Starting phenix.real_space_refine on Fri May 30 06:28:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rn5_19387/05_2025/8rn5_19387.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rn5_19387/05_2025/8rn5_19387.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rn5_19387/05_2025/8rn5_19387.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rn5_19387/05_2025/8rn5_19387.map" model { file = "/net/cci-nas-00/data/ceres_data/8rn5_19387/05_2025/8rn5_19387.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rn5_19387/05_2025/8rn5_19387.cif" } resolution = 2.88 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= -0.001 sd= 0.094 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 127 5.16 5 C 10438 2.51 5 N 2832 2.21 5 O 3089 1.98 5 H 16596 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 33083 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 11308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 705, 11308 Classifications: {'peptide': 705} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 26, 'TRANS': 678} Chain breaks: 1 Chain: "B" Number of atoms: 11167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 713, 11167 Classifications: {'peptide': 713} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 33, 'TRANS': 679} Chain breaks: 4 Chain: "C" Number of atoms: 9782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 9782 Classifications: {'peptide': 604} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 20, 'TRANS': 583} Chain breaks: 2 Chain: "D" Number of atoms: 379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 379 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 2, 'TRANS': 20} Chain: "E" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 446 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 15.96, per 1000 atoms: 0.48 Number of scatterers: 33083 At special positions: 0 Unit cell: (115.08, 132.72, 140.28, 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 127 16.00 Mg 1 11.99 O 3089 8.00 N 2832 7.00 C 10438 6.00 H 16596 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: 8.19 Conformation dependent library (CDL) restraints added in 2.6 seconds 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3866 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 21 sheets defined 49.8% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.61 Creating SS restraints... Processing helix chain 'A' and resid 1 through 9 Processing helix chain 'A' and resid 10 through 24 Processing helix chain 'A' and resid 31 through 49 Processing helix chain 'A' and resid 84 through 100 Processing helix chain 'A' and resid 127 through 140 removed outlier: 3.524A pdb=" N TYR A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 184 removed outlier: 3.553A pdb=" N LYS A 167 " --> pdb=" O ASP A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 removed outlier: 4.330A pdb=" N GLU A 197 " --> pdb=" O GLU A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 214 Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 237 through 245 removed outlier: 3.586A pdb=" N ARG A 245 " --> pdb=" O ARG A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 271 Processing helix chain 'A' and resid 301 through 313 Processing helix chain 'A' and resid 313 through 319 Processing helix chain 'A' and resid 332 through 349 Processing helix chain 'A' and resid 360 through 366 removed outlier: 3.838A pdb=" N TRP A 364 " --> pdb=" O ASN A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 383 removed outlier: 3.538A pdb=" N ALA A 380 " --> pdb=" O MET A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 411 removed outlier: 4.366A pdb=" N GLN A 404 " --> pdb=" O ALA A 400 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER A 411 " --> pdb=" O MET A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 447 Processing helix chain 'A' and resid 449 through 472 removed outlier: 3.699A pdb=" N THR A 453 " --> pdb=" O CYS A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 533 removed outlier: 3.634A pdb=" N TRP A 533 " --> pdb=" O SER A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 572 Processing helix chain 'A' and resid 574 through 595 removed outlier: 3.917A pdb=" N LEU A 578 " --> pdb=" O ARG A 574 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN A 583 " --> pdb=" O GLN A 579 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N MET A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 606 Processing helix chain 'A' and resid 629 through 646 Processing helix chain 'A' and resid 648 through 670 removed outlier: 4.101A pdb=" N ARG A 660 " --> pdb=" O ALA A 656 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU A 661 " --> pdb=" O GLU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 688 Processing helix chain 'A' and resid 693 through 716 Processing helix chain 'B' and resid 7 through 12 removed outlier: 4.157A pdb=" N ASP B 11 " --> pdb=" O PHE B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 22 removed outlier: 3.875A pdb=" N THR B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 117 removed outlier: 3.533A pdb=" N VAL B 116 " --> pdb=" O GLU B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 124 Processing helix chain 'B' and resid 138 through 152 removed outlier: 3.548A pdb=" N LEU B 152 " --> pdb=" O THR B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 162 through 174 removed outlier: 3.785A pdb=" N PHE B 166 " --> pdb=" O GLY B 162 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU B 174 " --> pdb=" O ILE B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 248 through 266 removed outlier: 4.149A pdb=" N ASN B 265 " --> pdb=" O ASN B 261 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU B 266 " --> pdb=" O ILE B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 293 removed outlier: 3.532A pdb=" N ALA B 280 " --> pdb=" O ASN B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 312 removed outlier: 3.569A pdb=" N GLU B 311 " --> pdb=" O LYS B 308 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N CYS B 312 " --> pdb=" O TRP B 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 308 through 312' Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 330 through 338 Processing helix chain 'B' and resid 338 through 346 removed outlier: 3.521A pdb=" N VAL B 342 " --> pdb=" O SER B 338 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN B 346 " --> pdb=" O VAL B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 376 removed outlier: 5.276A pdb=" N PHE B 374 " --> pdb=" O PRO B 371 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE B 376 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 381 Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 413 through 426 removed outlier: 3.524A pdb=" N SER B 417 " --> pdb=" O PHE B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 472 removed outlier: 3.522A pdb=" N LEU B 472 " --> pdb=" O THR B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 536 Processing helix chain 'B' and resid 539 through 559 Processing helix chain 'B' and resid 569 through 582 removed outlier: 4.152A pdb=" N ILE B 574 " --> pdb=" O LYS B 570 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU B 580 " --> pdb=" O LYS B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 593 Processing helix chain 'B' and resid 599 through 603 removed outlier: 3.809A pdb=" N LEU B 603 " --> pdb=" O LEU B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 611 Processing helix chain 'B' and resid 616 through 624 removed outlier: 3.773A pdb=" N GLY B 621 " --> pdb=" O PRO B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 640 removed outlier: 4.051A pdb=" N GLU B 637 " --> pdb=" O LEU B 634 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLY B 638 " --> pdb=" O SER B 635 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LYS B 640 " --> pdb=" O GLU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 699 Processing helix chain 'B' and resid 700 through 705 removed outlier: 4.254A pdb=" N TYR B 704 " --> pdb=" O ASN B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 731 removed outlier: 3.554A pdb=" N ALA B 716 " --> pdb=" O SER B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 735 through 750 Processing helix chain 'C' and resid 2 through 15 removed outlier: 4.228A pdb=" N ASP C 15 " --> pdb=" O GLN C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 25 removed outlier: 3.589A pdb=" N LYS C 19 " --> pdb=" O ASP C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 36 removed outlier: 3.628A pdb=" N PHE C 36 " --> pdb=" O ILE C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 55 removed outlier: 3.649A pdb=" N CYS C 54 " --> pdb=" O LYS C 50 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER C 55 " --> pdb=" O TRP C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 69 Processing helix chain 'C' and resid 94 through 104 removed outlier: 3.503A pdb=" N VAL C 98 " --> pdb=" O SER C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 117 Processing helix chain 'C' and resid 117 through 130 Processing helix chain 'C' and resid 157 through 170 Processing helix chain 'C' and resid 184 through 196 Processing helix chain 'C' and resid 201 through 214 Processing helix chain 'C' and resid 227 through 233 removed outlier: 4.039A pdb=" N MET C 233 " --> pdb=" O GLU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 238 Processing helix chain 'C' and resid 257 through 275 removed outlier: 3.701A pdb=" N VAL C 274 " --> pdb=" O ARG C 270 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA C 275 " --> pdb=" O ARG C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 288 removed outlier: 3.797A pdb=" N LEU C 281 " --> pdb=" O ASN C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 317 Processing helix chain 'C' and resid 392 through 408 removed outlier: 3.630A pdb=" N GLN C 408 " --> pdb=" O MET C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 415 removed outlier: 3.512A pdb=" N PHE C 413 " --> pdb=" O ASP C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 443 Processing helix chain 'C' and resid 446 through 452 removed outlier: 4.325A pdb=" N GLN C 450 " --> pdb=" O ASP C 446 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLY C 452 " --> pdb=" O PHE C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 519 removed outlier: 3.894A pdb=" N VAL C 519 " --> pdb=" O ALA C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 705 through 709 Processing helix chain 'C' and resid 713 through 720 removed outlier: 3.653A pdb=" N LYS C 719 " --> pdb=" O GLU C 715 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU C 720 " --> pdb=" O GLU C 716 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 766 Processing helix chain 'D' and resid 369 through 373 Processing helix chain 'E' and resid 360 through 366 removed outlier: 3.962A pdb=" N TRP E 364 " --> pdb=" O ASN E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 383 Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 79 removed outlier: 3.527A pdb=" N THR A 124 " --> pdb=" O PHE A 148 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASP A 153 " --> pdb=" O SER A 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 255 through 256 Processing sheet with id=AA4, first strand: chain 'A' and resid 291 through 295 removed outlier: 4.344A pdb=" N SER A 492 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N TYR A 497 " --> pdb=" O PHE A 521 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LYS A 551 " --> pdb=" O SER A 543 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N SER A 543 " --> pdb=" O LYS A 551 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL A 553 " --> pdb=" O ILE A 541 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL A 538 " --> pdb=" O ILE A 325 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 291 through 295 removed outlier: 4.344A pdb=" N SER A 492 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ILE A 481 " --> pdb=" O TYR A 497 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N LEU A 499 " --> pdb=" O ILE A 479 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE A 479 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL A 501 " --> pdb=" O LYS A 477 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LYS A 477 " --> pdb=" O VAL A 501 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 373 through 374 removed outlier: 5.753A pdb=" N GLN A 373 " --> pdb=" O LYS B 365 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N GLN B 367 " --> pdb=" O GLN A 373 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 623 through 628 removed outlier: 6.417A pdb=" N GLY A 627 " --> pdb=" O SER A 616 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N SER A 616 " --> pdb=" O GLY A 627 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AB1, first strand: chain 'B' and resid 178 through 188 Processing sheet with id=AB2, first strand: chain 'B' and resid 240 through 243 removed outlier: 4.171A pdb=" N THR B 226 " --> pdb=" O ARG B 350 