Starting phenix.real_space_refine on Thu Sep 18 17:58:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6tw1_10603/09_2025/6tw1_10603.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tw1_10603/09_2025/6tw1_10603.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6tw1_10603/09_2025/6tw1_10603.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tw1_10603/09_2025/6tw1_10603.map" model { file = "/net/cci-nas-00/data/ceres_data/6tw1_10603/09_2025/6tw1_10603.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tw1_10603/09_2025/6tw1_10603.cif" } resolution = 2.7 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= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 45 5.49 5 Mg 4 5.21 5 S 108 5.16 5 C 11508 2.51 5 N 3231 2.21 5 O 3731 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18627 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 703, 5733 Classifications: {'peptide': 703} Link IDs: {'PTRANS': 25, 'TRANS': 677} Chain breaks: 2 Chain: "B" Number of atoms: 5925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5925 Classifications: {'peptide': 740} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 711} Chain breaks: 1 Chain: "C" Number of atoms: 5879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5879 Classifications: {'peptide': 740} Link IDs: {'PTRANS': 30, 'TRANS': 709} Chain: "V" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 703 Classifications: {'RNA': 33} Modifications used: {'p5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 8, 'rna3p_pur': 11, 'rna3p_pyr': 8} Link IDs: {'rna2p': 14, 'rna3p': 18} Chain breaks: 1 Chain: "M" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 214 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 4} Link IDs: {'rna3p': 9} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Unusual residues: {' MG': 2, 'M4H': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 11 Unusual residues: {' MG': 2, 'POP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "V" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "M" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 4.69, per 1000 atoms: 0.25 Number of scatterers: 18627 At special positions: 0 Unit cell: (121.092, 122.718, 119.467, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 108 16.00 P 45 15.00 Mg 4 11.99 O 3731 8.00 N 3231 7.00 C 11508 6.00 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: 1.73 Conformation dependent library (CDL) restraints added in 735.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4104 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 25 sheets defined 48.2% alpha, 14.8% beta 12 base pairs and 22 stacking pairs defined. Time for finding SS restraints: 2.53 Creating SS restraints... Processing helix chain 'A' and resid 2 through 9 Processing helix chain 'A' and resid 10 through 24 Processing helix chain 'A' and resid 31 through 48 Processing helix chain 'A' and resid 83 through 98 Processing helix chain 'A' and resid 126 through 138 removed outlier: 3.994A pdb=" N TYR A 130 " --> pdb=" O LYS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 185 removed outlier: 3.841A pdb=" N ARG A 168 " --> pdb=" O ASP A 164 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 193 removed outlier: 3.643A pdb=" N GLN A 193 " --> pdb=" O ASP A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 240 through 249 Processing helix chain 'A' and resid 302 through 312 Processing helix chain 'A' and resid 330 through 347 removed outlier: 3.692A pdb=" N TYR A 334 " --> pdb=" O VAL A 330 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU A 347 " --> pdb=" O GLU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 365 Processing helix chain 'A' and resid 375 through 379 Processing helix chain 'A' and resid 400 through 410 removed outlier: 3.506A pdb=" N SER A 410 " --> pdb=" O PHE A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 446 removed outlier: 3.722A pdb=" N PHE A 440 " --> pdb=" O ARG A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 471 removed outlier: 3.502A pdb=" N GLU A 452 " --> pdb=" O CYS A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 533 removed outlier: 3.866A pdb=" N GLU A 533 " --> pdb=" O HIS A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 574 Processing helix chain 'A' and resid 575 through 577 No H-bonds generated for 'chain 'A' and resid 575 through 577' Processing helix chain 'A' and resid 578 through 599 removed outlier: 3.646A pdb=" N GLN A 586 " --> pdb=" O GLN A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 609 Processing helix chain 'A' and resid 627 through 645 Processing helix chain 'A' and resid 647 through 669 removed outlier: 4.211A pdb=" N LYS A 659 " --> pdb=" O ALA A 655 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU