Starting phenix.real_space_refine on Tue Aug 26 10:48:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rn9_19391/08_2025/8rn9_19391.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rn9_19391/08_2025/8rn9_19391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rn9_19391/08_2025/8rn9_19391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rn9_19391/08_2025/8rn9_19391.map" model { file = "/net/cci-nas-00/data/ceres_data/8rn9_19391/08_2025/8rn9_19391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rn9_19391/08_2025/8rn9_19391.cif" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.086 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 138 5.16 5 C 11329 2.51 5 N 3066 2.21 5 O 3343 1.98 5 H 18026 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35902 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 11470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 716, 11470 Classifications: {'peptide': 716} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 26, 'TRANS': 689} Chain: "B" Number of atoms: 11272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 11272 Classifications: {'peptide': 718} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 684} Chain breaks: 4 Chain: "C" Number of atoms: 12335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 760, 12335 Classifications: {'peptide': 760} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 28, 'TRANS': 731} Chain breaks: 1 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} Time building chain proxies: 5.05, per 1000 atoms: 0.14 Number of scatterers: 35902 At special positions: 0 Unit cell: (112.56, 144.48, 139.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 138 16.00 O 3343 8.00 N 3066 7.00 C 11329 6.00 H 18026 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: 2.71 Conformation dependent library (CDL) restraints added in 760.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4184 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 25 sheets defined 49.2% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 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 50 Processing helix chain 'A' and resid 84 through 100 Processing helix chain 'A' and resid 127 through 140 Processing helix chain 'A' and resid 163 through 184 Processing helix chain 'A' and resid 185 through 190 removed outlier: 4.194A pdb=" N VAL A 189 " --> pdb=" O ASN A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 215 Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 237 through 246 removed outlier: 3.627A pdb=" N ARG A 245 " --> pdb=" O ARG A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 270 Processing helix chain 'A' and resid 301 through 313 Processing helix chain 'A' and resid 313 through 318 Processing helix chain 'A' and resid 332 through 349 Processing helix chain 'A' and resid 360 through 366 removed outlier: 3.852A pdb=" N TRP A 364 " --> pdb=" O ASN A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 383 removed outlier: 3.617A pdb=" N ALA A 380 " --> pdb=" O MET A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 410 Processing helix chain 'A' and resid 429 through 447 removed outlier: 3.807A pdb=" N GLU A 445 " --> pdb=" O TYR A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 472 removed outlier: 3.697A pdb=" N THR A 453 " --> pdb=" O CYS A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 533 removed outlier: 4.279A pdb=" N SER A 530 " --> pdb=" O ARG A 527 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLY A 531 " --> pdb=" O VAL A 528 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS A 532 " --> pdb=" O ASP A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 572 removed outlier: 4.000A pdb=" N MET A 571 " --> pdb=" O MET A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 595 removed outlier: 4.144A pdb=" N LEU A 578 " --> pdb=" O ARG A 574 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN A 583 " --> pdb=" O GLN A 579 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N MET A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 605 removed outlier: 3.537A pdb=" N PHE A 604 " --> pdb=" O THR A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 646 Processing helix chain 'A' and resid 648 through 670 removed outlier: 3.572A pdb=" N GLU A 657 " --> pdb=" O GLY A 653 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ARG A 660 " --> pdb=" O ALA A 656 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU A 661 " --> pdb=" O GLU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 688 Processing helix chain 'A' and resid 693 through 714 Processing helix chain 'B' and resid 7 through 12 removed outlier: 3.917A pdb=" N ASP B 11 " --> pdb=" O PHE B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 22 removed outlier: 3.986A pdb=" N THR B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE B 22 " --> pdb=" O ILE B 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 17 through 22' Processing helix chain 'B' and resid 35 through 50 removed outlier: 3.734A pdb=" N SER B 50 " --> pdb=" O THR B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 117 Processing helix chain 'B' and resid 118 through 124 Processing helix chain 'B' and resid 138 through 153 removed outlier: 3.917A pdb=" N LEU B 152 " --> pdb=" O THR B 148 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN B 153 " --> pdb=" O SER B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 174 removed outlier: 3.813A pdb=" N PHE B 166 " --> pdb=" O GLY B 162 " (cutoff:3.500A) removed outlier: 3.695A 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 245 through 266 removed outlier: 3.597A pdb=" N ARG B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLY B 250 " --> pdb=" O ILE B 246 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN B 265 " --> pdb=" O ASN B 261 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU B 266 " --> pdb=" O ILE B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 293 removed outlier: 3.542A pdb=" N LYS B 279 " --> pdb=" O GLY B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 removed outlier: 3.589A pdb=" N PHE B 318 " --> pdb=" O ASN B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 338 Processing helix chain 'B' and resid 338 through 346 removed outlier: 3.598A pdb=" N