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR B 401 " --> pdb=" O ASN B 397 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 488 through 491 Processing sheet with id=AB4, first strand: chain 'C' and resid 59 through 61 removed outlier: 4.259A pdb=" N GLN C 91 " --> pdb=" O LEU C 61 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 131 through 136 removed outlier: 5.825A pdb=" N TRP C 132 " --> pdb=" O HIS C 247 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N HIS C 247 " --> pdb=" O TRP C 132 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ARG C 134 " --> pdb=" O ILE C 245 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 143 through 148 Processing sheet with id=AB7, first strand: chain 'C' and resid 289 through 291 removed outlier: 3.587A pdb=" N THR C 531 " --> pdb=" O VAL C 290 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 325 through 327 removed outlier: 6.962A pdb=" N GLU C 364 " --> pdb=" O ILE C 335 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N SER C 379 " --> pdb=" O LEU C 383 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LEU C 383 " --> pdb=" O SER C 379 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 340 through 347 Processing sheet with id=AC1, first strand: chain 'C' and resid 498 through 499 Processing sheet with id=AC2, first strand: chain 'C' and resid 698 through 700 Processing sheet with id=AC3, first strand: chain 'D' and resid 355 through 359 819 hydrogen bonds defined for protein. 2280 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.00 Time building geometry restraints manager: 9.92 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: 16556 1.03 - 1.23: 63 1.23 - 1.42: 6805 1.42 - 1.62: 9745 1.62 - 1.81: 214 Bond restraints: 33383 Sorted by residual: bond pdb=" CB GLU C 179 " pdb=" CG GLU C 179 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.25e+00 bond pdb=" CA ASP B 444 " pdb=" CB ASP B 444 " ideal model delta sigma weight residual 1.541 1.553 -0.012 1.20e-02 6.94e+03 1.01e+00 bond pdb=" CA VAL A 250 " pdb=" CB VAL A 250 " ideal model delta sigma weight residual 1.530 1.540 -0.009 1.05e-02 9.07e+03 8.17e-01 bond pdb=" CB ASP B 444 " pdb=" CG ASP B 444 " ideal model delta sigma weight residual 1.516 1.539 -0.023 2.50e-02 1.60e+03 8.14e-01 bond pdb=" CA SER B 443 " pdb=" C SER B 443 " ideal model delta sigma weight residual 1.531 1.522 0.009 1.08e-02 8.57e+03 7.46e-01 ... (remaining 33378 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 59180 1.38 - 2.77: 1124 2.77 - 4.15: 113 4.15 - 5.53: 12 5.53 - 6.91: 2 Bond angle restraints: 60431 Sorted by residual: angle pdb=" C ASN C 692 " pdb=" CA ASN C 692 " pdb=" CB ASN C 692 " ideal model delta sigma weight residual 117.23 112.07 5.16 1.36e+00 5.41e-01 1.44e+01 angle pdb=" N GLY A 542 " pdb=" CA GLY A 542 " pdb=" C GLY A 542 " ideal model delta sigma weight residual 111.42 115.83 -4.41 1.51e+00 4.39e-01 8.52e+00 angle pdb=" CA ASP B 444 " pdb=" CB ASP B 444 " pdb=" CG ASP B 444 " ideal model delta sigma weight residual 112.60 115.45 -2.85 1.00e+00 1.00e+00 8.11e+00 angle pdb=" N ASP B 444 " pdb=" CA ASP B 444 " pdb=" CB ASP B 444 " ideal model delta sigma weight residual 114.17 111.32 2.85 1.14e+00 7.69e-01 6.26e+00 angle pdb=" N SER C 298 " pdb=" CA SER C 298 " pdb=" C SER C 298 " ideal model delta sigma weight residual 113.18 110.04 3.14 1.33e+00 5.65e-01 5.58e+00 ... (remaining 60426 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 13605 17.85 - 35.71: 1343 35.71 - 53.56: 502 53.56 - 71.42: 116 71.42 - 89.27: 22 Dihedral angle restraints: 15588 sinusoidal: 8662 harmonic: 6926 Sorted by residual: dihedral pdb=" CA PHE C 365 " pdb=" C PHE C 365 " pdb=" N HIS C 366 " pdb=" CA HIS C 366 " ideal model delta harmonic sigma weight residual 180.00 159.34 20.66 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA LYS A 327 " pdb=" C LYS A 327 " pdb=" N SER A 328 " pdb=" CA SER A 328 " ideal model delta harmonic sigma weight residual 180.00 -159.87 -20.13 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA PHE A 677 " pdb=" C PHE A 677 " pdb=" N ASP A 678 " pdb=" CA ASP A 678 " ideal model delta harmonic sigma weight residual 180.00 161.42 18.58 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 15585 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1593 0.028 - 0.057: 630 0.057 - 0.085: 133 0.085 - 0.113: 101 0.113 - 0.141: 33 Chirality restraints: 2490 Sorted by residual: chirality pdb=" CA VAL A 514 " pdb=" N VAL A 514 " pdb=" C VAL A 514 " pdb=" CB VAL A 514 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.99e-01 chirality pdb=" CA ILE D 368 " pdb=" N ILE D 368 " pdb=" C ILE D 368 " pdb=" CB ILE D 368 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.95e-01 chirality pdb=" CA ILE B 368 " pdb=" N ILE B 368 " pdb=" C ILE B 368 " pdb=" CB ILE B 368 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.86e-01 ... (remaining 2487 not shown) Planarity restraints: 4879 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 444 " 0.014 2.00e-02 2.50e+03 2.70e-02 7.27e+00 pdb=" C ASP B 444 " -0.047 2.00e-02 2.50e+03 pdb=" O ASP B 444 " 0.017 2.00e-02 2.50e+03 pdb=" N ASP B 445 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 734 " 0.037 5.00e-02 4.00e+02 5.57e-02 4.96e+00 pdb=" N PRO C 735 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO C 735 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 735 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 253 " 0.028 5.00e-02 4.00e+02 4.23e-02 2.86e+00 pdb=" N PRO A 254 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 254 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 254 " 0.023 5.00e-02 4.00e+02 ... (remaining 4876 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 753 2.12 - 2.74: 60009 2.74 - 3.36: 96446 3.36 - 3.98: 122770 3.98 - 4.60: 193926 Nonbonded interactions: 473904 Sorted by model distance: nonbonded pdb="HD21 ASN B 306 " pdb=" O ASP B 444 " model vdw 1.497 2.450 nonbonded pdb=" OD2 ASP B 521 " pdb=" HH TYR B 558 " model vdw 1.573 2.450 nonbonded pdb=" OE1 GLN C 323 " pdb=" H GLN C 323 " model vdw 1.575 2.450 nonbonded pdb=" O SER B 58 " pdb=" H GLY B 62 " model vdw 1.601 2.450 nonbonded pdb=" OE1 GLU A 488 " pdb=" H GLU A 488 " model vdw 1.606 2.450 ... (remaining 473899 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=0.00 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: 6.940 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: 0.600 Extract box with map and model: 1.450 Check model and map are aligned: 0.270 Set scattering table: 0.330 Process input model: 67.400 Find NCS groups from input model: 0.380 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: 0.010 Load rotamer database and sin/cos tables:11.