A 660 " --> pdb=" O GLU A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 687 Processing helix chain 'A' and resid 692 through 713 Processing helix chain 'B' and resid 7 through 12 removed outlier: 4.227A pdb=" N LYS B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 22 removed outlier: 5.904A pdb=" N SER B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE B 22 " --> pdb=" O SER B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 116 removed outlier: 3.509A pdb=" N GLN B 115 " --> pdb=" O ILE B 111 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN B 116 " --> pdb=" O ASP B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 125 removed outlier: 3.566A pdb=" N LYS B 121 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY B 125 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 153 Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 162 through 173 Processing helix chain 'B' and resid 174 through 176 No H-bonds generated for 'chain 'B' and resid 174 through 176' Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 245 through 265 removed outlier: 3.555A pdb=" N ARG B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLY B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ARG B 265 " --> pdb=" O ASN B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 292 Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 330 through 338 Processing helix chain 'B' and resid 338 through 346 Processing helix chain 'B' and resid 369 through 373 removed outlier: 3.542A pdb=" N LEU B 373 " --> pdb=" O ALA B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 381 removed outlier: 3.501A pdb=" N PHE B 381 " --> pdb=" O LEU B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 391 Processing helix chain 'B' and resid 412 through 427 removed outlier: 4.098A pdb=" N GLY B 427 " --> pdb=" O VAL B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 455 through 473 Processing helix chain 'B' and resid 505 through 512 Proline residue: B 510 - end of helix Processing helix chain 'B' and resid 518 through 536 Processing helix chain 'B' and resid 540 through 559 Processing helix chain 'B' and resid 572 through 582 Processing helix chain 'B' and resid 585 through 589 Processing helix chain 'B' and resid 590 through 594 Processing helix chain 'B' and resid 607 through 613 Processing helix chain 'B' and resid 614 through 616 No H-bonds generated for 'chain 'B' and resid 614 through 616' Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 679 through 697 removed outlier: 5.205A pdb=" N ASP B 685 " --> pdb=" O GLY B 681 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N GLU B 686 " --> pdb=" O ILE B 682 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG B 687 " --> pdb=" O LEU B 683 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU B 697 " --> pdb=" O CYS B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 704 removed outlier: 4.242A pdb=" N THR B 704 " --> pdb=" O PRO B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 732 Processing helix chain 'B' and resid 736 through 756 removed outlier: 3.858A pdb=" N GLN B 756 " --> pdb=" O ALA B 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 0 through 12 removed outlier: 3.915A pdb=" N ILE C 4 " --> pdb=" O GLY C 0 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 23 Processing helix chain 'C' and resid 24 through 33 removed outlier: 3.870A pdb=" N ALA C 29 " --> pdb=" O VAL C 25 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYS C 33 " --> pdb=" O ALA C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 51 Processing helix chain 'C' and resid 62 through 67 Processing helix chain 'C' and resid 92 through 103 removed outlier: 3.937A pdb=" N VAL C 96 " --> pdb=" O SER C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'C' and resid 115 through 127 Processing helix chain 'C' and resid 155 through 168 Processing helix chain 'C' and resid 169 through 172 removed outlier: 3.932A pdb=" N VAL C 172 " --> pdb=" O PRO C 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 169 through 172' Processing helix chain 'C' and resid 179 through 193 Processing helix chain 'C' and resid 199 through 212 Processing helix chain 'C' and resid 225 through 230 removed outlier: 3.535A pdb=" N GLU C 230 " --> pdb=" O SER C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 251 through 271 removed outlier: 3.841A pdb=" N ILE C 260 " --> pdb=" O ASP C 256 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE C 271 " --> pdb=" O VAL C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 285 Processing helix chain 'C' and resid 293 through 298 removed outlier: 3.522A pdb=" N ILE C 297 " --> pdb=" O PRO C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 