VAL B 342 " --> pdb=" O SER B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 376 removed outlier: 4.794A pdb=" N PHE B 374 " --> pdb=" O PRO B 371 " (cutoff:3.500A) removed outlier: 4.047A 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 394 through 396 No H-bonds generated for 'chain 'B' and resid 394 through 396' Processing helix chain 'B' and resid 413 through 426 Processing helix chain 'B' and resid 454 through 471 Processing helix chain 'B' and resid 517 through 537 removed outlier: 3.835A pdb=" N GLY B 537 " --> pdb=" O MET B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 558 Processing helix chain 'B' and resid 569 through 582 removed outlier: 3.951A pdb=" N ILE B 574 " --> pdb=" O LYS B 570 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU B 580 " --> pdb=" O LYS B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 593 removed outlier: 3.702A pdb=" N GLY B 593 " --> pdb=" O VAL B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 603 removed outlier: 3.694A 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 Processing helix chain 'B' and resid 632 through 639 removed outlier: 3.950A pdb=" N GLU B 637 " --> pdb=" O LEU B 634 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLY B 638 " --> pdb=" O SER B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 699 Processing helix chain 'B' and resid 712 through 731 Processing helix chain 'B' and resid 735 through 750 removed outlier: 3.598A pdb=" N GLY B 750 " --> pdb=" O LEU B 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 15 removed outlier: 4.065A pdb=" N ASP C 15 " --> pdb=" O GLN C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 25 Processing helix chain 'C' and resid 29 through 35 Processing helix chain 'C' and resid 44 through 55 removed outlier: 3.590A pdb=" N CYS C 54 " --> pdb=" O LYS C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 70 Processing helix chain 'C' and resid 94 through 104 removed outlier: 3.655A pdb=" N VAL C 98 " --> pdb=" O SER C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 116 removed outlier: 4.225A pdb=" N ARG C 115 " --> pdb=" O GLU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 129 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 removed outlier: 3.585A pdb=" N LEU C 205 " --> pdb=" O THR C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 233 removed outlier: 4.029A 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: 3.767A pdb=" N VAL C 274 " --> pdb=" O ARG C 270 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA C 275 " --> pdb=" O ARG C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 289 removed outlier: 3.970A 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: 3.548A pdb=" N GLN C 408 " --> pdb=" O MET C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 415 Processing helix chain 'C' and resid 431 through 443 Processing helix chain 'C' and resid 446 through 452 removed outlier: 4.282A pdb=" N GLN C 450 " --> pdb=" O ASP C 446 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLY C 452 " --> pdb=" O PHE C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 557 Processing helix chain 'C' and resid 557 through 568 removed outlier: 3.570A pdb=" N LEU C 561 " --> pdb=" O ASN C 557 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU C 566 " --> pdb=" O LYS C 562 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU C 567 " --> pdb=" O ALA C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 573 Processing helix chain 'C' and resid 575 through 577 No H-bonds generated for 'chain 'C' and resid 575 through 577' Processing helix chain 'C' and resid 578 through 583 Processing helix chain 'C' and resid 586 through 608 removed outlier: 4.718A pdb=" N GLY C 591 " --> pdb=" O GLN C 587 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N GLN C 592 " --> pdb=" O LYS C 588 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU C 608 " --> pdb=" O MET C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 611 through 619 Processing helix chain 'C' and resid 620 through 623 removed outlier: 3.721A pdb=" N PHE C 623 " --> pdb=" O PRO C 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 620 through 623' Processing helix chain 'C' and resid 680 through 689 Processing helix chain 'C' and resid 705 through 709 removed outlier: 3.622A pdb=" N LEU C 708 " --> pdb=" O ASP C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 720 removed outlier: 3.698A pdb=" N LYS C 719 " --> pdb=" O GLU C 715 " (cutoff:3.500A) removed outlier: 3.933A 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: 3.951A 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 52 through 54 Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 79 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: 3.569A pdb=" N THR A 295 " --> pdb=" O SER A 492 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N SER A 492 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N TYR A 497 " --> pdb=" O PHE A 521 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 416 through 417 removed outlier: 6.302A pdb=" N LYS A 477 " --> pdb=" O VAL A 501 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N VAL A 501 " --> pdb=" O LYS A 477 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE A 479 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LEU A 499 " --> pdb=" O ILE A 479 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ILE A 481 " --> pdb=" O TYR A 497 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N TYR A 497 " --> pdb=" O PHE A 521 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 373 through 374 removed outlier: 6.040A pdb=" N GLN A 373 " --> pdb=" O LYS B 365 " (cutoff:3.500A) removed outlier: 8.553A 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: 6.173A pdb=" N LYS A 623 " --> pdb=" O THR A 619 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N THR A 619 " --> pdb=" O LYS A 623 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL A 625 " --> pdb=" O ILE A 617 " (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: 6.512A pdb=" N LEU B 224 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 488 through 491 removed outlier: 3.943A pdb=" N PHE B 495 " --> pdb=" O SER B 502 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 641 through 642 