Starting phenix.real_space_refine on Tue Aug 26 14:27:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rnb_19393/08_2025/8rnb_19393.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rnb_19393/08_2025/8rnb_19393.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 { model { file = "/net/cci-nas-00/data/ceres_data/8rnb_19393/08_2025/8rnb_19393.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rnb_19393/08_2025/8rnb_19393.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8rnb_19393/08_2025/8rnb_19393.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rnb_19393/08_2025/8rnb_19393.map" } 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= 0.074 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 139 5.16 5 C 11975 2.51 5 N 3228 2.21 5 O 3535 1.98 5 H 19011 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 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: 37888 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 11270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 703, 11270 Classifications: {'peptide': 703} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 26, 'TRANS': 676} Chain breaks: 1 Chain: "E" Number of atoms: 11310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 11310 Classifications: {'peptide': 720} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 685} Chain breaks: 2 Chain: "F" Number of atoms: 10555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 653, 10555 Classifications: {'peptide': 653} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 631} Chain breaks: 2 Chain: "G" Number of atoms: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 2502 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 5, 'TRANS': 149} Chain: "C" Number of atoms: 2251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 2251 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 7, 'TRANS': 130} Time building chain proxies: 5.60, per 1000 atoms: 0.15 Number of scatterers: 37888 At special positions: 0 Unit cell: (131.88, 141.96, 126.84, 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 139 16.00 O 3535 8.00 N 3228 7.00 C 11975 6.00 H 19011 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: 2.64 Conformation dependent library (CDL) restraints added in 933.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4698 Ramachandran restraints generated. 2349 Oldfield, 0 Emsley, 2349 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4412 Finding SS restraints... Secondary structure from input PDB file: 101 helices and 28 sheets defined 49.2% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'D' and resid 1 through 9 removed outlier: 3.548A pdb=" N PHE D 9 " --> pdb=" O ILE D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 22 Processing helix chain 'D' and resid 23 through 25 No H-bonds generated for 'chain 'D' and resid 23 through 25' Processing helix chain 'D' and resid 32 through 49 Processing helix chain 'D' and resid 84 through 100 Processing helix chain 'D' and resid 127 through 140 removed outlier: 4.295A pdb=" N TYR D 131 " --> pdb=" O LEU D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 182 removed outlier: 3.691A pdb=" N SER D 182 " --> pdb=" O GLN D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 185 No H-bonds generated for 'chain 'D' and resid 183 through 185' Processing helix chain 'D' and resid 193 through 198 removed outlier: 3.734A pdb=" N VAL D 196 " --> pdb=" O GLU D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 214 Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 237 through 246 removed outlier: 3.677A pdb=" N ARG D 245 " --> pdb=" O ARG D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 266 through 271 Processing helix chain 'D' and resid 301 through 313 Processing helix chain 'D' and resid 313 through 318 Processing helix chain 'D' and resid 332 through 349 Processing helix chain 'D' and resid 358 through 366 removed outlier: 4.268A pdb=" N ALA D 362 " --> pdb=" O LYS D 358 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR D 366 " --> pdb=" O ALA D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 383 removed outlier: 3.501A pdb=" N ALA D 380 " --> pdb=" O MET D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 411 removed outlier: 4.462A pdb=" N GLN D 404 " --> pdb=" O ALA D 400 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR D 405 " --> pdb=" O ALA D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 447 Processing helix chain 'D' and resid 449 through 469 removed outlier: 3.547A pdb=" N THR D 453 " --> pdb=" O CYS D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 533 removed outlier: 3.967A pdb=" N SER D 530 " --> pdb=" O ARG D 527 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLY D 531 " --> pdb=" O VAL D 528 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TRP D 533 " --> pdb=" O SER D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 573 Processing helix chain 'D' and resid 575 through 595 removed outlier: 3.606A pdb=" N GLN D 595 " --> pdb=" O GLU D 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 605 Processing helix chain 'D' and resid 629 through 646 Processing helix chain 'D' and resid 648 through 670 removed outlier: 3.959A pdb=" N ARG D 660 " --> pdb=" O ALA D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 678 through 688 Processing helix chain 'D' and resid 693 through 715 removed outlier: 3.950A pdb=" N LYS D 715 " --> pdb=" O LYS D 711 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 12 removed outlier: 3.992A pdb=" N ASP E 11 " --> pdb=" O PHE E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 18 Processing helix chain 'E' and resid 35 through 49 Processing helix chain 'E' and resid 84 through 99 Processing helix chain 'E' and resid 101 through 117 removed outlier: 3.791A pdb=" N ALA E 105 " --> pdb=" O GLY E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 124 Processing helix chain 'E' and resid 138 through 153 Processing helix chain 'E' and resid 156 through 161 removed outlier: 3.933A pdb=" N LYS E 160 " --> pdb=" O ASN E 156 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY E 161 " --> pdb=" O GLY E 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 156 through 161' Processing helix chain 'E' and resid 162 through 174 removed outlier: 3.563A pdb=" N PHE E 166 " --> pdb=" O GLY E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 222 Processing helix chain 'E' and resid 248 through 265 removed outlier: 4.112A pdb=" N ASN E 265 " --> pdb=" O ASN E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 292 removed outlier: 4.056A pdb=" N LYS E 279 " --> pdb=" O GLY E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 326 Processing helix chain 'E' and resid 330 through 346 removed outlier: 4.359A pdb=" N ALA E 340 " --> pdb=" O PHE E 336 " (cutoff:3.500A) Proline residue: E 341 - end of helix Processing helix chain 'E' and resid 371 through 373 No H-bonds generated for 'chain 'E' and resid 371 through 373' Processing helix chain 'E' and resid 377 through 381 Processing helix chain 'E' and resid 382 through 393 Processing helix chain 'E' and resid 413 through 426 Processing helix chain 'E' and resid 454 through 472 Processing helix chain 'E' and resid 477 through 480 removed outlier: 3.603A pdb=" N LYS E 480 " --> pdb=" O SER E 477 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 