316 removed outlier: 3.586A pdb=" N ILE C 310 " --> pdb=" O GLN C 306 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU C 315 " --> pdb=" O CYS C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 405 removed outlier: 3.602A pdb=" N ASN C 396 " --> pdb=" O GLU C 392 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU C 397 " --> pdb=" O ASP C 393 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE C 399 " --> pdb=" O LEU C 395 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N MET C 402 " --> pdb=" O MET C 398 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE C 404 " --> pdb=" O THR C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 413 Processing helix chain 'C' and resid 429 through 439 removed outlier: 3.836A pdb=" N GLN C 433 " --> pdb=" O ASN C 429 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU C 435 " --> pdb=" O MET C 431 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN C 439 " --> pdb=" O LEU C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 446 removed outlier: 3.777A pdb=" N LEU C 446 " --> pdb=" O SER C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 518 Processing helix chain 'C' and resid 541 through 556 removed outlier: 3.581A pdb=" N LEU C 546 " --> pdb=" O PRO C 542 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR C 547 " --> pdb=" O GLU C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 566 removed outlier: 4.255A pdb=" N THR C 562 " --> pdb=" O GLU C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 573 removed outlier: 3.652A pdb=" N ASN C 573 " --> pdb=" O THR C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 583 Processing helix chain 'C' and resid 585 through 587 No H-bonds generated for 'chain 'C' and resid 585 through 587' Processing helix chain 'C' and resid 588 through 606 removed outlier: 3.501A pdb=" N THR C 598 " --> pdb=" O GLY C 594 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN C 602 " --> pdb=" O THR C 598 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG C 604 " --> pdb=" O PHE C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 611 through 619 removed outlier: 3.651A pdb=" N LYS C 617 " --> pdb=" O ILE C 613 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 622 No H-bonds generated for 'chain 'C' and resid 620 through 622' Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 62 Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 259 Processing sheet with id=AA4, first strand: chain 'A' and resid 274 through 275 removed outlier: 6.428A pdb=" N LYS A 274 " --> pdb=" O LYS A 397 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 290 through 293 removed outlier: 7.173A pdb=" N ARG A 491 " --> pdb=" O ASP A 486 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ASP A 486 " --> pdb=" O ARG A 491 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N THR A 493 " --> pdb=" O CYS A 484 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N CYS A 484 " --> pdb=" O THR A 493 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N LEU A 495 " --> pdb=" O THR A 482 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N THR A 482 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLY A 497 " --> pdb=" O ILE A 480 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN A 476 " --> pdb=" O LYS A 501 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TYR A 475 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 317 through 324 removed outlier: 10.071A pdb=" N TRP A 317 " --> pdb=" O MET A 543 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N MET A 543 " --> pdb=" O TRP A 317 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N LYS A 319 " --> pdb=" O GLY A 541 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLY A 541 " --> pdb=" O LYS A 319 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL A 537 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL A 556 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ASP A 542 " --> pdb=" O LYS A 554 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LYS A 554 " --> pdb=" O ASP A 542 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLU A 544 " --> pdb=" O ILE A 552 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE A 552 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N TYR A 496 " --> pdb=" O PHE A 520 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ARG A 491 " --> pdb=" O ASP A 486 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ASP A 486 " --> pdb=" O ARG A 491 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N THR A 493 " --> pdb=" O CYS A 484 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N CYS A 484 " --> pdb=" O THR A 493 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N LEU A 495 " --> pdb=" O