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 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 0.034 16787 Z= 0.107 Angle : 0.474 6.913 22601 Z= 0.249 Chirality : 0.037 0.141 2490 Planarity : 0.003 0.057 2899 Dihedral : 17.736 89.270 6415 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.80 % Favored : 96.15 % Rotamer: Outliers : 2.60 % Allowed : 24.74 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.19), residues: 2050 helix: 2.12 (0.18), residues: 902 sheet: -0.60 (0.35), residues: 209 loop : -0.68 (0.20), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 437 HIS 0.003 0.001 HIS C 235 PHE 0.016 0.001 PHE B 511 TYR 0.018 0.001 TYR B 496 ARG 0.003 0.000 ARG B 220 Details of bonding type rmsd hydrogen bonds : bond 0.13535 ( 814) hydrogen bonds : angle 5.44583 ( 2280) covalent geometry : bond 0.00244 (16787) covalent geometry : angle 0.47380 (22601) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 196 time to evaluate : 2.643 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: B 86 ASP cc_start: 0.7638 (p0) cc_final: 0.7263 (m-30) outliers start: 47 outliers final: 44 residues processed: 243 average time/residue: 2.0480 time to fit residues: 576.3817 Evaluate side-chains 231 residues out of total 1811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 187 time to evaluate : 2.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 475 LYS Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 595 GLN Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 306 ASN Chi-restraints excluded: chain B residue 309 TRP Chi-restraints excluded: chain B residue 437 TRP Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 503 ASN Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 456 SER Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain C residue 732 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 160 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 186 optimal weight: 10.0000 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN C 517 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.211047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.140737 restraints weight = 54036.970| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.42 r_work: 0.3532 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.0667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16787 Z= 0.205 Angle : 0.533 5.295 22601 Z= 0.284 Chirality : 0.040 0.171 2490 Planarity : 0.004 0.049 2899 Dihedral : 7.150 73.501 2312 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.88 % Favored : 95.07 % Rotamer: Outliers : 3.81 % Allowed : 24.24 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.19), residues: 2050 helix: 1.86 (0.17), residues: 905 sheet: -0.68 (0.33), residues: 230 loop : -0.78 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 437 HIS 0.004 0.001 HIS C 366 PHE 0.016 0.001 PHE B 449 TYR 0.019 0.002 TYR B 466 ARG 0.003 0.000 ARG C 126 Details of bonding type rmsd hydrogen bonds : bond 0.04645 ( 814) hydrogen bonds : angle 4.68914 ( 2280) covalent geometry : bond 0.00479 (16787) covalent geometry : angle 0.53325 (22601) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 192 time to evaluate : 2.446 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: A 272 HIS cc_start: 0.8513 (OUTLIER) cc_final: 0.8160 (m90) REVERT: A 332 ASN cc_start: 0.8328 (OUTLIER) cc_final: 0.7738 (t0) REVERT: A 581 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8385 (ttp) REVERT: A 621 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.6789 (mp0) REVERT: B 412 MET cc_start: 0.7945 (mmt) cc_final: 0.7620 (mmm) REVERT: B 568 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.6939 (mp0) REVERT: C 144 ARG cc_start: 0.6385 (ttp-170) cc_final: 0.5943 (ttm110) REVERT: C 155 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.6608 (tm-30) REVERT: C 193 GLU cc_start: 0.7612 (tp30) cc_final: 0.7407 (tp30) outliers start: 69 outliers final: 38 residues processed: 247 average time/residue: 2.1804 time to fit residues: 624.8872 Evaluate side-chains 229 residues out of total 1811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 185 time to evaluate : 2.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 272 HIS Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 475 LYS Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 595 GLN Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 621 GLU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 309 TRP Chi-restraints excluded: chain B residue 367 GLN Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 503 ASN Chi-restraints excluded: chain B residue 568 GLU Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 732 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 5 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 128 optimal weight: 0.3980 chunk 127 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 23 optimal weight: 0.4980 chunk 162 optimal weight: 8.9990 chunk 140 optimal weight: 6.9990 chunk 166 optimal weight: 9.9990 chunk 76 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 ASN C 517 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.211851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.147454 restraints weight = 54288.360| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.68 r_work: 0.3523 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.0862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16787 Z= 0.164 Angle : 0.506 9.319 22601 Z= 0.268 Chirality : 0.040 0.450 2490 Planarity : 0.004 0.045 2899 Dihedral : 6.381 67.380 2288 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.10 % Favored : 95.85 % Rotamer: Outliers : 3.09 % Allowed : 24.57 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.56 (0.19), residues: 2050 helix: 1.85 (0.17), residues: 905 sheet: -0.65 (0.33), residues: 230 loop : -0.86 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 437 HIS 0.004 0.001 HIS C 366 PHE 0.014 0.001 PHE B 449 TYR 0.016 0.001 TYR B 466 ARG 0.002 0.000 ARG A 169 Details of bonding type rmsd hydrogen bonds : bond 0.04356 ( 814) hydrogen bonds : angle 4.55292 ( 2280) covalent geometry : bond 0.00386 (16787) covalent geometry : angle 0.50636 (22601) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 195 time to