477 through 480' Processing helix chain 'E' and resid 517 through 536 Processing helix chain 'E' and resid 539 through 559 Processing helix chain 'E' and resid 569 through 582 removed outlier: 4.634A pdb=" N ILE E 574 " --> pdb=" O LYS E 570 " (cutoff:3.500A) Processing helix chain 'E' and resid 589 through 593 Processing helix chain 'E' and resid 599 through 603 removed outlier: 3.521A pdb=" N LEU E 603 " --> pdb=" O LEU E 600 " (cutoff:3.500A) Processing helix chain 'E' and resid 606 through 612 Processing helix chain 'E' and resid 613 through 615 No H-bonds generated for 'chain 'E' and resid 613 through 615' Processing helix chain 'E' and resid 616 through 624 Processing helix chain 'E' and resid 675 through 684 Processing helix chain 'E' and resid 687 through 702 removed outlier: 3.617A pdb=" N ALA E 697 " --> pdb=" O ASN E 693 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N CYS E 698 " --> pdb=" O LEU E 694 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ALA E 702 " --> pdb=" O CYS E 698 " (cutoff:3.500A) Processing helix chain 'E' and resid 712 through 732 Processing helix chain 'E' and resid 735 through 750 removed outlier: 3.587A pdb=" N GLY E 750 " --> pdb=" O LEU E 746 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 15 removed outlier: 3.854A pdb=" N ASP F 15 " --> pdb=" O GLN F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 25 removed outlier: 3.515A pdb=" N LYS F 19 " --> pdb=" O ASP F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 39 removed outlier: 3.561A pdb=" N ASN F 31 " --> pdb=" O VAL F 27 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE F 32 " --> pdb=" O ASP F 28 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE F 33 " --> pdb=" O GLN F 29 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG F 34 " --> pdb=" O TYR F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 55 removed outlier: 3.501A pdb=" N LYS F 50 " --> pdb=" O SER F 46 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N CYS F 54 " --> pdb=" O LYS F 50 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER F 55 " --> pdb=" O TRP F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 70 removed outlier: 3.694A pdb=" N ILE F 70 " --> pdb=" O MET F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 105 removed outlier: 4.020A pdb=" N VAL F 98 " --> pdb=" O SER F 94 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR F 99 " --> pdb=" O ILE F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 117 removed outlier: 3.563A pdb=" N VAL F 116 " --> pdb=" O GLY F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 129 removed outlier: 3.614A pdb=" N PHE F 121 " --> pdb=" O TYR F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 232 removed outlier: 4.040A pdb=" N GLU F 232 " --> pdb=" O ALA F 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 228 through 232' Processing helix chain 'F' and resid 233 through 237 Processing helix chain 'F' and resid 255 through 275 removed outlier: 4.101A pdb=" N VAL F 263 " --> pdb=" O GLN F 259 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL F 274 " --> pdb=" O ARG F 270 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA F 275 " --> pdb=" O ARG F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 288 removed outlier: 4.168A pdb=" N LEU F 281 " --> pdb=" O ASN F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 303 Processing helix chain 'F' and resid 308 through 318 Processing helix chain 'F' and resid 392 through 408 removed outlier: 3.577A pdb=" N MET F 396 " --> pdb=" O LYS F 392 " (cutoff:3.500A) Processing helix chain 'F' and resid 409 through 415 Processing helix chain 'F' and resid 431 through 443 Processing helix chain 'F' and resid 444 through 452 removed outlier: 4.021A pdb=" N GLY F 452 " --> pdb=" O PHE F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 534 through 541 removed outlier: 4.013A pdb=" N MET F 537 " --> pdb=" O THR F 534 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N GLU F 539 " --> pdb=" O LYS F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 542 through 557 Processing helix chain 'F' and resid 557 through 568 removed outlier: 3.517A pdb=" N LEU F 567 " --> pdb=" O ALA F 563 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY F 568 " --> pdb=" O GLN F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 574 removed outlier: 3.716A pdb=" N PHE F 573 " --> pdb=" O GLU F 570 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN F 574 " --> pdb=" O ASP F 571 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 570 through 574' Processing helix chain 'F' and resid 575 through 583 removed outlier: 3.975A pdb=" N SER F 583 " --> pdb=" O GLU F 579 " (cutoff:3.500A) Processing helix chain 'F' and resid 586 through 607 removed outlier: 4.423A pdb=" N GLY F 591 " --> pdb=" O GLN F 587 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N GLN F 592 " --> pdb=" O LYS F 588 " (cutoff:3.500A) Processing helix chain 'F' and resid 611 through 619 Processing helix chain 'F' and resid 620 through 623 removed outlier: 3.762A pdb=" N PHE F 623 " --> pdb=" O PRO F 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 620 through 623' Processing helix chain 'F' and resid 682 through 686 removed outlier: 3.705A pdb=" N ARG F 686 " --> pdb=" O ASP F 683 " (cutoff:3.500A) Processing helix chain 'F' and resid 705 through 709 Processing helix chain 'F' and resid 713 through 719 removed outlier: 3.524A pdb=" N LYS F 719 " --> pdb=" O GLU F 715 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 12 Processing helix chain 'G' and resid 81 through 87 removed outlier: 3.814A pdb=" N GLU G 85 " --> pdb=" O GLU G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 112 Proline residue: G 108 - end of helix removed outlier: 3.861A pdb=" N LYS G 111 " --> pdb=" O PRO G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 139 Processing helix chain 'C' and resid 542 through 557 Processing helix chain 'C' and resid 557 through 568 removed outlier: 3.659A pdb=" N LEU C 561 " --> pdb=" O ASN C 557 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU C 566 " --> pdb=" O LYS C 562 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU C 567 " --> pdb=" O ALA C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 584 removed outlier: 4.034A pdb=" N PHE C 581 " --> pdb=" O ALA C 577 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE C 584 " --> pdb=" O ALA C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 608 removed outlier: 4.821A pdb=" N GLY C 591 " --> pdb=" O GLN C 587 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N GLN C 592 " --> pdb=" O LYS C 588 " (cutoff:3.500A) removed outlier: 3.664A 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: 3.950A 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 sheet with id=AA1, first strand: chain 'D' and resid 77 through 79 removed outlier: 3.741A pdb=" N ARG D 117 " --> pdb=" O ASP D 112 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N PHE D 118 " --> pdb=" O GLU D 144 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N MET D 146 " --> pdb=" O PHE D 118 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLU D 120 " --> pdb=" O MET D 146 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N PHE D 148 " --> pdb=" O GLU D 120 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLY D 122 " --> pdb=" O