Processing sheet with id=AB5, first strand: chain 'C' and resid 59 through 61 removed outlier: 3.979A pdb=" N MET C 92 " --> pdb=" O THR C 81 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 73 through 74 Processing sheet with id=AB7, first strand: chain 'C' and resid 131 through 136 removed outlier: 5.945A pdb=" N TRP C 132 " --> pdb=" O HIS C 247 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N HIS C 247 " --> pdb=" O TRP C 132 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ARG C 134 " --> pdb=" O ILE C 245 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 143 through 148 Processing sheet with id=AB9, first strand: chain 'C' and resid 290 through 291 Processing sheet with id=AC1, first strand: chain 'C' and resid 325 through 327 removed outlier: 6.988A pdb=" N GLU C 364 " --> pdb=" O ILE C 335 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N SER C 379 " --> pdb=" O LEU C 383 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LEU C 383 " --> pdb=" O SER C 379 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 340 through 347 Processing sheet with id=AC3, first strand: chain 'C' and resid 498 through 499 Processing sheet with id=AC4, first strand: chain 'C' and resid 639 through 641 Processing sheet with id=AC5, first strand: chain 'C' and resid 659 through 662 Processing sheet with id=AC6, first strand: chain 'C' and resid 698 through 700 Processing sheet with id=AC7, first strand: chain 'D' and resid 355 through 359 882 hydrogen bonds defined for protein. 2463 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: 7.02 Time building geometry restraints manager: 3.61 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: 17984 1.03 - 1.23: 45 1.23 - 1.42: 7403 1.42 - 1.62: 10568 1.62 - 1.81: 234 Bond restraints: 36234 Sorted by residual: bond pdb=" N ILE B 749 " pdb=" CA ILE B 749 " ideal model delta sigma weight residual 1.461 1.496 -0.034 1.17e-02 7.31e+03 8.60e+00 bond pdb=" C LYS B 741 " pdb=" O LYS B 741 " ideal model delta sigma weight residual 1.236 1.269 -0.033 1.16e-02 7.43e+03 8.13e+00 bond pdb=" C ALA B 744 " pdb=" O ALA B 744 " ideal model delta sigma weight residual 1.236 1.267 -0.031 1.16e-02 7.43e+03 7.25e+00 bond pdb=" N ILE B 752 " pdb=" H ILE B 752 " ideal model delta sigma weight residual 0.860 0.914 -0.054 2.00e-02 2.50e+03 7.25e+00 bond pdb=" N TYR B 751 " pdb=" H TYR B 751 " ideal model delta sigma weight residual 0.860 0.913 -0.053 2.00e-02 2.50e+03 7.02e+00 ... (remaining 36229 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 64840 1.62 - 3.25: 675 3.25 - 4.87: 89 4.87 - 6.50: 12 6.50 - 8.12: 2 Bond angle restraints: 65618 Sorted by residual: angle pdb=" C GLU C 179 " pdb=" CA GLU C 179 " pdb=" CB GLU C 179 " ideal model delta sigma weight residual 111.22 117.23 -6.01 1.23e+00 6.61e-01 2.39e+01 angle pdb=" C GLU B 748 " pdb=" N ILE B 749 " pdb=" CA ILE B 749 " ideal model delta sigma weight residual 120.53 126.91 -6.38 1.41e+00 5.03e-01 2.05e+01 angle pdb=" C GLU A 70 " pdb=" CA GLU A 70 " pdb=" CB GLU A 70 " ideal model delta sigma weight residual 117.23 111.29 5.94 1.36e+00 5.41e-01 1.91e+01 angle pdb=" CA MET B 743 " pdb=" C MET B 743 " pdb=" O MET B 743 " ideal model delta sigma weight residual 120.82 116.52 4.30 1.05e+00 9.07e-01 1.68e+01 angle pdb=" N ILE A 80 " pdb=" CA ILE A 80 " pdb=" C ILE A 80 " ideal model delta sigma weight residual 112.96 108.90 4.06 1.00e+00 1.00e+00 1.65e+01 ... (remaining 65613 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 14793 17.55 - 35.10: 1501 35.10 - 52.65: 478 52.65 - 70.20: 116 70.20 - 87.75: 25 Dihedral angle restraints: 16913 sinusoidal: 9402 harmonic: 7511 Sorted by residual: 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 -157.17 -22.83 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA GLN A 595 " pdb=" C GLN A 595 " pdb=" N GLY A 596 " pdb=" CA GLY A 596 " ideal model delta harmonic sigma weight residual -180.00 -158.13 -21.87 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA MET C 537 " pdb=" C MET C 537 " pdb=" N TRP C 538 " pdb=" CA TRP C 538 " ideal model delta harmonic sigma weight residual -180.00 -159.32 -20.68 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 16910 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2113 0.040 - 0.080: 402 0.080 - 0.120: 150 0.120 - 0.160: 22 0.160 - 0.199: 2 Chirality restraints: 2689 Sorted by residual: chirality pdb=" CA ILE B 752 " pdb=" N ILE B 752 " pdb=" C ILE B 752 " pdb=" CB ILE B 752 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.94e-01 chirality pdb=" CB VAL A 443 " pdb=" CA VAL A 443 " pdb=" CG1 VAL A 443 " pdb=" CG2 VAL A 443 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.38e-01 chirality pdb=" CA LEU B 746 " pdb=" N LEU B 746 " pdb=" C LEU B 746 " pdb=" CB LEU B 746 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.06e-01 ... (remaining 2686 not shown) Planarity restraints: 5294 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 722 " -0.399 9.50e-02 1.11e+02 1.33e-01 1.88e+01 pdb=" NE ARG B 722 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG B 722 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG B 722 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 722 " -0.002 2.00e-02 2.50e+03 pdb="HH11 ARG B 722 " 0.006 2.00e-02 2.50e+03 pdb="HH12 ARG B 722 " -0.005 2.00e-02 2.50e+03 pdb="HH21 ARG B 722 " -0.009 2.00e-02 2.50e+03 pdb="HH22 ARG B 722 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 429 " 0.027 5.00e-02 4.00e+02 4.09e-02 2.68e+00 pdb=" N PRO A 430 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 430 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 430 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 179 " 0.008 2.00e-02 2.50e+03 1.52e-02 2.30e+00 pdb=" C GLU C 179 " -0.026 2.00e-02 2.50e+03 pdb=" O GLU C 179 " 0.010 2.00e-02 2.50e+03 pdb=" N SER C 180 " 0.009 2.00e-02 2.50e+03 ... (remaining 5291 not shown) Histogram of nonbonded interaction distances: 1.33 - 1.98: 280 1.98 - 2.64: 48229 2.64 - 3.29: 108986 3.29 - 3.95: 135574 3.95 - 4.60: 215628 Nonbonded interactions: 508697 Sorted by model distance: nonbonded pdb=" HA2 GLY A 570 " pdb=" HH TYR A 644 " model vdw 1.328 2.270 nonbonded pdb=" H GLY B 515 " pdb=" OD2 ASP B 521 " model vdw 1.555 2.450 nonbonded