evaluate : 2.399 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: A 272 HIS cc_start: 0.8549 (OUTLIER) cc_final: 0.8195 (m90) REVERT: A 332 ASN cc_start: 0.8339 (OUTLIER) cc_final: 0.7797 (t0) REVERT: A 382 ASP cc_start: 0.8213 (m-30) cc_final: 0.7910 (m-30) REVERT: A 577 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8248 (mp) REVERT: A 581 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.8297 (ttp) REVERT: A 621 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.6736 (mp0) REVERT: B 412 MET cc_start: 0.7910 (mmt) cc_final: 0.7567 (mmm) REVERT: B 568 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6926 (mp0) REVERT: B 690 LYS cc_start: 0.6316 (mttt) cc_final: 0.5699 (mmpt) REVERT: C 144 ARG cc_start: 0.6603 (ttp-170) cc_final: 0.6140 (ttm110) REVERT: C 155 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.6532 (tm-30) REVERT: C 193 GLU cc_start: 0.7685 (tp30) cc_final: 0.7442 (tp30) outliers start: 56 outliers final: 35 residues processed: 236 average time/residue: 2.2044 time to fit residues: 596.2650 Evaluate side-chains 229 residues out of total 1811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 187 time to evaluate : 2.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 272 HIS Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 475 LYS Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 595 GLN Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 621 GLU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 309 TRP Chi-restraints excluded: chain B residue 367 GLN Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 503 ASN Chi-restraints excluded: chain B residue 568 GLU Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 723 MET Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 456 SER Chi-restraints excluded: chain C residue 732 GLN Chi-restraints excluded: chain D residue 361 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 199 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 173 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 127 optimal weight: 2.9990 chunk 197 optimal weight: 0.9990 chunk 168 optimal weight: 0.0870 chunk 186 optimal weight: 10.0000 chunk 131 optimal weight: 3.9990 chunk 192 optimal weight: 5.9990 overall best weight: 1.3364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 ASN C 517 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.210871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.146200 restraints weight = 54227.705| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.64 r_work: 0.3531 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16787 Z= 0.162 Angle : 0.500 5.528 22601 Z= 0.265 Chirality : 0.039 0.161 2490 Planarity : 0.004 0.046 2899 Dihedral : 6.156 62.666 2280 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.54 % Favored : 95.41 % Rotamer: Outliers : 2.93 % Allowed : 25.12 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.19), residues: 2050 helix: 1.83 (0.17), residues: 905 sheet: -0.65 (0.33), residues: 236 loop : -0.93 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 437 HIS 0.003 0.001 HIS C 366 PHE 0.014 0.001 PHE B 695 TYR 0.016 0.001 TYR B 466 ARG 0.002 0.000 ARG A 169 Details of bonding type rmsd hydrogen bonds : bond 0.04084 ( 814) hydrogen bonds : angle 4.46298 ( 2280) covalent geometry : bond 0.00382 (16787) covalent geometry : angle 0.50037 (22601) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 192 time to evaluate : 2.866 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: A 272 HIS cc_start: 0.8523 (OUTLIER) cc_final: 0.8214 (m90) REVERT: A 332 ASN cc_start: 0.8349 (OUTLIER) cc_final: 0.7809 (t0) REVERT: A 577 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8293 (mp) REVERT: B 409 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.7846 (mpt) REVERT: B 412 MET cc_start: 0.7923 (mmt) cc_final: 0.7571 (mmm) REVERT: B 568 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.6949 (mp0) REVERT: B 585 ARG cc_start: 0.7061 (OUTLIER) cc_final: 0.6401 (mtm180) REVERT: B 708 VAL cc_start: 0.6556 (OUTLIER) cc_final: 0.6347 (m) REVERT: C 144 ARG cc_start: 0.6550 (ttp-170) cc_final: 0.6161 (ttm110) REVERT: C 155 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.6557 (tm-30) REVERT: C 178 ARG cc_start: 0.5607 (OUTLIER) cc_final: 0.4524 (mtm110) REVERT: C 300 LEU cc_start: 0.2658 (OUTLIER) cc_final: 0.2351 (mp) outliers start: 53 outliers final: 33 residues processed: 232 average time/residue: 2.3058 time to fit residues: 611.3300 Evaluate side-chains 226 residues out of total 1811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 183 time to evaluate : 2.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 272 HIS Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 475 LYS Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 595 GLN Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 621 GLU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 309 TRP Chi-restraints excluded: chain B residue 367 GLN Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 503 ASN Chi-restraints excluded: chain B residue 568 GLU Chi-restraints excluded: chain B residue 585 ARG Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 723 MET Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain D residue 361 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 108 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 chunk 190 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 12 optimal weight: 9.9990 chunk 132 optimal weight: 7.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 ASN B 700 ASN C 517 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.210553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.146881 restraints weight = 54047.878| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.60 r_work: 0.3524 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16787 Z= 0.183 Angle : 0.516 5.068 22601 Z= 0.273 Chirality : 0.040 0.157 2490 Planarity : 0.004 0.046 2899 Dihedral : 6.013 61.124 2275 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.49 % Favored : 95.46 % Rotamer: Outliers : 3.59 % Allowed : 24.46 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.19), residues: 2050 helix: 1.73 (0.17), residues: 916 sheet: -0.69 (0.33), residues: 236 loop : -1.03 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 437 HIS 0.004 0.001 HIS C 366 PHE 0.016 0.001 PHE B 695 TYR 0.017 0.002 TYR C 246 ARG 0.002 0.000 ARG B 249 Details of bonding type rmsd hydrogen bonds : bond 0.04193 ( 