cc_start: 0.7804 (tp30) cc_final: 0.7387 (tp30) REVERT: B 7 LEU cc_start: 0.8433 (mp) cc_final: 0.7906 (mp) REVERT: B 305 ASP cc_start: 0.7394 (OUTLIER) cc_final: 0.7121 (m-30) REVERT: B 380 TYR cc_start: 0.7228 (m-80) cc_final: 0.7021 (m-80) REVERT: B 634 HIS cc_start: 0.5316 (OUTLIER) cc_final: 0.4099 (m-70) REVERT: C 333 THR cc_start: 0.5020 (OUTLIER) cc_final: 0.4667 (m) REVERT: C 365 MET cc_start: 0.4874 (mpp) cc_final: 0.4577 (mpp) REVERT: C 384 LEU cc_start: 0.3010 (tt) cc_final: 0.2663 (tp) REVERT: C 473 MET cc_start: 0.3106 (tpt) cc_final: 0.2883 (tpt) REVERT: C 476 ARG cc_start: 0.6307 (ttm170) cc_final: 0.4673 (ttp80) REVERT: C 752 LYS cc_start: 0.6972 (mmmt) cc_final: 0.6561 (pttp) outliers start: 35 outliers final: 29 residues processed: 256 average time/residue: 0.7192 time to fit residues: 268.7405 Evaluate side-chains 267 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 234 time to evaluate : 2.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 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 609 LYS Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 247 GLN Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 602 ARG Chi-restraints excluded: chain B residue 634 HIS Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 755 ARG Chi-restraints excluded: chain C residue 243 MET 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 402 MET Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 751 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 5 optimal weight: 9.9990 chunk 126 optimal weight: 0.0070 chunk 160 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 163 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 196 optimal weight: 6.9990 chunk 193 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 overall best weight: 1.1602 ------------------------------------------------------------------------------- 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 = 0.4283 r_free = 0.4283 target = 0.166486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.135512 restraints weight = 82881.706| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.93 r_work: 0.3771 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16487 Z= 0.111 Angle : 0.492 7.949 22214 Z= 0.258 Chirality : 0.038 0.150 2452 Planarity : 0.004 0.059 2867 Dihedral : 3.820 21.618 2205 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.90 % Allowed : 24.99 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.19), residues: 2001 helix: 1.65 (0.17), residues: 921 sheet: -0.31 (0.34), residues: 243 loop : -1.59 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 368 HIS 0.004 0.001 HIS A 452 PHE 0.009 0.001 PHE B 185 TYR 0.010 0.001 TYR A 564 ARG 0.003 0.000 ARG A 196 Details of bonding type rmsd hydrogen bonds : bond 0.03498 ( 806) hydrogen bonds : angle 4.40308 ( 2244) covalent geometry : bond 0.00253 (16487) covalent geometry : angle 0.49236 (22214) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 236 time to evaluate : 2.644 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: symmetry clash REVERT: A 423 VAL cc_start: 0.7442 (OUTLIER) cc_final: 0.7207 (p) REVERT: A 599 GLU cc_start: 0.7772 (tp30) cc_final: 0.7359 (tp30) REVERT: B 7 LEU cc_start: 0.8440 (mp) cc_final: 0.7918 (mp) REVERT: B 305 ASP cc_start: 0.7360 (OUTLIER) cc_final: 0.7087 (m-30) REVERT: B 634 HIS cc_start: 0.5248 (OUTLIER) cc_final: 0.3917 (m-70) REVERT: C 333 THR cc_start: 0.5081 (OUTLIER) cc_final: 0.4724 (m) REVERT: C 365 MET cc_start: 0.4841 (mpp) cc_final: 0.4541 (mpp) REVERT: C 384 LEU cc_start: 0.3249 (tt) cc_final: 0.2910 (tp) REVERT: C 473 MET cc_start: 0.3222 (tpt) cc_final: 0.2924 (tpt) REVERT: C 476 ARG cc_start: 0.6317 (ttm170) cc_final: 0.4732 (ttm110) REVERT: C 752 LYS cc_start: 0.6960 (mmmt) cc_final: 0.6560 (pttp) outliers start: 34 outliers final: 30 residues processed: 258 average time/residue: 0.7216 time to fit residues: 270.9028 Evaluate side-chains 267 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 233 time to evaluate : 2.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 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 594 SER Chi-restraints excluded: chain A residue 609 LYS Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 247 GLN Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 602 ARG Chi-restraints excluded: chain B residue 634 HIS Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 755 ARG Chi-restraints excluded: chain C residue 243 MET 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 751 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 152 optimal weight: 2.9990 chunk 96 optimal weight: 8.9990 chunk 115 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 194 optimal weight: 4.9990 chunk 192 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 162 optimal weight: 4.9990 chunk 156 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 247 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.164005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.133109 restraints weight = 83296.854| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.90 r_work: 0.3744 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.2580 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= 0.180 Angle : 0.545 9.012 22214 Z= 0.292 Chirality : 0.040 0.154 2452 Planarity : 0.004 0.060 2867 Dihedral : 4.108 21.269 2205 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.23 % Allowed : 24.76 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.19), residues: 2001 helix: 1.28 (0.17), residues: 915 sheet: -0.35 (0.34), residues: 236 loop : -1.79 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 422 HIS 0.005 0.001 HIS A 535 PHE 0.013 0.001 PHE B 505 TYR 0.012 0.002 TYR C 55 ARG 0.004 0.000 ARG B 706 Details of bonding type rmsd hydrogen bonds : bond 0.04093 ( 806) hydrogen bonds : angle 4.63977 ( 2244) covalent geometry : bond 0.00413 (16487) covalent geometry : angle 0.54534 (22214) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14055.60 seconds wall clock time: 242 minutes 0.96 seconds (14520.96 seconds total)