pdb=" OD1 ASN B 153 " pdb=" H THR B 180 " model vdw 1.561 2.450 nonbonded pdb=" HD1 TYR A 644 " pdb=" HA2 GLY B 26 " model vdw 1.565 2.270 nonbonded pdb=" HH TYR A 279 " pdb=" O LEU A 283 " model vdw 1.570 2.450 ... (remaining 508692 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: 9.950 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: 0.230 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 27.340 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 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 : 0.003 0.038 18208 Z= 0.134 Angle : 0.529 8.122 24510 Z= 0.291 Chirality : 0.038 0.199 2689 Planarity : 0.004 0.171 3147 Dihedral : 16.684 87.749 6971 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.81 % Favored : 95.15 % Rotamer: Outliers : 0.31 % Allowed : 19.83 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.18), residues: 2226 helix: 1.53 (0.17), residues: 979 sheet: -0.96 (0.33), residues: 245 loop : -1.02 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 257 TYR 0.020 0.001 TYR A 644 PHE 0.017 0.001 PHE B 504 TRP 0.011 0.001 TRP B 437 HIS 0.004 0.001 HIS B 745 Details of bonding type rmsd covalent geometry : bond 0.00263 (18208) covalent geometry : angle 0.52899 (24510) hydrogen bonds : bond 0.12990 ( 867) hydrogen bonds : angle 5.51203 ( 2463) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 281 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 285 average time/residue: 0.2891 time to fit residues: 124.0589 Evaluate side-chains 277 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 274 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 607 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 10.0000 chunk 212 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 583 GLN ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.166031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.129220 restraints weight = 87219.209| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.53 r_work: 0.3514 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.0831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 18208 Z= 0.276 Angle : 0.593 5.993 24510 Z= 0.320 Chirality : 0.042 0.156 2689 Planarity : 0.005 0.062 3147 Dihedral : 4.838 55.209 2433 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.02 % Favored : 93.94 % Rotamer: Outliers : 1.73 % Allowed : 20.34 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.18), residues: 2226 helix: 1.01 (0.16), residues: 996 sheet: -1.15 (0.33), residues: 236 loop : -1.32 (0.20), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 212 TYR 0.022 0.002 TYR B 554 PHE 0.014 0.002 PHE A 539 TRP 0.015 0.002 TRP C 100 HIS 0.006 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00627 (18208) covalent geometry : angle 0.59263 (24510) hydrogen bonds : bond 0.04596 ( 867) hydrogen bonds : angle 5.02943 ( 2463) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 282 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 VAL cc_start: 0.7732 (t) cc_final: 0.7357 (m) REVERT: A 308 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7516 (tm-30) REVERT: A 567 MET cc_start: 0.7813 (mmm) cc_final: 0.7602 (mmm) REVERT: B 256 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7658 (mt-10) REVERT: B 311 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8343 (mt-10) REVERT: B 409 MET cc_start: 0.6421 (mmp) cc_final: 0.6162 (mmm) REVERT: B 530 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8115 (ptmm) REVERT: B 748 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7630 (tm-30) REVERT: C 179 GLU cc_start: 0.8689 (tt0) cc_final: 0.8033 (tm-30) REVERT: D 363 ARG cc_start: 0.8488 (mtp85) cc_final: 0.8283 (mtt-85) outliers start: 34 outliers final: 24 residues processed: 310 average time/residue: 0.3573 time to fit residues: 165.6310 Evaluate side-chains 296 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 270 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain B residue 692 CYS Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 456 SER Chi-restraints excluded: chain C residue 545 GLU Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 713 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 81 optimal weight: 3.9990 chunk 198 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 189 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 148 optimal weight: 9.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 579 GLN A 583 GLN ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.168833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.132572 restraints weight = 86324.347| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.51 r_work: 0.3551 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18208 Z= 0.128 Angle : 0.504 5.666 24510 Z= 0.265 Chirality : 0.038 0.149 2689 Planarity : 0.004 0.038 3147 Dihedral : 4.565 56.272 2430 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.72 % Favored : 95.24 % Rotamer: Outliers : 1.63 % Allowed : 20.23 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.18), residues: 2226 helix: 1.19 (0.17), residues: 1000 sheet: -1.27 (0.33), residues: 232 loop : -1.25 (0.20), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 686 TYR 0.016 0.001 TYR B 554 PHE 0.009 0.001 PHE B 550 TRP 0.011 0.001 TRP A 695 HIS 0.003 0.001 HIS B 604 Details of bonding type rmsd covalent geometry : bond 0.00290 (18208) covalent geometry : angle 0.50369 (24510) hydrogen bonds : bond 0.03971 ( 867) hydrogen bonds : angle 4.63844 ( 2463) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 283 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 VAL cc_start: 0.7703 (t) cc_final: 0.7433 (m) REVERT: A 123 ILE cc_start: 0.7865 (mt) cc_final: 0.7302 (pt) REVERT: A 308 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7549 (tm-30) REVERT: A 567 MET cc_start: 0.7707 (mmm) cc_final: 0.7380 (mmm) REVERT: C 136 THR cc_start: 0.8819 (m) cc_final: 0.8546 (p) REVERT: C 179 GLU cc_start: 0.8749 (tt0) cc_final: 0.8122 (tm-30) REVERT: C 524 SER cc_start: 0.6865 (OUTLIER) cc_final: 0.6421 (t) REVERT: C 596 PHE cc_start: 0.7158 (t80) cc_final: 0.6899 (t80) outliers start: 32 outliers final: 22 residues processed: 309 average time/residue: 0.3328 time to fit residues: 157.4499 Evaluate side-chains 295 