814) hydrogen bonds : angle 4.46184 ( 2280) covalent geometry : bond 0.00433 (16787) covalent geometry : angle 0.51550 (22601) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 188 time to evaluate : 2.565 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: A 272 HIS cc_start: 0.8521 (OUTLIER) cc_final: 0.8211 (m90) REVERT: A 332 ASN cc_start: 0.8353 (OUTLIER) cc_final: 0.7810 (t0) REVERT: A 577 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8304 (mp) REVERT: B 412 MET cc_start: 0.7917 (mmt) cc_final: 0.7575 (mmm) REVERT: B 568 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.6934 (mp0) REVERT: B 585 ARG cc_start: 0.7136 (OUTLIER) cc_final: 0.6476 (mtm180) REVERT: C 144 ARG cc_start: 0.6575 (ttp-170) cc_final: 0.6187 (ttm110) REVERT: C 155 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.6509 (tm-30) REVERT: C 178 ARG cc_start: 0.5640 (OUTLIER) cc_final: 0.4541 (mtm110) outliers start: 65 outliers final: 42 residues processed: 238 average time/residue: 2.2843 time to fit residues: 621.9656 Evaluate side-chains 231 residues out of total 1811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 182 time to evaluate : 2.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 272 HIS Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 475 LYS Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 595 GLN Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 621 GLU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 309 TRP Chi-restraints excluded: chain B residue 367 GLN Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 437 TRP Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 503 ASN Chi-restraints excluded: chain B residue 568 GLU Chi-restraints excluded: chain B residue 585 ARG Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 723 MET Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 456 SER Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain D residue 361 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 103 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 138 optimal weight: 9.9990 chunk 141 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 chunk 197 optimal weight: 5.9990 chunk 187 optimal weight: 9.9990 chunk 24 optimal weight: 0.7980 chunk 164 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 ASN B 700 ASN C 68 ASN C 517 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.211469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.145621 restraints weight = 54266.541| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.44 r_work: 0.3547 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16787 Z= 0.139 Angle : 0.491 5.125 22601 Z= 0.259 Chirality : 0.038 0.158 2490 Planarity : 0.004 0.046 2899 Dihedral : 5.910 57.764 2275 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.87 % Allowed : 25.23 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.19), residues: 2050 helix: 1.81 (0.17), residues: 916 sheet: -0.67 (0.32), residues: 240 loop : -1.04 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 437 HIS 0.004 0.001 HIS C 235 PHE 0.014 0.001 PHE B 511 TYR 0.015 0.001 TYR B 466 ARG 0.002 0.000 ARG B 571 Details of bonding type rmsd hydrogen bonds : bond 0.03865 ( 814) hydrogen bonds : angle 4.37484 ( 2280) covalent geometry : bond 0.00326 (16787) covalent geometry : angle 0.49077 (22601) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 192 time to evaluate : 2.741 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: A 195 ASP cc_start: 0.4618 (OUTLIER) cc_final: 0.4274 (p0) REVERT: A 272 HIS cc_start: 0.8488 (OUTLIER) cc_final: 0.8166 (m90) REVERT: A 332 ASN cc_start: 0.8337 (OUTLIER) cc_final: 0.7803 (t0) REVERT: A 577 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8278 (mp) REVERT: B 386 ARG cc_start: 0.8404 (ttm170) cc_final: 0.7935 (ttm170) REVERT: B 412 MET cc_start: 0.7900 (mmt) cc_final: 0.7562 (mmm) REVERT: B 568 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.6887 (mp0) REVERT: B 585 ARG cc_start: 0.7103 (OUTLIER) cc_final: 0.6455 (mtm180) REVERT: C 144 ARG cc_start: 0.6556 (ttp-170) cc_final: 0.6174 (ttm110) REVERT: C 155 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.6543 (tm-30) REVERT: C 178 ARG cc_start: 0.5650 (OUTLIER) cc_final: 0.4530 (mtm110) REVERT: C 300 LEU cc_start: 0.2652 (OUTLIER) cc_final: 0.2349 (mp) REVERT: C 381 MET cc_start: 0.5729 (ptm) cc_final: 0.5348 (ptm) outliers start: 52 outliers final: 36 residues processed: 235 average time/residue: 2.3361 time to fit residues: 625.4252 Evaluate side-chains 232 residues out of total 1811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 187 time to evaluate : 2.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 272 HIS Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 475 LYS Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 595 GLN Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 309 TRP Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 437 TRP Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 568 GLU Chi-restraints excluded: chain B residue 585 ARG Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 723 MET Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 323 GLN Chi-restraints excluded: chain C residue 456 SER Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain D residue 361 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 90 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 173 optimal weight: 8.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 180 optimal weight: 9.9990 chunk 132 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 548 GLN B 700 ASN C 517 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.209352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.142923 restraints weight = 53899.232| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.56 r_work: 0.3496 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 16787 Z= 0.202 Angle : 0.529 6.194 22601 Z= 0.281 Chirality : 0.040 0.157 2490 Planarity : 0.004 0.046 2899 Dihedral : 5.969 59.357 2273 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.48 % Allowed : 25.12 % Favored : 71.