PHE D 148 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASP D 153 " --> pdb=" O SER D 149 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 255 through 256 removed outlier: 3.851A pdb=" N ASP E 445 " --> pdb=" O SER E 442 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 294 through 295 removed outlier: 4.444A pdb=" N SER D 492 " --> pdb=" O THR D 295 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ILE D 481 " --> pdb=" O TYR D 497 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N LEU D 499 " --> pdb=" O ILE D 479 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE D 479 " --> pdb=" O LEU D 499 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL D 501 " --> pdb=" O LYS D 477 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LYS D 477 " --> pdb=" O VAL D 501 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 294 through 295 removed outlier: 4.444A pdb=" N SER D 492 " --> pdb=" O THR D 295 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N TYR D 497 " --> pdb=" O PHE D 521 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR D 562 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N LYS D 551 " --> pdb=" O SER D 543 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N SER D 543 " --> pdb=" O LYS D 551 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL D 553 " --> pdb=" O ILE D 541 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 373 through 374 removed outlier: 5.786A pdb=" N GLN D 373 " --> pdb=" O LYS E 365 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N GLN E 367 " --> pdb=" O GLN D 373 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 623 through 628 removed outlier: 3.734A pdb=" N GLY D 618 " --> pdb=" O VAL D 625 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLY D 627 " --> pdb=" O SER D 616 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N SER D 616 " --> pdb=" O GLY D 627 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 54 through 57 Processing sheet with id=AA8, first strand: chain 'E' and resid 128 through 130 Processing sheet with id=AA9, first strand: chain 'E' and resid 178 through 188 Processing sheet with id=AB1, first strand: chain 'E' and resid 243 through 244 removed outlier: 4.004A pdb=" N THR E 401 " --> pdb=" O ASN E 397 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 488 through 490 Processing sheet with id=AB3, first strand: chain 'F' and resid 59 through 60 Processing sheet with id=AB4, first strand: chain 'F' and resid 73 through 74 Processing sheet with id=AB5, first strand: chain 'F' and resid 131 through 132 Processing sheet with id=AB6, first strand: chain 'F' and resid 135 through 137 Processing sheet with id=AB7, first strand: chain 'F' and resid 294 through 295 removed outlier: 3.704A pdb=" N GLU F 294 " --> pdb=" O ILE F 291 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 325 through 326 Processing sheet with id=AB9, first strand: chain 'F' and resid 334 through 337 removed outlier: 6.915A pdb=" N GLU F 364 " --> pdb=" O ILE F 335 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N CYS F 372 " --> pdb=" O CYS F 369 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 334 through 337 removed outlier: 6.915A pdb=" N GLU F 364 " --> pdb=" O ILE F 335 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYS F 385 " --> pdb=" O LYS F 377 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 340 through 347 removed outlier: 3.969A pdb=" N ILE F 346 " --> pdb=" O GLN F 354 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN F 354 " --> pdb=" O ILE F 346 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 453 through 455 Processing sheet with id=AC4, first strand: chain 'F' and resid 498 through 499 removed outlier: 3.616A pdb=" N SER F 498 " --> pdb=" O ILE F 506 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET F 514 " --> pdb=" O LEU F 505 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 639 through 641 Processing sheet with id=AC6, first strand: chain 'F' and resid 660 through 662 Processing sheet with id=AC7, first strand: chain 'F' and resid 698 through 702 removed outlier: 7.314A pdb=" N LYS F 737 " --> pdb=" O SER F 701 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 24 through 25 removed outlier: 6.948A pdb=" N LEU G 24 " --> pdb=" O ILE G 50 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 639 through 641 Processing sheet with id=AD1, first strand: chain 'C' and resid 659 through 662 869 hydrogen bonds defined for protein. 2430 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.89 Time building geometry restraints manager: 3.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 18967 1.03 - 1.23: 379 1.23 - 1.43: 7504 1.43 - 1.63: 11156 1.63 - 1.82: 234 Bond restraints: 38240 Sorted by residual: bond pdb=" C HIS E 745 " pdb=" O HIS E 745 " ideal model delta sigma weight residual 1.236 1.277 -0.040 1.15e-02 7.56e+03 1.23e+01 bond pdb=" C ALA E 744 " pdb=" O ALA E 744 " ideal model delta sigma weight residual 1.237 1.276 -0.040 1.16e-02 7.43e+03 1.17e+01 bond pdb=" N ILE E 749 " pdb=" CA ILE E 749 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.17e-02 7.31e+03 9.42e+00 bond pdb=" N LEU E 746 " pdb=" H LEU E 746 " ideal model delta sigma weight residual 0.860 0.916 -0.056 2.00e-02 2.50e+03 7.87e+00 bond pdb=" C GLY E 747 " pdb=" O GLY E 747 " ideal model delta sigma weight residual 1.234 1.267 -0.033 1.20e-02 6.94e+03 7.68e+00 ... (remaining 38235 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.01: 69133 3.01 - 6.03: 114 6.03 - 9.04: 1 9.04 - 12.05: 0 12.05 - 15.06: 1 Bond angle restraints: 69249 Sorted by residual: angle pdb=" CB MET E 409 " pdb=" CG MET E 409 " pdb=" SD MET E 409 " ideal model delta sigma weight residual 112.70 127.76 -15.06 3.00e+00 1.11e-01 2.52e+01 angle pdb=" C ALA E 744 " pdb=" N HIS E 745 " pdb=" CA HIS E 745 " ideal model delta sigma weight residual 120.44 126.21 -5.77 1.30e+00 5.92e-01 1.97e+01 angle pdb=" CA ILE E 749 " pdb=" C ILE E 749 " pdb=" O ILE E 749 " ideal model delta sigma weight residual 121.05 116.57 4.48 1.04e+00 9.25e-01 1.85e+01 angle pdb=" C LEU E 746 " pdb=" N GLY E 747 " pdb=" CA GLY E 747 " ideal model delta sigma weight residual 119.98 124.75 -4.77 1.11e+00 8.12e-01 1.85e+01 angle pdb=" C HIS E 745 " pdb=" N LEU E 746 " pdb=" CA LEU E 746 " ideal model delta sigma weight residual 120.31 126.31 -6.00 1.52e+00 4.33e-01 1.56e+01 ... (remaining 69244 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 15723 17.70 - 35.39: 1507 35.39 - 53.09: 474 53.09 - 70.78: 130 70.78 - 88.48: 20 Dihedral angle restraints: 17854 sinusoidal: 9916 harmonic: 7938 Sorted by residual: dihedral pdb=" CA MET F 690 " pdb=" C MET F 690 " pdb=" N GLY F 691 " pdb=" CA GLY F 691 " ideal model delta harmonic sigma weight residual 180.00 -158.66 -21.34 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA ARG F 688 " pdb=" C ARG F 688 " pdb=" N SER F 689 " pdb=" CA SER F 689 " ideal model delta harmonic sigma weight residual -180.00 -159.82 -20.18 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA SER E 442 " pdb=" C SER E 442 " pdb=" N SER E 443 " pdb=" CA SER E 443 " ideal model delta harmonic sigma weight residual 180.00 160.95 19.05 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 17851 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1984 0.032 - 0.064: 606 0.064 - 