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 272 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 367 GLN Chi-restraints excluded: chain B residue 687 CYS Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 524 SER Chi-restraints excluded: chain C residue 545 GLU Chi-restraints excluded: chain C residue 610 MET Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 713 THR Chi-restraints excluded: chain D residue 372 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 54 optimal weight: 4.9990 chunk 73 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 200 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 212 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 198 optimal weight: 5.9990 chunk 202 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN C 437 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.163608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.128020 restraints weight = 87103.182| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.46 r_work: 0.3498 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 18208 Z= 0.266 Angle : 0.591 5.542 24510 Z= 0.318 Chirality : 0.042 0.166 2689 Planarity : 0.004 0.040 3147 Dihedral : 4.925 57.202 2430 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.19 % Favored : 92.77 % Rotamer: Outliers : 2.70 % Allowed : 20.34 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.18), residues: 2226 helix: 0.77 (0.16), residues: 997 sheet: -1.28 (0.33), residues: 239 loop : -1.47 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 212 TYR 0.019 0.002 TYR B 554 PHE 0.021 0.002 PHE A 442 TRP 0.013 0.002 TRP B 437 HIS 0.006 0.002 HIS B 711 Details of bonding type rmsd covalent geometry : bond 0.00609 (18208) covalent geometry : angle 0.59093 (24510) hydrogen bonds : bond 0.04359 ( 867) hydrogen bonds : angle 4.90767 ( 2463) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 282 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 VAL cc_start: 0.7803 (t) cc_final: 0.7525 (m) REVERT: A 123 ILE cc_start: 0.7882 (mt) cc_final: 0.7356 (pt) REVERT: A 308 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7445 (tm-30) REVERT: A 650 GLN cc_start: 0.8981 (OUTLIER) cc_final: 0.8683 (mt0) REVERT: B 256 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7655 (mt-10) REVERT: B 530 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8067 (ptmm) REVERT: C 59 LEU cc_start: 0.6417 (OUTLIER) cc_final: 0.6170 (mp) REVERT: C 125 MET cc_start: 0.8482 (tmm) cc_final: 0.8229 (tmm) REVERT: C 136 THR cc_start: 0.8791 (m) cc_final: 0.8550 (p) REVERT: C 179 GLU cc_start: 0.8631 (tt0) cc_final: 0.8122 (tm-30) REVERT: C 219 PHE cc_start: 0.8334 (OUTLIER) cc_final: 0.7953 (t80) REVERT: C 524 SER cc_start: 0.7059 (OUTLIER) cc_final: 0.6635 (t) REVERT: C 596 PHE cc_start: 0.7234 (t80) cc_final: 0.7033 (t80) outliers start: 53 outliers final: 42 residues processed: 326 average time/residue: 0.3445 time to fit residues: 171.1065 Evaluate side-chains 316 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 269 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 367 GLN Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain B residue 687 CYS Chi-restraints excluded: chain B residue 692 CYS Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 456 SER Chi-restraints excluded: chain C residue 524 SER Chi-restraints excluded: chain C residue 545 GLU Chi-restraints excluded: chain C residue 610 MET Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 648 ASN Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 713 THR Chi-restraints excluded: chain D residue 372 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 80 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 219 optimal weight: 7.9990 chunk 156 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 157 optimal weight: 0.5980 chunk 214 optimal weight: 3.9990 chunk 8 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 ASN ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.166457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.131269 restraints weight = 86454.333| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.80 r_work: 0.3509 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 18208 Z= 0.164 Angle : 0.523 5.431 24510 Z= 0.277 Chirality : 0.039 0.153 2689 Planarity : 0.004 0.058 3147 Dihedral : 4.784 57.534 2430 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.39 % Favored : 94.56 % Rotamer: Outliers : 2.19 % Allowed : 21.05 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.18), residues: 2226 helix: 0.95 (0.16), residues: 997 sheet: -1.30 (0.33), residues: 237 loop : -1.41 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 324 TYR 0.016 0.001 TYR B 554 PHE 0.030 0.001 PHE B 504 TRP 0.011 0.001 TRP C 100 HIS 0.004 0.001 HIS C 235 Details of bonding type rmsd covalent geometry : bond 0.00375 (18208) covalent geometry : angle 0.52326 (24510) hydrogen bonds : bond 0.03861 ( 867) hydrogen bonds : angle 4.64842 ( 2463) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 272 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 VAL cc_start: 0.7699 (t) cc_final: 0.7426 (m) REVERT: A 123 ILE cc_start: 0.7832 (mt) cc_final: 0.7283 (pt) REVERT: A 308 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7754 (tm-30) REVERT: A 704 ASN cc_start: 0.7892 (m-40) cc_final: 0.7303 (m110) REVERT: B 179 MET cc_start: 0.8873 (tpt) cc_final: 0.8120 (tpt) REVERT: B 256 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7694 (mt-10) REVERT: B 311 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8398 (mt-10) REVERT: C 59 LEU cc_start: 0.6427 (OUTLIER) cc_final: 0.6206 (mp) REVERT: C 125 MET cc_start: 0.8488 (tmm) cc_final: 0.8211 (tmm) REVERT: C 136 THR cc_start: 0.8776 (m) cc_final: 0.8533 (p) REVERT: C 179 GLU cc_start: 0.8708 (tt0) cc_final: 0.8183 (tm-30) REVERT: C 219 PHE cc_start: 0.8325 (OUTLIER) cc_final: 0.7954 (t80) REVERT: C 524 SER cc_start: 0.6947 (OUTLIER) cc_final: 0.6524 (t) REVERT: C 596 PHE cc_start: 0.7230 (t80) cc_final: 0.7016 (t80) outliers start: 43 outliers final: 30 residues processed: 307 average time/residue: 0.3423 time to fit residues: 159.5470 Evaluate side-chains 301 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 266 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 