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.19), residues: 2050 helix: 1.64 (0.17), residues: 918 sheet: -0.78 (0.32), residues: 236 loop : -1.10 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 437 HIS 0.004 0.001 HIS C 366 PHE 0.017 0.001 PHE B 695 TYR 0.020 0.002 TYR C 246 ARG 0.002 0.000 ARG B 705 Details of bonding type rmsd hydrogen bonds : bond 0.04278 ( 814) hydrogen bonds : angle 4.45272 ( 2280) covalent geometry : bond 0.00485 (16787) covalent geometry : angle 0.52914 (22601) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 192 time to evaluate : 2.443 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: A 195 ASP cc_start: 0.4613 (OUTLIER) cc_final: 0.4291 (p0) REVERT: A 272 HIS cc_start: 0.8562 (OUTLIER) cc_final: 0.8282 (m90) REVERT: A 332 ASN cc_start: 0.8450 (OUTLIER) cc_final: 0.8035 (t0) REVERT: B 41 ASP cc_start: 0.8316 (OUTLIER) cc_final: 0.8050 (m-30) REVERT: B 412 MET cc_start: 0.7901 (mmt) cc_final: 0.7644 (mmm) REVERT: B 568 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7039 (mp0) REVERT: B 585 ARG cc_start: 0.7396 (OUTLIER) cc_final: 0.6635 (mtm180) REVERT: C 144 ARG cc_start: 0.6774 (ttp-170) cc_final: 0.6410 (ttm110) REVERT: C 155 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.6552 (tm-30) REVERT: C 178 ARG cc_start: 0.5825 (OUTLIER) cc_final: 0.4636 (mtm110) REVERT: C 300 LEU cc_start: 0.2762 (OUTLIER) cc_final: 0.2423 (mp) REVERT: C 372 CYS cc_start: 0.4555 (OUTLIER) cc_final: 0.3787 (t) outliers start: 63 outliers final: 39 residues processed: 243 average time/residue: 2.2897 time to fit residues: 633.8066 Evaluate side-chains 235 residues out of total 1811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 186 time to evaluate : 2.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 272 HIS Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 475 LYS Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 595 GLN Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 309 TRP Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 437 TRP Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 568 GLU Chi-restraints excluded: chain B residue 585 ARG Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 723 MET Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 48 ARG Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 372 CYS Chi-restraints excluded: chain C residue 456 SER Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain D residue 361 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 108 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 201 optimal weight: 4.9990 chunk 199 optimal weight: 7.9990 chunk 147 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 chunk 95 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 113 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 ASN B 367 GLN C 24 GLN C 517 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.211317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.145072 restraints weight = 53819.066| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.35 r_work: 0.3523 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16787 Z= 0.114 Angle : 0.486 6.120 22601 Z= 0.257 Chirality : 0.038 0.159 2490 Planarity : 0.003 0.045 2899 Dihedral : 5.804 58.604 2273 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.82 % Allowed : 25.90 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.19), residues: 2050 helix: 1.90 (0.18), residues: 910 sheet: -0.70 (0.32), residues: 240 loop : -1.01 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 437 HIS 0.004 0.001 HIS C 235 PHE 0.016 0.001 PHE B 511 TYR 0.016 0.001 TYR B 496 ARG 0.002 0.000 ARG A 169 Details of bonding type rmsd hydrogen bonds : bond 0.03665 ( 814) hydrogen bonds : angle 4.32748 ( 2280) covalent geometry : bond 0.00262 (16787) covalent geometry : angle 0.48643 (22601) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 194 time to evaluate : 2.734 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: A 272 HIS cc_start: 0.8524 (OUTLIER) cc_final: 0.8239 (m90) REVERT: A 456 MET cc_start: 0.8780 (mmm) cc_final: 0.8564 (mmm) REVERT: A 577 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8481 (mp) REVERT: B 41 ASP cc_start: 0.8277 (OUTLIER) cc_final: 0.8003 (m-30) REVERT: B 412 MET cc_start: 0.7916 (mmt) cc_final: 0.7610 (mmm) REVERT: B 568 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.6910 (mp0) REVERT: B 585 ARG cc_start: 0.7386 (OUTLIER) cc_final: 0.6611 (mtm180) REVERT: C 144 ARG cc_start: 0.6715 (ttp-170) cc_final: 0.6346 (ttm110) REVERT: C 155 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.6560 (tm-30) REVERT: C 178 ARG cc_start: 0.5793 (OUTLIER) cc_final: 0.4570 (mtm110) REVERT: C 300 LEU cc_start: 0.2894 (OUTLIER) cc_final: 0.2583 (mp) outliers start: 51 outliers final: 30 residues processed: 237 average time/residue: 2.4049 time to fit residues: 650.7779 Evaluate side-chains 220 residues out of total 1811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 182 time to evaluate : 2.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 272 HIS Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 475 LYS Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 595 GLN Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 309 TRP Chi-restraints excluded: chain B residue 437 TRP Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 568 GLU Chi-restraints excluded: chain B residue 585 ARG Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 456 SER Chi-restraints excluded: chain C residue 485 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 108 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 51 optimal weight: 0.0870 chunk 176 optimal weight: 9.9990 chunk 86 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 167 optimal weight: 9.9990 chunk 168 optimal weight: 0.8980 chunk 36 optimal weight: 0.0070 chunk 140 optimal weight: 9.9990 chunk 183 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN C 517 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.211559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.145819 restraints weight = 53758.837| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.36 r_work: 0.3528 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16787 Z= 0.122 Angle : 0.490 6.608 22601 Z= 0.256 Chirality : 0.038 0.157 2490 Planarity : 0.003 0.045 2899 Dihedral : 5.615 58.651 2271 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.60 % Allowed : 26.23 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.19), residues: 2050 helix: 1.97 (0.18), residues: 909 sheet: -0.74 (0.32), residues: 242 loop : -0.97 (0.20), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 437 HIS 0.004 0.001 HIS C 235 PHE 0.012 0.001 PHE B 511 TYR 0.019 0.001 TYR B 496 ARG 0.003 0.000 ARG B 386 Details of bonding type rmsd hydrogen bonds : bond 0.03579 ( 814) hydrogen bonds : angle 4.26347 ( 2280) covalent