0.096: 153 0.096 - 0.128: 91 0.128 - 0.160: 8 Chirality restraints: 2842 Sorted by residual: chirality pdb=" CA HIS E 745 " pdb=" N HIS E 745 " pdb=" C HIS E 745 " pdb=" CB HIS E 745 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.38e-01 chirality pdb=" CA LEU E 746 " pdb=" N LEU E 746 " pdb=" C LEU E 746 " pdb=" CB LEU E 746 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" CA ILE E 368 " pdb=" N ILE E 368 " pdb=" C ILE E 368 " pdb=" CB ILE E 368 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.00e-01 ... (remaining 2839 not shown) Planarity restraints: 5597 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE E 749 " 0.013 2.00e-02 2.50e+03 2.42e-02 5.85e+00 pdb=" N GLY E 750 " -0.042 2.00e-02 2.50e+03 pdb=" CA GLY E 750 " 0.011 2.00e-02 2.50e+03 pdb=" H GLY E 750 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU E 748 " -0.010 2.00e-02 2.50e+03 1.88e-02 3.53e+00 pdb=" N ILE E 749 " 0.032 2.00e-02 2.50e+03 pdb=" CA ILE E 749 " -0.008 2.00e-02 2.50e+03 pdb=" H ILE E 749 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE E 376 " 0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO E 377 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO E 377 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 377 " 0.023 5.00e-02 4.00e+02 ... (remaining 5594 not shown) Histogram of nonbonded interaction distances: 1.23 - 1.90: 182 1.90 - 2.58: 39625 2.58 - 3.25: 116879 3.25 - 3.93: 144312 3.93 - 4.60: 230371 Nonbonded interactions: 531369 Sorted by model distance: nonbonded pdb=" HB3 LEU E 746 " pdb="HD13 ILE E 752 " model vdw 1.231 2.440 nonbonded pdb=" O ASN G 127 " pdb="HD21 ASN G 127 " model vdw 1.475 2.450 nonbonded pdb="HG22 ILE E 749 " pdb=" HD2 TYR E 751 " model vdw 1.490 2.270 nonbonded pdb=" OE1 GLU F 647 " pdb=" H GLU F 647 " model vdw 1.509 2.450 nonbonded pdb=" H SER C 656 " pdb=" O PHE C 659 " model vdw 1.541 2.450 ... (remaining 531364 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.780 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: 0.220 Extract box with map and model: 0.410 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 30.550 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 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 0.043 19229 Z= 0.127 Angle : 0.491 15.064 25890 Z= 0.264 Chirality : 0.037 0.160 2842 Planarity : 0.003 0.045 3330 Dihedral : 16.176 88.478 7350 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.77 % Favored : 95.15 % Rotamer: Outliers : 0.38 % Allowed : 19.28 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % 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: 0.46 (0.18), residues: 2349 helix: 1.82 (0.17), residues: 1025 sheet: -1.05 (0.32), residues: 266 loop : -0.84 (0.20), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 549 TYR 0.013 0.001 TYR E 554 PHE 0.013 0.001 PHE F 623 TRP 0.011 0.001 TRP E 437 HIS 0.004 0.001 HIS E 745 Details of bonding type rmsd covalent geometry : bond 0.00252 (19229) covalent geometry : angle 0.49087 (25890) hydrogen bonds : bond 0.13891 ( 863) hydrogen bonds : angle 5.29355 ( 2430) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4698 Ramachandran restraints generated. 2349 Oldfield, 0 Emsley, 2349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4698 Ramachandran restraints generated. 2349 Oldfield, 0 Emsley, 2349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 688 is missing expected H atoms. Skipping. Evaluate side-chains 302 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 294 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 743 MET cc_start: 0.5328 (mmm) cc_final: 0.4948 (mtp) REVERT: F 724 GLU cc_start: 0.7523 (tt0) cc_final: 0.7262 (tm-30) REVERT: C 579 GLU cc_start: 0.7348 (mt-10) cc_final: 0.7049 (mt-10) outliers start: 8 outliers final: 5 residues processed: 298 average time/residue: 0.2834 time to fit residues: 128.5491 Evaluate side-chains 274 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 269 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 437 TRP Chi-restraints excluded: chain F residue 517 ASN Chi-restraints excluded: chain G residue 127 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 314 ASN F 91 GLN G 92 HIS G 94 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.166020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.126469 restraints weight = 92457.239| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 3.49 r_work: 0.3417 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.0739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19229 Z= 0.167 Angle : 0.508 8.995 25890 Z= 0.270 Chirality : 0.038 0.154 2842 Planarity : 0.003 0.043 3330 Dihedral : 4.079 36.331 2562 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.19 % Favored : 94.72 % Rotamer: Outliers : 1.20 % Allowed : 19.09 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % 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: 0.30 (0.18), residues: 2349 helix: 1.70 (0.17), residues: 1033 sheet: -1.05 (0.32), residues: 260 loop : -0.99 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 316 TYR 0.016 0.001 TYR E 554 PHE 0.011 0.001 PHE E 511 TRP 0.016 0.001 TRP E 437 HIS 0.003 0.001 HIS E 47 Details of bonding type rmsd covalent geometry : bond 0.00378 (19229) covalent geometry : angle 0.50762 (25890) hydrogen bonds : bond 0.04439 ( 863) hydrogen bonds : angle 4.57512 ( 2430) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4698 Ramachandran restraints generated. 2349 Oldfield, 0 Emsley, 2349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4698 Ramachandran restraints generated. 2349 Oldfield, 0 Emsley, 2349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 688 is missing expected H atoms. Skipping. Evaluate side-chains 292 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 267 time to evaluate : 0.856 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: D 416 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.7940 (mtpp) REVERT: D 427 ASP cc_start: 0.8123 (OUTLIER) cc_final: 0.7894 (m-30) REVERT: E 743 MET cc_start: 0.5443 (mmm) cc_final: 0.5060 (mmt) REVERT: F 724 GLU cc_start: 0.7892 (tt0) cc_final: 0.7544 (tm-30) outliers start: 25 outliers final: 17 residues processed: 283 average time/residue: 0.2918 time to fit residues: 125.4978 Evaluate side-chains 278 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 259 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 314 ASN Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain E residue 527 THR Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 279 LEU Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 603 GLN Chi-restraints excluded: chain F residue 700 VAL Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 131 TYR Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 656 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 21 optimal weight: 3.9990 chunk 31 optimal weight: 0.2980 chunk 223 optimal weight: 3.9990 chunk 134 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 154 optimal weight: 3.9990 chunk 231 optimal weight: 0.0370 chunk 180 optimal weight: 8.9990 chunk 93 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 overall best weight: 1.4462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 548 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.167307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.123397 