628 SER Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 367 GLN Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 687 CYS Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 524 SER Chi-restraints excluded: chain C residue 545 GLU Chi-restraints excluded: chain C residue 610 MET Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 713 THR Chi-restraints excluded: chain D residue 372 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 15 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 215 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 213 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 218 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 167 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 583 GLN ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.164303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.128888 restraints weight = 86572.463| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.46 r_work: 0.3519 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 18208 Z= 0.200 Angle : 0.538 5.762 24510 Z= 0.286 Chirality : 0.040 0.154 2689 Planarity : 0.004 0.076 3147 Dihedral : 4.827 58.543 2430 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.74 % Favored : 93.22 % Rotamer: Outliers : 2.96 % Allowed : 20.59 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.18), residues: 2226 helix: 0.93 (0.16), residues: 990 sheet: -1.30 (0.33), residues: 244 loop : -1.38 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 324 TYR 0.017 0.001 TYR B 554 PHE 0.019 0.001 PHE B 504 TRP 0.012 0.001 TRP B 437 HIS 0.004 0.001 HIS C 235 Details of bonding type rmsd covalent geometry : bond 0.00461 (18208) covalent geometry : angle 0.53771 (24510) hydrogen bonds : bond 0.03872 ( 867) hydrogen bonds : angle 4.65824 ( 2463) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 276 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 VAL cc_start: 0.7741 (t) cc_final: 0.7483 (m) REVERT: A 123 ILE cc_start: 0.7861 (mt) cc_final: 0.7316 (pt) REVERT: A 308 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7720 (tm-30) REVERT: A 650 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.8695 (mt0) REVERT: A 704 ASN cc_start: 0.7958 (m-40) cc_final: 0.7365 (m110) REVERT: B 179 MET cc_start: 0.8923 (tpt) cc_final: 0.8175 (tpt) REVERT: B 207 LYS cc_start: 0.7633 (mttt) cc_final: 0.7302 (mmtt) REVERT: B 256 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7642 (mt-10) REVERT: B 311 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8469 (mt-10) REVERT: C 59 LEU cc_start: 0.6369 (OUTLIER) cc_final: 0.6119 (mp) REVERT: C 136 THR cc_start: 0.8774 (m) cc_final: 0.8517 (p) REVERT: C 179 GLU cc_start: 0.8596 (tt0) cc_final: 0.8159 (tm-30) REVERT: C 219 PHE cc_start: 0.8351 (OUTLIER) cc_final: 0.7911 (t80) REVERT: C 524 SER cc_start: 0.6995 (OUTLIER) cc_final: 0.6562 (t) outliers start: 58 outliers final: 40 residues processed: 324 average time/residue: 0.2973 time to fit residues: 145.8527 Evaluate side-chains 318 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 272 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 628 SER Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 367 GLN Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 687 CYS Chi-restraints excluded: chain B residue 692 CYS Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 456 SER Chi-restraints excluded: chain C residue 524 SER Chi-restraints excluded: chain C residue 545 GLU Chi-restraints excluded: chain C residue 610 MET Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 648 ASN Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 713 THR Chi-restraints excluded: chain D residue 372 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 131 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 185 optimal weight: 7.9990 chunk 211 optimal weight: 8.9990 chunk 169 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 129 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 595 GLN ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 ASN ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 244 GLN ** C 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.163338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.127746 restraints weight = 87488.920| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.48 r_work: 0.3503 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 18208 Z= 0.221 Angle : 0.554 5.661 24510 Z= 0.296 Chirality : 0.041 0.155 2689 Planarity : 0.004 0.073 3147 Dihedral : 4.929 59.029 2430 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.29 % Favored : 93.67 % Rotamer: Outliers : 3.41 % Allowed : 20.80 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.18), residues: 2226 helix: 0.82 (0.16), residues: 996 sheet: -1.36 (0.33), residues: 235 loop : -1.48 (0.20), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 324 TYR 0.018 0.001 TYR B 554 PHE 0.033 0.002 PHE B 504 TRP 0.012 0.001 TRP B 437 HIS 0.004 0.001 HIS C 235 Details of bonding type rmsd covalent geometry : bond 0.00507 (18208) covalent geometry : angle 0.55359 (24510) hydrogen bonds : bond 0.03964 ( 867) hydrogen bonds : angle 4.72051 ( 2463) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 279 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 VAL cc_start: 0.7733 (t) cc_final: 0.7216 (m) REVERT: A 123 ILE cc_start: 0.7902 (mt) cc_final: 0.7352 (pt) REVERT: A 308 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7738 (tm-30) REVERT: A 650 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8709 (mt0) REVERT: A 704 ASN cc_start: 0.7930 (m-40) cc_final: 0.7364 (m110) REVERT: B 179 MET cc_start: 0.8902 (tpt) cc_final: 0.8158 (tpt) REVERT: B 207 LYS cc_start: 0.7667 (mttt) cc_final: 0.7340 (mmtt) REVERT: B 256 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7655 (mt-10) REVERT: B 311 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8533 (mt-10) REVERT: B 530 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.7944 (ptmm) REVERT: B 685 GLU cc_start: 0.6054 (OUTLIER) cc_final: 0.3564 (mm-30) REVERT: C 59 LEU cc_start: 0.6282 (OUTLIER) cc_final: 0.6016 (mp) REVERT: C 136 THR cc_start: 0.8741 (m) cc_final: 0.8484 (p) REVERT: C 179 GLU cc_start: 0.8612 (tt0) cc_final: 0.8239 (tm-30) REVERT: C 219 PHE