THR A 482 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N THR A 482 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLY A 497 " --> pdb=" O ILE A 480 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN A 476 " --> pdb=" O LYS A 501 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 372 through 374 removed outlier: 4.297A pdb=" N GLN B 367 " --> pdb=" O MET A 374 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 622 through 626 removed outlier: 6.121A pdb=" N GLY A 626 " --> pdb=" O PRO A 615 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AB1, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AB2, first strand: chain 'B' and resid 178 through 192 removed outlier: 7.665A pdb=" N ASN B 678 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ARG B 203 " --> pdb=" O ASN B 678 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 240 through 244 removed outlier: 3.763A pdb=" N THR B 226 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 489 through 492 Processing sheet with id=AB5, first strand: chain 'C' and resid 57 through 60 Processing sheet with id=AB6, first strand: chain 'C' and resid 129 through 135 removed outlier: 4.746A pdb=" N GLN C 243 " --> pdb=" O GLY C 131 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N VAL C 133 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N GLU C 241 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 141 through 148 removed outlier: 6.365A pdb=" N ARG C 214 " --> pdb=" O ILE C 147 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 287 through 289 Processing sheet with id=AB9, first strand: chain 'C' and resid 323 through 325 removed outlier: 3.636A pdb=" N PHE C 325 " --> pdb=" O TYR C 328 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASN C 329 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS C 331 " --> pdb=" O ASN C 364 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N GLU C 362 " --> pdb=" O VAL C 333 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS C 376 " --> pdb=" O GLU C 361 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N ARG C 479 " --> pdb=" O ILE C 382 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ALA C 384 " --> pdb=" O ARG C 479 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 338 through 339 Processing sheet with id=AC2, first strand: chain 'C' and resid 342 through 345 Processing sheet with id=AC3, first strand: chain 'C' and resid 462 through 463 Processing sheet with id=AC4, first strand: chain 'C' and resid 496 through 497 removed outlier: 7.432A pdb=" N ASN C 506 " --> pdb=" O LEU C 511 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N LEU C 511 " --> pdb=" O ASN C 506 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 635 through 640 Processing sheet with id=AC6, first strand: chain 'C' and resid 657 through 659 Processing sheet with id=AC7, first strand: chain 'C' and resid 686 through 687 removed outlier: 3.516A pdb=" N ILE C 696 " --> pdb=" O GLU C 687 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU C 733 " --> pdb=" O LEU C 697 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N LYS C 699 " --> pdb=" O THR C 731 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N THR C 731 " --> pdb=" O LYS C 699 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS C 736 " --> pdb=" O GLU C 720 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N GLU C 720 " --> pdb=" O LYS C 736 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N LEU C 708 " --> pdb=" O LEU C 725 " (cutoff:3.500A) 832 hydrogen bonds defined for protein. 2298 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 30 hydrogen bonds 60 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 22 stacking parallelities Total time for adding SS restraints: 4.13 Time building geometry restraints manager: 2.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3317 1.32 - 1.44: 4917 1.44 - 1.57: 10426 1.57 - 1.69: 85 1.69 - 1.81: 190 Bond restraints: 18935 Sorted by residual: bond pdb=" O POP B 803 " pdb=" P2 POP B 803 " ideal model delta sigma weight residual 1.661 1.598 0.063 2.00e-02 2.50e+03 9.91e+00 bond pdb=" O POP B 803 " pdb=" P1 POP B 803 " ideal model delta sigma weight residual 1.660 1.602 0.058 2.00e-02 2.50e+03 8.27e+00 bond pdb=" C19 M4H A 801 " pdb=" C20 M4H A 801 " ideal model delta sigma weight residual 1.414 1.462 -0.048 2.00e-02 2.50e+03 5.74e+00 bond pdb=" C1 M4H A 801 " pdb=" C6 M4H A 801 " ideal model delta sigma weight residual 1.437 1.477 -0.040 2.00e-02 2.50e+03 3.99e+00 bond pdb=" C13 M4H A 801 " pdb=" N18 M4H A 801 " ideal model delta sigma weight residual 1.459 1.498 -0.039 2.00e-02 2.50e+03 3.84e+00 ... (remaining 18930 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 25434 2.75 - 5.51: 278 5.51 - 8.26: 29 8.26 - 11.01: 4 11.01 - 13.76: 2 Bond angle restraints: 25747 Sorted by residual: angle pdb=" C MET B 407 " pdb=" N MET B 408 " pdb=" CA MET B 408 " ideal model delta sigma weight residual 121.54 132.57 -11.03 1.91e+00 2.74e-01 3.34e+01 angle pdb=" N18 M4H A 801 " pdb=" C19 M4H A 801 " pdb=" N26 M4H A 801 " ideal model delta sigma weight residual 125.81 139.57 -13.76 3.00e+00 1.11e-01 2.10e+01 angle pdb=" N MET B 408 " pdb=" CA MET B 408 " pdb=" C MET B 408 " ideal model delta sigma weight residual 110.80 101.48 9.32 2.13e+00 2.20e-01 1.92e+01 angle pdb=" O4' A V 7 " pdb=" C1' A V 7 " pdb=" N9 A V 7 " ideal model delta sigma weight residual 108.20 113.54 -5.34 1.50e+00 4.44e-01 1.27e+01 angle pdb=" P1 POP B 803 " pdb=" O POP B 803 " pdb=" P2 POP B 803 " ideal model delta sigma weight residual 139.66 129.33 10.33 3.00e+00 1.11e-01 1.19e+01 ... (remaining 25742 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 10244 17.97 - 35.94: 970 35.94 - 53.91: 249 53.91 - 71.87: 106 71.87 - 89.84: 42 Dihedral angle restraints: 11611 sinusoidal: 5262 harmonic: 6349 Sorted by residual: dihedral pdb=" CA MET B 407 " pdb=" C MET B 407 " pdb=" N MET B 408 " pdb=" CA MET B 408 " ideal model delta harmonic sigma weight residual 180.00 150.00 30.00 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA ILE A 481 " pdb=" C ILE A 481 " pdb=" N THR A 482 " pdb=" CA THR A 482 " ideal model delta harmonic sigma weight residual 180.00 153.18 26.82 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA LEU A 219 " pdb=" C LEU A 219 " pdb=" N PRO A 220 " pdb=" CA PRO A 220 " ideal model delta harmonic sigma weight residual 180.00 160.08 19.92 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 11608 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1884 0.047 - 0.095: 778 0.095 - 0.142: 179 0.142 - 0.189: 23 0.189 - 0.236: 3 Chirality restraints: 2867 Sorted by residual: chirality pdb=" C1' A V 4 " pdb=" O4' A V 4 " pdb=" C2' A V 4 " pdb=" N9 A V 4 " both_signs ideal model delta sigma weight residual False 2.46 2.22 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" C1' A V 7 " pdb=" O4' A V 7 " pdb=" C2' A V 7 " pdb=" N9 A V 7 " both_signs ideal model delta sigma weight residual False 2.44 2.22 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CB ILE B 392 " pdb=" CA ILE B 392 " pdb=" CG1 ILE B 392 " pdb=" CG2 ILE B 392 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 2864 not shown) Planarity restraints: 3153 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A V 7 " -0.038 2.00e-02 2.50e+03 1.77e-02 8.61e+00 pdb=" N9 A V 7 " 0.040 2.00e-02 2.50e+03 pdb=" C8 A V 7 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A V 7 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A V 7 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A V 7 " -0.014 2.00e-02 2.50e+03 pdb=" N6 A V 7 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A V 7 " 0.000 2.00e-02 2.50e+03 pdb=" C2 A V 7 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A V 7 " 0.006 2.00e-02 2.50e+03 pdb=" C4 A V 7 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 619 " -0.046 5.00e-02 4.00e+02 6.93e-02 7.68e+00 pdb=" N PRO A 620 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO A 620 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 620 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A V 4 " -0.037 2.00e-02 2.50e+03 1.66e-02 7.56e+00 pdb=" N9 A V 4 " 0.037 2.00e-02 2.50e+03 pdb=" C8 A V 4 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A V 4 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A V 4 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A V 4 " -0.008 2.00e-02 2.50e+03 pdb=" N6 A V 4 " -0.008 2.00e-02 2.50e+03 pdb=" N1 A V 4 " -0.004 2.00e-02 2.50e+03 pdb=" C2 A V 4 " 0.004 2.00e-02 2.50e+03 pdb=" N3 A V 4 " 0.007 2.00e-02 2.50e+03 pdb=" C4 A V 4 " 0.004 2.00e-02 2.50e+03 ... (remaining 3150 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 280 2.60 - 3.17: 14261 3.17 - 3.75: 30435 3.75 - 4.32: 44853 4.32 - 4.90: 70545 Nonbonded interactions: 160374 Sorted by model distance: nonbonded pdb=" OD1 ASP A 108 " pdb="MG MG A 802 " model vdw 2.024 2.170 nonbonded pdb=" O11 M4H A 801 " pdb="MG MG A 803 " model vdw 2.035 2.170 nonbonded pdb=" OD1 ASP B 305 " pdb="MG MG B 801 " model vdw 2.036 2.170 nonbonded pdb=" OD2 ASP A 108 " pdb="MG MG A 803 " model vdw 2.055 2.170 nonbonded pdb=" OD1 ASP B 445 " pdb="MG MG B 801 " model vdw 2.059 2.170 ... (remaining 160369 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: 2.650 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: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.040 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 