restraints weight = 92663.068| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.93 r_work: 0.3427 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.0930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19229 Z= 0.132 Angle : 0.484 7.542 25890 Z= 0.255 Chirality : 0.037 0.150 2842 Planarity : 0.003 0.046 3330 Dihedral : 3.790 21.049 2552 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.07 % Favored : 94.85 % Rotamer: Outliers : 1.59 % Allowed : 18.80 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % 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: 2349 helix: 1.60 (0.16), residues: 1043 sheet: -1.09 (0.32), residues: 260 loop : -1.03 (0.19), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 115 TYR 0.016 0.001 TYR E 554 PHE 0.009 0.001 PHE E 511 TRP 0.013 0.001 TRP E 437 HIS 0.002 0.001 HIS E 47 Details of bonding type rmsd covalent geometry : bond 0.00304 (19229) covalent geometry : angle 0.48373 (25890) hydrogen bonds : bond 0.03955 ( 863) hydrogen bonds : angle 4.40436 ( 2430) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4698 Ramachandran restraints generated. 2349 Oldfield, 0 Emsley, 2349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4698 Ramachandran restraints generated. 2349 Oldfield, 0 Emsley, 2349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 688 is missing expected H atoms. Skipping. Evaluate side-chains 306 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 273 time to evaluate : 0.939 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: D 416 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.7978 (mtpp) REVERT: E 743 MET cc_start: 0.5470 (mmm) cc_final: 0.5120 (mmt) REVERT: F 69 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7453 (ttt180) REVERT: F 724 GLU cc_start: 0.7922 (tt0) cc_final: 0.7542 (tm-30) outliers start: 33 outliers final: 23 residues processed: 294 average time/residue: 0.2826 time to fit residues: 126.9792 Evaluate side-chains 289 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 264 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 488 MET Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain E residue 527 THR Chi-restraints excluded: chain F residue 69 ARG Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 279 LEU Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 517 ASN Chi-restraints excluded: chain F residue 564 GLN Chi-restraints excluded: chain F residue 701 SER Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 131 TYR Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 656 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 58 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 234 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 190 optimal weight: 7.9990 chunk 89 optimal weight: 0.3980 chunk 206 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 chunk 210 optimal weight: 8.9990 chunk 232 optimal weight: 8.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 360 ASN E 314 ASN ** F 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 450 GLN G 92 HIS G 127 ASN C 548 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.165361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.124817 restraints weight = 92025.267| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.99 r_work: 0.3413 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19229 Z= 0.140 Angle : 0.481 7.822 25890 Z= 0.254 Chirality : 0.038 0.148 2842 Planarity : 0.003 0.048 3330 Dihedral : 3.821 21.400 2552 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.28 % Favored : 94.64 % Rotamer: Outliers : 1.97 % Allowed : 18.85 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % 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: 0.17 (0.18), residues: 2349 helix: 1.58 (0.16), residues: 1044 sheet: -1.13 (0.31), residues: 261 loop : -1.08 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 673 TYR 0.017 0.001 TYR E 554 PHE 0.015 0.001 PHE D 335 TRP 0.014 0.001 TRP E 437 HIS 0.006 0.001 HIS G 92 Details of bonding type rmsd covalent geometry : bond 0.00322 (19229) covalent geometry : angle 0.48066 (25890) hydrogen bonds : bond 0.03677 ( 863) hydrogen bonds : angle 4.29320 ( 2430) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4698 Ramachandran restraints generated. 2349 Oldfield, 0 Emsley, 2349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4698 Ramachandran restraints generated. 2349 Oldfield, 0 Emsley, 2349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 688 is missing expected H atoms. Skipping. Evaluate side-chains 310 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 269 time to evaluate : 1.047 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: E 743 MET cc_start: 0.5375 (mmm) cc_final: 0.5014 (mmt) REVERT: F 49 MET cc_start: 0.8686 (tpp) cc_final: 0.8268 (tpp) REVERT: F 69 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7430 (ttt180) REVERT: F 724 GLU cc_start: 0.7827 (tt0) cc_final: 0.7537 (tm-30) REVERT: C 662 ASN cc_start: 0.7542 (OUTLIER) cc_final: 0.7287 (p0) outliers start: 41 outliers final: 31 residues processed: 298 average time/residue: 0.2945 time to fit residues: 134.4537 Evaluate side-chains 293 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 260 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 522 SER Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 437 TRP Chi-restraints excluded: chain E residue 488 MET Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain E residue 527 THR Chi-restraints excluded: chain E residue 567 VAL Chi-restraints excluded: chain F residue 69 ARG Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 279 LEU Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 517 ASN Chi-restraints excluded: chain F residue 564 GLN Chi-restraints excluded: chain F residue 656 SER Chi-restraints excluded: chain F residue 701 SER Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 127 ASN Chi-restraints excluded: chain G residue 131 TYR Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 662 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 77 optimal weight: 0.7980 chunk 13 optimal weight: 9.9990 chunk 131 optimal weight: 0.8980 chunk 122 optimal weight: 0.4980 chunk 127 optimal weight: 4.9990 chunk 103 optimal weight: 0.5980 chunk 123 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 176 optimal weight: 4.9990 chunk 210 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 360 ASN C 548 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.166206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.125637 restraints weight = 91815.778| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 3.19 r_work: 0.3428 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 19229 Z= 0.107 Angle : 0.471 9.553 25890 Z= 0.246 Chirality : 0.037 0.145 2842 Planarity : 0.003 0.049 3330 Dihedral : 3.794 21.064 2552 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.94 % Favored : 94.98 % Rotamer: Outliers : 1.92 % Allowed : 18.94 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % 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: 0.29 (0.18), residues: 2349 helix: 1.73 (0.16), residues: 1032 sheet: -1.03 (0.32), residues: 251 loop : -1.05 (0.19), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 134 TYR 0.014 0.001 TYR E 554 PHE 0.010 0.001 PHE F 623 TRP 0.013 0.001 TRP E 437 HIS 0.003 0.000 HIS G 92 Details of bonding type rmsd covalent geometry : bond 0.00246 (19229) covalent geometry : angle 0.47099 (25890) hydrogen bonds : bond 0.03477 ( 863) hydrogen bonds : angle 4.19734 ( 2430) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4698 Ramachandran restraints generated. 