cc_start: 0.8390 (OUTLIER) cc_final: 0.7927 (t80) REVERT: C 298 SER cc_start: 0.7806 (OUTLIER) cc_final: 0.7278 (t) REVERT: C 454 GLU cc_start: 0.6751 (tp30) cc_final: 0.6485 (tp30) REVERT: C 524 SER cc_start: 0.6994 (OUTLIER) cc_final: 0.6591 (t) outliers start: 67 outliers final: 49 residues processed: 334 average time/residue: 0.3293 time to fit residues: 167.5743 Evaluate side-chains 330 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 272 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 628 SER Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 367 GLN Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 504 PHE Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain B residue 687 CYS Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 244 GLN Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 456 SER Chi-restraints excluded: chain C residue 524 SER Chi-restraints excluded: chain C residue 545 GLU Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 610 MET Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 648 ASN Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 713 THR Chi-restraints excluded: chain D residue 372 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 131 optimal weight: 7.9990 chunk 101 optimal weight: 0.9980 chunk 92 optimal weight: 9.9990 chunk 130 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 212 optimal weight: 1.9990 chunk 149 optimal weight: 0.0970 chunk 195 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 145 optimal weight: 0.0870 chunk 197 optimal weight: 10.0000 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 ASN ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.166704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.130622 restraints weight = 86657.133| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.54 r_work: 0.3535 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18208 Z= 0.113 Angle : 0.509 6.781 24510 Z= 0.268 Chirality : 0.038 0.151 2689 Planarity : 0.004 0.050 3147 Dihedral : 4.743 59.310 2430 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.44 % Favored : 94.52 % Rotamer: Outliers : 1.89 % Allowed : 22.58 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.18), residues: 2226 helix: 1.11 (0.16), residues: 994 sheet: -1.29 (0.33), residues: 240 loop : -1.32 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 324 TYR 0.015 0.001 TYR B 554 PHE 0.023 0.001 PHE B 504 TRP 0.011 0.001 TRP C 100 HIS 0.004 0.001 HIS B 604 Details of bonding type rmsd covalent geometry : bond 0.00259 (18208) covalent geometry : angle 0.50914 (24510) hydrogen bonds : bond 0.03577 ( 867) hydrogen bonds : angle 4.45968 ( 2463) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 275 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 VAL cc_start: 0.7450 (t) cc_final: 0.7175 (m) REVERT: A 123 ILE cc_start: 0.7864 (mt) cc_final: 0.7291 (pt) REVERT: A 308 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7758 (tm-30) REVERT: A 704 ASN cc_start: 0.7910 (m-40) cc_final: 0.7341 (m110) REVERT: B 207 LYS cc_start: 0.7681 (mttt) cc_final: 0.7307 (mmtt) REVERT: B 256 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7668 (mt-10) REVERT: B 311 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8385 (mt-10) REVERT: B 530 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.7889 (ptmm) REVERT: B 685 GLU cc_start: 0.5921 (OUTLIER) cc_final: 0.3354 (mm-30) REVERT: C 59 LEU cc_start: 0.6203 (OUTLIER) cc_final: 0.5948 (mp) REVERT: C 136 THR cc_start: 0.8783 (m) cc_final: 0.8533 (p) REVERT: C 179 GLU cc_start: 0.8608 (tt0) cc_final: 0.8194 (tm-30) REVERT: C 219 PHE cc_start: 0.8403 (OUTLIER) cc_final: 0.7913 (t80) REVERT: C 454 GLU cc_start: 0.6844 (tp30) cc_final: 0.6553 (tp30) REVERT: C 524 SER cc_start: 0.6926 (OUTLIER) cc_final: 0.6590 (t) outliers start: 37 outliers final: 22 residues processed: 306 average time/residue: 0.3425 time to fit residues: 158.3484 Evaluate side-chains 298 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 269 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 504 PHE Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain B residue 687 CYS Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 524 SER Chi-restraints excluded: chain C residue 545 GLU Chi-restraints excluded: chain C residue 610 MET Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 713 THR Chi-restraints excluded: chain D residue 372 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 188 optimal weight: 10.0000 chunk 139 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 180 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 176 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 91 optimal weight: 0.0000 chunk 62 optimal weight: 0.5980 chunk 81 optimal weight: 3.9990 overall best weight: 2.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.164607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.129225 restraints weight = 87203.217| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.49 r_work: 0.3515 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 18208 Z= 0.167 Angle : 0.521 5.763 24510 Z= 0.276 Chirality : 0.039 0.207 2689 Planarity : 0.004 0.050 3147 Dihedral : 4.602 55.762 2428 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.93 % Favored : 94.03 % Rotamer: Outliers : 2.14 % Allowed : 22.68 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.18), residues: 2226 helix: 1.09 (0.16), residues: 992 sheet: -1.33 (0.32), residues: 258 loop : -1.32 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 324 TYR 0.020 0.001 TYR A 644 PHE 0.024 0.001 PHE B 504 TRP 0.012 0.001 TRP B 437 HIS 0.004 0.001 HIS C 235 Details of bonding type rmsd covalent geometry : bond 0.00385 (18208) covalent geometry : angle 0.52084 (24510) hydrogen bonds : bond 0.03667 ( 867) hydrogen bonds : angle 4.49967 ( 2463) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 274 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 VAL cc_start: 0.7541 (t) cc_final: 0.7309 (m) REVERT: A 123 ILE cc_start: 0.7896 (mt) cc_final: 0.7320 (pt) REVERT: A 308 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7732 (tm-30) REVERT: A 650 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.8698 (mt0) REVERT: A 704 ASN cc_start: 0.7865 (m-40) cc_final: 