geometry : bond 0.00287 (16787) covalent geometry : angle 0.48966 (22601) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 192 time to evaluate : 2.572 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: A 195 ASP cc_start: 0.4628 (OUTLIER) cc_final: 0.4342 (p0) REVERT: A 272 HIS cc_start: 0.8471 (OUTLIER) cc_final: 0.8155 (m90) REVERT: A 572 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.5890 (mp0) REVERT: B 216 GLU cc_start: 0.7287 (mt-10) cc_final: 0.6735 (tp30) REVERT: B 412 MET cc_start: 0.7917 (mmt) cc_final: 0.7612 (mmm) REVERT: B 568 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.6879 (mp0) REVERT: B 585 ARG cc_start: 0.7407 (OUTLIER) cc_final: 0.6609 (mtm180) REVERT: C 144 ARG cc_start: 0.6707 (ttp-170) cc_final: 0.6336 (ttm110) REVERT: C 155 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.6470 (tm-30) REVERT: C 178 ARG cc_start: 0.5827 (OUTLIER) cc_final: 0.4614 (mtm110) REVERT: C 185 ARG cc_start: 0.6797 (OUTLIER) cc_final: 0.6588 (ptp-170) REVERT: C 372 CYS cc_start: 0.4537 (OUTLIER) cc_final: 0.3825 (t) REVERT: C 760 MET cc_start: 0.1636 (OUTLIER) cc_final: 0.0899 (ttp) outliers start: 47 outliers final: 31 residues processed: 233 average time/residue: 2.3451 time to fit residues: 622.3973 Evaluate side-chains 229 residues out of total 1811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 188 time to evaluate : 2.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 272 HIS Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 475 LYS Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 595 GLN Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 309 TRP Chi-restraints excluded: chain B residue 437 TRP Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 568 GLU Chi-restraints excluded: chain B residue 585 ARG Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 185 ARG Chi-restraints excluded: chain C residue 372 CYS Chi-restraints excluded: chain C residue 456 SER Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 760 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 8 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 173 optimal weight: 9.9990 chunk 23 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 101 optimal weight: 0.5980 chunk 137 optimal weight: 5.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 ASN B 700 ASN C 24 GLN C 517 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.209943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.143369 restraints weight = 53706.939| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.34 r_work: 0.3502 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 16787 Z= 0.192 Angle : 0.526 6.440 22601 Z= 0.276 Chirality : 0.040 0.156 2490 Planarity : 0.004 0.046 2899 Dihedral : 5.557 58.707 2268 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.65 % Allowed : 26.23 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.19), residues: 2050 helix: 1.79 (0.17), residues: 912 sheet: -0.74 (0.32), residues: 240 loop : -1.07 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 437 HIS 0.004 0.001 HIS C 366 PHE 0.017 0.001 PHE B 695 TYR 0.020 0.002 TYR B 496 ARG 0.002 0.000 ARG B 467 Details of bonding type rmsd hydrogen bonds : bond 0.04041 ( 814) hydrogen bonds : angle 4.35305 ( 2280) covalent geometry : bond 0.00461 (16787) covalent geometry : angle 0.52568 (22601) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 187 time to evaluate : 2.377 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: A 195 ASP cc_start: 0.4626 (OUTLIER) cc_final: 0.4325 (p0) REVERT: A 272 HIS cc_start: 0.8561 (OUTLIER) cc_final: 0.8242 (m90) REVERT: A 572 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.5907 (mp0) REVERT: B 41 ASP cc_start: 0.8303 (OUTLIER) cc_final: 0.8035 (m-30) REVERT: B 412 MET cc_start: 0.7925 (mmt) cc_final: 0.7607 (mmm) REVERT: B 568 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.6932 (mp0) REVERT: B 585 ARG cc_start: 0.7451 (OUTLIER) cc_final: 0.6674 (mtm180) REVERT: C 144 ARG cc_start: 0.6703 (ttp-170) cc_final: 0.6300 (ttm110) REVERT: C 155 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.6507 (tm-30) REVERT: C 178 ARG cc_start: 0.5766 (OUTLIER) cc_final: 0.4579 (mtm110) REVERT: C 372 CYS cc_start: 0.4471 (OUTLIER) cc_final: 0.3745 (t) outliers start: 48 outliers final: 31 residues processed: 230 average time/residue: 2.3024 time to fit residues: 602.0052 Evaluate side-chains 228 residues out of total 1811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 188 time to evaluate : 2.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 272 HIS Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 475 LYS Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 595 GLN Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 309 TRP Chi-restraints excluded: chain B residue 437 TRP Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 568 GLU Chi-restraints excluded: chain B residue 585 ARG Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 372 CYS Chi-restraints excluded: chain C residue 456 SER Chi-restraints excluded: chain C residue 485 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 0 optimal weight: 10.0000 chunk 191 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 115 optimal weight: 0.9980 chunk 145 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 700 ASN C 24 GLN C 517 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.211516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.142831 restraints weight = 53741.235| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.14 r_work: 0.3538 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16787 Z= 0.123 Angle : 0.494 6.798 22601 Z= 0.258 Chirality : 0.038 0.158 2490 Planarity : 0.003 0.045 2899 Dihedral : 5.444 58.960 2268 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.37 % Allowed : 26.34 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.19), residues: 2050 helix: 1.91 (0.17), residues: 915 sheet: -0.74 (0.32), residues: 236 loop : -1.01 (0.20), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 437 HIS 0.004 0.001 HIS C 235 PHE 0.017 0.001 PHE B 511 TYR 0.013 0.001 TYR B 554 ARG 0.002 0.000 ARG B 386 Details of bonding type rmsd hydrogen bonds : bond 0.03606 ( 814) hydrogen bonds : angle 4.26972 ( 2280) covalent geometry : bond 0.00289 (16787) covalent geometry : angle 0.49358 (22601) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24256.98 seconds wall clock time: 414 minutes 40.86 seconds (24880.86 seconds total)