2349 Oldfield, 0 Emsley, 2349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4698 Ramachandran restraints generated. 2349 Oldfield, 0 Emsley, 2349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 688 is missing expected H atoms. Skipping. Evaluate side-chains 313 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 273 time to evaluate : 0.720 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: D 504 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.8035 (pm20) REVERT: E 743 MET cc_start: 0.5363 (mmm) cc_final: 0.5002 (mmt) REVERT: F 49 MET cc_start: 0.8666 (tpp) cc_final: 0.8273 (tpp) REVERT: F 69 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7453 (ttt180) REVERT: F 724 GLU cc_start: 0.7865 (tt0) cc_final: 0.7536 (tm-30) outliers start: 40 outliers final: 32 residues processed: 302 average time/residue: 0.2936 time to fit residues: 135.7304 Evaluate side-chains 301 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 267 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 522 SER Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 437 TRP Chi-restraints excluded: chain E residue 488 MET Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain E residue 527 THR Chi-restraints excluded: chain E residue 567 VAL Chi-restraints excluded: chain F residue 69 ARG Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 279 LEU Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 517 ASN Chi-restraints excluded: chain F residue 564 GLN Chi-restraints excluded: chain F residue 603 GLN Chi-restraints excluded: chain F residue 656 SER Chi-restraints excluded: chain F residue 701 SER Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 131 TYR Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 656 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 127 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 181 optimal weight: 8.9990 chunk 106 optimal weight: 0.7980 chunk 199 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 138 optimal weight: 9.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 306 ASN E 382 ASN C 548 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.161966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.122307 restraints weight = 92359.407| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.78 r_work: 0.3372 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 19229 Z= 0.250 Angle : 0.551 8.579 25890 Z= 0.296 Chirality : 0.040 0.157 2842 Planarity : 0.004 0.051 3330 Dihedral : 4.121 22.359 2552 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.90 % Favored : 93.02 % Rotamer: Outliers : 2.88 % Allowed : 18.65 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % 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: -0.23 (0.17), residues: 2349 helix: 1.33 (0.16), residues: 1027 sheet: -1.28 (0.32), residues: 257 loop : -1.35 (0.18), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 673 TYR 0.023 0.002 TYR E 554 PHE 0.015 0.001 PHE F 623 TRP 0.015 0.001 TRP E 437 HIS 0.004 0.001 HIS D 643 Details of bonding type rmsd covalent geometry : bond 0.00579 (19229) covalent geometry : angle 0.55107 (25890) hydrogen bonds : bond 0.04124 ( 863) hydrogen bonds : angle 4.55285 ( 2430) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4698 Ramachandran restraints generated. 2349 Oldfield, 0 Emsley, 2349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4698 Ramachandran restraints generated. 2349 Oldfield, 0 Emsley, 2349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 688 is missing expected H atoms. Skipping. Evaluate side-chains 325 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 265 time to evaluate : 0.862 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: D 416 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8126 (mtpp) REVERT: D 427 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7947 (m-30) REVERT: D 657 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7972 (mm-30) REVERT: E 117 THR cc_start: 0.7773 (OUTLIER) cc_final: 0.7316 (t) REVERT: E 379 GLU cc_start: 0.9037 (OUTLIER) cc_final: 0.8422 (mp0) REVERT: E 743 MET cc_start: 0.5194 (mmm) cc_final: 0.4867 (mmt) REVERT: F 69 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7504 (ttt180) REVERT: F 685 GLU cc_start: 0.5807 (OUTLIER) cc_final: 0.5590 (tm-30) REVERT: F 724 GLU cc_start: 0.7842 (tt0) cc_final: 0.7534 (tm-30) REVERT: C 662 ASN cc_start: 0.7535 (OUTLIER) cc_final: 0.7335 (p0) outliers start: 60 outliers final: 44 residues processed: 309 average time/residue: 0.2738 time to fit residues: 130.3974 Evaluate side-chains 309 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 258 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 329 GLU Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 444 ASN Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 522 SER Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 557 CYS Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain E residue 488 MET Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain E residue 567 VAL Chi-restraints excluded: chain F residue 69 ARG Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 279 LEU Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain F residue 517 ASN Chi-restraints excluded: chain F residue 564 GLN Chi-restraints excluded: chain F residue 603 GLN Chi-restraints excluded: chain F residue 656 SER Chi-restraints excluded: chain F residue 685 GLU Chi-restraints excluded: chain F residue 692 ASN Chi-restraints excluded: chain F residue 701 SER Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 131 TYR Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 610 MET Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 662 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 78 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 223 optimal weight: 1.9990 chunk 217 optimal weight: 0.8980 chunk 147 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 131 optimal weight: 0.6980 chunk 189 optimal weight: 5.9990 chunk 138 optimal weight: 10.0000 chunk 109 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.164364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.124314 restraints weight = 91922.089| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.88 r_work: 0.3404 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19229 Z= 0.123 Angle : 0.493 11.851 25890 Z= 0.258 Chirality : 0.038 0.147 2842 Planarity : 0.003 0.061 3330 Dihedral : 3.953 21.812 2552 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.02 % Favored : 94.89 % Rotamer: Outliers : 2.36 % Allowed : 19.42 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % 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: 0.03 (0.17), residues: 2349 helix: 1.54 (0.16), residues: 1027 sheet: -1.15 (0.32), residues: 257 loop : -1.21 (0.19), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 134 TYR 0.016 0.001 TYR E 554 PHE 0.013 0.001 PHE F 623 TRP 0.014 0.001 TRP E 437 HIS 0.002 0.001 HIS D 643 Details of bonding type rmsd covalent geometry : bond 0.00284 (19229) covalent geometry : angle 0.49255 (25890) hydrogen bonds : bond 0.03593 ( 863) hydrogen bonds : angle 4.29934 ( 2430) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4698 Ramachandran restraints generated. 