0.7313 (m110) REVERT: B 179 MET cc_start: 0.8885 (tpt) cc_final: 0.8167 (tpt) REVERT: B 207 LYS cc_start: 0.7729 (mttt) cc_final: 0.7363 (mmtt) REVERT: B 256 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7690 (mt-10) REVERT: B 311 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8446 (mt-10) REVERT: B 530 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.7905 (ptmm) REVERT: B 685 GLU cc_start: 0.5936 (OUTLIER) cc_final: 0.3516 (mm-30) REVERT: C 59 LEU cc_start: 0.6263 (OUTLIER) cc_final: 0.6005 (mp) REVERT: C 136 THR cc_start: 0.8769 (m) cc_final: 0.8508 (p) REVERT: C 179 GLU cc_start: 0.8579 (tt0) cc_final: 0.8207 (tm-30) REVERT: C 219 PHE cc_start: 0.8409 (OUTLIER) cc_final: 0.7929 (t80) REVERT: C 454 GLU cc_start: 0.6915 (tp30) cc_final: 0.6638 (tp30) REVERT: C 524 SER cc_start: 0.6957 (OUTLIER) cc_final: 0.6622 (t) outliers start: 42 outliers final: 30 residues processed: 310 average time/residue: 0.3474 time to fit residues: 163.5352 Evaluate side-chains 309 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 271 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 504 PHE Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain B residue 687 CYS Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 524 SER Chi-restraints excluded: chain C residue 545 GLU Chi-restraints excluded: chain C residue 610 MET Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 713 THR Chi-restraints excluded: chain D residue 372 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 7 optimal weight: 4.9990 chunk 201 optimal weight: 9.9990 chunk 169 optimal weight: 0.0970 chunk 211 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 90 optimal weight: 0.0970 chunk 104 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 47 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 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.167420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.131478 restraints weight = 86602.293| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.54 r_work: 0.3549 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 18208 Z= 0.108 Angle : 0.502 6.196 24510 Z= 0.263 Chirality : 0.038 0.168 2689 Planarity : 0.004 0.056 3147 Dihedral : 4.456 57.022 2428 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.81 % Favored : 95.10 % Rotamer: Outliers : 1.68 % Allowed : 23.09 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.18), residues: 2226 helix: 1.30 (0.17), residues: 987 sheet: -1.29 (0.33), residues: 245 loop : -1.21 (0.20), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 324 TYR 0.022 0.001 TYR A 644 PHE 0.021 0.001 PHE B 504 TRP 0.012 0.001 TRP B 437 HIS 0.004 0.001 HIS C 235 Details of bonding type rmsd covalent geometry : bond 0.00248 (18208) covalent geometry : angle 0.50190 (24510) hydrogen bonds : bond 0.03394 ( 867) hydrogen bonds : angle 4.31396 ( 2463) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 275 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 VAL cc_start: 0.7541 (t) cc_final: 0.7282 (m) REVERT: A 308 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7676 (tm-30) REVERT: A 330 LYS cc_start: 0.8660 (mmtp) cc_final: 0.8150 (mmtt) REVERT: A 650 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8691 (mt0) REVERT: A 704 ASN cc_start: 0.7844 (m-40) cc_final: 0.7281 (m110) REVERT: B 179 MET cc_start: 0.8837 (tpt) cc_final: 0.8217 (tpt) REVERT: B 207 LYS cc_start: 0.7737 (mttt) cc_final: 0.7356 (mmtt) REVERT: B 256 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7674 (mt-10) REVERT: B 311 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8310 (mt-10) REVERT: B 530 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.7871 (ptmm) REVERT: B 576 LYS cc_start: 0.8069 (mttm) cc_final: 0.7815 (mmtt) REVERT: B 685 GLU cc_start: 0.5844 (OUTLIER) cc_final: 0.3275 (mm-30) REVERT: C 59 LEU cc_start: 0.6223 (OUTLIER) cc_final: 0.5976 (mp) REVERT: C 136 THR cc_start: 0.8762 (m) cc_final: 0.8479 (p) REVERT: C 179 GLU cc_start: 0.8570 (tt0) cc_final: 0.8219 (tm-30) REVERT: C 219 PHE cc_start: 0.8388 (OUTLIER) cc_final: 0.7897 (t80) REVERT: C 454 GLU cc_start: 0.6879 (tp30) cc_final: 0.6614 (tp30) REVERT: C 523 GLU cc_start: 0.6786 (tp30) cc_final: 0.6534 (tp30) REVERT: C 524 SER cc_start: 0.6877 (OUTLIER) cc_final: 0.6449 (t) outliers start: 33 outliers final: 20 residues processed: 302 average time/residue: 0.3274 time to fit residues: 148.1961 Evaluate side-chains 296 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 268 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 504 PHE Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain B residue 687 CYS Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 524 SER Chi-restraints excluded: chain C residue 545 GLU Chi-restraints excluded: chain C residue 610 MET Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain D residue 372 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 205 optimal weight: 7.9990 chunk 116 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 206 optimal weight: 4.9990 chunk 208 optimal weight: 9.9990 chunk 182 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.165389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.129956 restraints weight = 86475.430| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.49 r_work: 0.3536 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18208 Z= 0.152 Angle : 0.513 5.777 24510 Z= 0.271 Chirality : 0.039 0.191 2689 Planarity : 0.004 0.085 3147 Dihedral : 4.492 58.093 2428 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.66 % Favored : 94.25 % Rotamer: Outliers : 1.58 % Allowed : 23.09 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.18), residues: 2226 helix: 1.23 (0.16), residues: 993 sheet: -1.27 (0.33), residues: 246 loop : -1.24 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 324 TYR 0.032 0.001 TYR C 74 PHE 0.021 0.001 PHE B 504 TRP 0.012 0.001 TRP B 437 HIS 0.004 0.001 HIS C 235 Details of bonding type rmsd covalent geometry : bond 0.00351 (18208) covalent geometry : angle 0.51337 (24510) hydrogen bonds : bond 0.03505 ( 867) hydrogen bonds : angle 4.37372 ( 2463) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9451.19 seconds wall clock time: 161 minutes 15.66 seconds (9675.66 seconds total)