2349 Oldfield, 0 Emsley, 2349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4698 Ramachandran restraints generated. 2349 Oldfield, 0 Emsley, 2349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 688 is missing expected H atoms. Skipping. Evaluate side-chains 319 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 270 time to evaluate : 0.664 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: D 416 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.7977 (mtpp) REVERT: D 567 MET cc_start: 0.8804 (mmp) cc_final: 0.8525 (mmp) REVERT: E 117 THR cc_start: 0.7657 (OUTLIER) cc_final: 0.7221 (t) REVERT: E 379 GLU cc_start: 0.8960 (OUTLIER) cc_final: 0.8332 (mp0) REVERT: E 743 MET cc_start: 0.5225 (mmm) cc_final: 0.4895 (mmt) REVERT: F 7 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7281 (pt0) REVERT: F 62 THR cc_start: 0.8750 (m) cc_final: 0.8427 (p) REVERT: F 69 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7512 (ttt180) REVERT: F 394 GLU cc_start: 0.8219 (pm20) cc_final: 0.7690 (pm20) REVERT: F 724 GLU cc_start: 0.7783 (tt0) cc_final: 0.7512 (tm-30) outliers start: 49 outliers final: 38 residues processed: 304 average time/residue: 0.2778 time to fit residues: 130.5935 Evaluate side-chains 304 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 262 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 522 SER Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 557 CYS Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain E residue 437 TRP Chi-restraints excluded: chain E residue 488 MET Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain E residue 567 VAL Chi-restraints excluded: chain F residue 69 ARG Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 279 LEU Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain F residue 517 ASN Chi-restraints excluded: chain F residue 564 GLN Chi-restraints excluded: chain F residue 656 SER Chi-restraints excluded: chain F residue 701 SER Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 131 TYR Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 610 MET Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 656 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 227 optimal weight: 8.9990 chunk 117 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 163 optimal weight: 8.9990 chunk 130 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 165 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 217 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 504 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.165962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.123846 restraints weight = 91568.822| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 3.21 r_work: 0.3405 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19229 Z= 0.114 Angle : 0.490 12.590 25890 Z= 0.255 Chirality : 0.037 0.145 2842 Planarity : 0.003 0.053 3330 Dihedral : 3.879 21.505 2552 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.19 % Favored : 94.72 % Rotamer: Outliers : 2.26 % Allowed : 19.71 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % 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: 0.14 (0.18), residues: 2349 helix: 1.64 (0.16), residues: 1023 sheet: -1.10 (0.32), residues: 257 loop : -1.13 (0.19), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 484 TYR 0.015 0.001 TYR E 554 PHE 0.017 0.001 PHE G 121 TRP 0.013 0.001 TRP E 437 HIS 0.002 0.000 HIS D 462 Details of bonding type rmsd covalent geometry : bond 0.00266 (19229) covalent geometry : angle 0.49044 (25890) hydrogen bonds : bond 0.03447 ( 863) hydrogen bonds : angle 4.23339 ( 2430) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4698 Ramachandran restraints generated. 2349 Oldfield, 0 Emsley, 2349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4698 Ramachandran restraints generated. 2349 Oldfield, 0 Emsley, 2349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 688 is missing expected H atoms. Skipping. Evaluate side-chains 315 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 268 time to evaluate : 1.050 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: D 567 MET cc_start: 0.8800 (mmp) cc_final: 0.8566 (mmp) REVERT: E 379 GLU cc_start: 0.9032 (OUTLIER) cc_final: 0.8361 (mp0) REVERT: E 743 MET cc_start: 0.5238 (mmm) cc_final: 0.4894 (mmt) REVERT: F 7 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7359 (pt0) REVERT: F 62 THR cc_start: 0.8721 (m) cc_final: 0.8384 (p) REVERT: F 69 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7549 (ttt180) REVERT: F 394 GLU cc_start: 0.8237 (pm20) cc_final: 0.7899 (pm20) REVERT: F 724 GLU cc_start: 0.7885 (tt0) cc_final: 0.7537 (tm-30) REVERT: C 662 ASN cc_start: 0.7585 (OUTLIER) cc_final: 0.7335 (p0) outliers start: 47 outliers final: 39 residues processed: 302 average time/residue: 0.2817 time to fit residues: 131.1915 Evaluate side-chains 303 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 261 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 522 SER Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 557 CYS Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain E residue 437 TRP Chi-restraints excluded: chain E residue 488 MET Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain E residue 567 VAL Chi-restraints excluded: chain F residue 69 ARG Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 279 LEU Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain F residue 517 ASN Chi-restraints excluded: chain F residue 564 GLN Chi-restraints excluded: chain F residue 656 SER Chi-restraints excluded: chain F residue 701 SER Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 131 TYR Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 610 MET Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 662 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 175 optimal weight: 7.9990 chunk 162 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 92 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 11 optimal weight: 0.0050 chunk 198 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 overall best weight: 0.8196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.165471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.124669 restraints weight = 92175.483| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 3.22 r_work: 0.3430 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 19229 Z= 0.103 Angle : 0.487 14.028 25890 Z= 0.252 Chirality : 0.037 0.142 2842 Planarity : 0.003 0.052 3330 Dihedral : 3.819 21.131 2552 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.02 % Favored : 94.89 % Rotamer: Outliers : 2.02 % Allowed : 19.81 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % 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: 0.23 (0.18), residues: 2349 helix: 1.68 (0.16), residues: 1032 sheet: -1.05 (0.32), residues: 257 loop : -1.09 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 484 TYR 0.013 0.001 TYR E 554 PHE 0.013 0.001 PHE F 623 TRP 0.012 0.001 TRP E 437 HIS 0.003 0.000 HIS D 506 Details of bonding type rmsd covalent geometry : bond 0.00238 (19229) covalent geometry : angle 0.48664 (25890) hydrogen bonds : bond 0.03348 ( 863) hydrogen bonds : angle 4.16166 ( 2430) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4698 Ramachandran restraints generated. 2349 Oldfield, 0 Emsley, 2349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4698 Ramachandran restraints generated. 2349 Oldfield, 0 Emsley, 2349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 688 is missing expected H atoms. Skipping. Evaluate side-chains 310 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 268 time to evaluate : 0.770 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: D 567 MET cc_start: 0.8834 (mmp) cc_final: 0.8562 (mmp) REVERT: E 379 GLU cc_start: 0.9000 (OUTLIER) cc_final: 0.8341 (mp0) REVERT: E 743 MET cc_start: 0.5295 (mmm) cc_final: 0.4921 (mmt) REVERT: F 7 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7359 (pt0) REVERT: F 62 THR cc_start: 0.8706 (m) cc_final: 0.8376 (p) REVERT: F 69 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7512 (ttt180) REVERT: F 394 GLU cc_start: 0.8251 (pm20) cc_final: 0.7919 (pm20) REVERT: F 724 GLU cc_start: 0.7925 (tt0) cc_final: 0.7563 (tm-30) REVERT: C 662 ASN cc_start: 0.7545 (OUTLIER) cc_final: 0.7294 (p0) outliers start: 42 outliers final: 37 residues processed: 298 average time/residue: 0.2992 time to fit residues: 136.7370 Evaluate side-chains 302 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 262 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 522 SER Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 557 CYS Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain E residue 437 TRP Chi-restraints excluded: chain E residue 488 MET Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain E residue 567 VAL Chi-restraints excluded: chain F residue 69 ARG Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 279 LEU Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain F residue 517 ASN Chi-restraints excluded: chain F residue 564 GLN Chi-restraints excluded: chain F residue 656 SER Chi-restraints excluded: chain F residue 701 SER Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 131 TYR Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 610 MET Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 662 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 16 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 141 optimal weight: 9.9990 chunk 50 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 145 optimal weight: 8.9990 chunk 166 optimal weight: 5.9990 chunk 179 optimal weight: 1.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 504 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.163617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.123481 restraints weight = 91831.722| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.93 r_work: 0.3410 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19229 Z= 0.164 Angle : 0.517 15.750 25890 Z= 0.270 Chirality : 0.038 0.146 2842 Planarity : 0.004 0.052 3330 Dihedral : 3.920 21.482 2552 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.05 % Favored : 93.87 % Rotamer: Outliers : 2.16 % Allowed : 19.86 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % 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: 0.05 (0.18), residues: 2349 helix: 1.56 (0.16), residues: 1033 sheet: -1.11 (0.32), residues: 257 loop : -1.22 (0.19), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 484 TYR 0.018 0.001 TYR E 554 PHE 0.014 0.001 PHE F 623 TRP 0.013 0.001 TRP E 437 HIS 0.003 0.001 HIS E 47 Details of bonding type rmsd covalent geometry : bond 0.00379 (19229) covalent geometry : angle 0.51745 (25890) hydrogen bonds : bond 0.03629 ( 863) hydrogen bonds : angle 4.28076 ( 2430) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4698 Ramachandran restraints generated. 2349 Oldfield, 0 Emsley, 2349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4698 Ramachandran restraints generated. 2349 Oldfield, 0 Emsley, 2349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 688 is missing expected H atoms. Skipping. Evaluate side-chains 304 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 259 time to evaluate : 0.855 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: D 504 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7825 (pp30) REVERT: D 567 MET cc_start: 0.8804 (mmp) cc_final: 0.8558 (mmp) REVERT: D 657 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7711 (mm-30) REVERT: E 117 THR cc_start: 0.7677 (OUTLIER) cc_final: 0.7256 (t) REVERT: E 379 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8334 (mp0) REVERT: E 743 MET cc_start: 0.5157 (mmm) cc_final: 0.4824 (mmt) REVERT: F 69 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7542 (ttt180) REVERT: F 394 GLU cc_start: 0.8251 (pm20) cc_final: 0.7920 (pm20) REVERT: C 662 ASN cc_start: 0.7642 (OUTLIER) cc_final: 0.7389 (p0) outliers start: 45 outliers final: 37 residues processed: 290 average time/residue: 0.3231 time to fit residues: 143.0740 Evaluate side-chains 300 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 258 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain D residue 416 LYS Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 522 SER Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 557 CYS Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain E residue 437 TRP Chi-restraints excluded: chain E residue 488 MET Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain E residue 567 VAL Chi-restraints excluded: chain F residue 69 ARG Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain F residue 517 ASN Chi-restraints excluded: chain F residue 564 GLN Chi-restraints excluded: chain F residue 656 SER Chi-restraints excluded: chain F residue 701 SER Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 131 TYR Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 589 MET Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 662 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 173 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 180 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 26 optimal weight: 0.0870 chunk 222 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.163694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.123494 restraints weight = 92135.133| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 3.17 r_work: 0.3405 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.257 19229 Z= 0.199 Angle : 0.709 59.194 25890 Z= 0.401 Chirality : 0.039 0.436 2842 Planarity : 0.004 0.052 3330 Dihedral : 3.921 21.477 2552 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.96 % Favored : 93.95 % Rotamer: Outliers : 2.07 % Allowed : 19.90 % Favored : 78.03 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.09 % 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: 0.05 (0.18), residues: 2349 helix: 1.55 (0.16), residues: 1033 sheet: -1.11 (0.32), residues: 257 loop : -1.22 (0.19), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 673 TYR 0.018 0.001 TYR E 554 PHE 0.013 0.001 PHE F 623 TRP 0.013 0.001 TRP E 437 HIS 0.003 0.001 HIS E 47 Details of bonding type rmsd covalent geometry : bond 0.00445 (19229) covalent geometry : angle 0.70921 (25890) hydrogen bonds : bond 0.03609 ( 863) hydrogen bonds : angle 4.27959 ( 2430) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9934.20 seconds wall clock time: 168 minutes 55.89 seconds (10135.89 seconds total)