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 : 0.008 0.068 18935 Z= 0.342 Angle : 0.818 13.764 25747 Z= 0.453 Chirality : 0.052 0.236 2867 Planarity : 0.006 0.069 3153 Dihedral : 16.612 89.842 7507 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.59 % Favored : 96.32 % Rotamer: Outliers : 5.99 % Allowed : 10.28 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -3.41 (0.14), residues: 2171 helix: -2.32 (0.12), residues: 972 sheet: -1.52 (0.31), residues: 241 loop : -2.26 (0.16), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 449 TYR 0.024 0.003 TYR B 557 PHE 0.029 0.003 PHE A 211 TRP 0.023 0.003 TRP C 49 HIS 0.005 0.001 HIS C 437 Details of bonding type rmsd covalent geometry : bond 0.00791 (18935) covalent geometry : angle 0.81794 (25747) hydrogen bonds : bond 0.19498 ( 858) hydrogen bonds : angle 6.97690 ( 2358) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 302 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.6005 (OUTLIER) cc_final: 0.5713 (tm-30) REVERT: A 82 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8233 (mm-40) REVERT: A 323 ILE cc_start: 0.8820 (OUTLIER) cc_final: 0.8467 (pp) REVERT: A 374 MET cc_start: 0.7722 (ttm) cc_final: 0.7347 (tpp) REVERT: A 492 ARG cc_start: 0.7632 (ttm-80) cc_final: 0.7407 (ttp-170) REVERT: B 202 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7294 (tm-30) REVERT: B 227 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.8197 (pmm) REVERT: B 296 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6877 (pt0) REVERT: B 384 ASP cc_start: 0.7767 (m-30) cc_final: 0.7494 (m-30) REVERT: B 619 ASP cc_start: 0.7874 (OUTLIER) cc_final: 0.7434 (p0) REVERT: B 633 HIS cc_start: 0.8233 (t-90) cc_final: 0.7928 (t-90) REVERT: C 138 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7187 (mp10) REVERT: C 141 VAL cc_start: 0.8949 (OUTLIER) cc_final: 0.8722 (p) REVERT: C 171 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.7880 (mm-30) REVERT: C 195 ASN cc_start: 0.6713 (m-40) cc_final: 0.6480 (m110) REVERT: C 392 GLU cc_start: 0.1944 (OUTLIER) cc_final: 0.1708 (tm-30) REVERT: C 394 ILE cc_start: 0.1343 (OUTLIER) cc_final: 0.0805 (mt) REVERT: C 395 LEU cc_start: 0.4315 (OUTLIER) cc_final: 0.4070 (tm) REVERT: C 431 MET cc_start: 0.5778 (mmm) cc_final: 0.5310 (mmm) REVERT: C 494 ILE cc_start: 0.4966 (OUTLIER) cc_final: 0.4623 (pt) REVERT: C 505 ARG cc_start: 0.5618 (OUTLIER) cc_final: 0.4562 (mtt90) REVERT: C 628 LEU cc_start: 0.5900 (OUTLIER) cc_final: 0.5664 (pt) REVERT: C 654 GLN cc_start: 0.7010 (pt0) cc_final: 0.6194 (mm110) REVERT: C 679 ILE cc_start: 0.2170 (OUTLIER) cc_final: 0.1589 (mt) outliers start: 116 outliers final: 42 residues processed: 388 average time/residue: 0.8027 time to fit residues: 343.1126 Evaluate side-chains 310 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 251 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 364 ASN Chi-restraints excluded: chain C residue 392 GLU Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 505 ARG Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain C residue 731 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 4.9990 chunk 212 optimal weight: 7.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 239 ASN A 256 GLN A 670 ASN B 127 GLN B 186 GLN B 216 ASN B 310 ASN B 372 ASN B 694 GLN B 745 ASN ** C 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 GLN C 148 ASN C 233 HIS C 301 ASN C 320 ASN C 563 GLN C 602 GLN C 614 GLN C 659 ASN C 663 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.166401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.126924 restraints weight = 20041.175| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.43 r_work: 0.3093 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18935 Z= 0.127 Angle : 0.530 8.678 25747 Z= 0.286 Chirality : 0.041 0.201 2867 Planarity : 0.004 0.049 3153 Dihedral : 13.123 89.493 3183 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.49 % Allowed : 14.93 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -1.54 (0.16), residues: 2171 helix: -0.25 (0.15), residues: 975 sheet: -0.92 (0.34), residues: 215 loop : -1.81 (0.17), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 503 TYR 0.029 0.001 TYR B 557 PHE 0.015 0.001 PHE A 211 TRP 0.014 0.001 TRP C 49 HIS 0.004 0.001 HIS C 551 Details of bonding type rmsd covalent geometry : bond 0.00270 (18935) covalent geometry : angle 0.52997 (25747) hydrogen bonds : bond 0.04801 ( 858) hydrogen bonds : angle 4.63554 ( 2358) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 289 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 MET cc_start: 0.7380 (tpp) cc_final: 0.6842 (tpt) REVERT: A 43 GLU cc_start: 0.7444 (tm-30) cc_final: 0.6832 (tm-30) REVERT: A 147 ILE cc_start: 0.8431 (mm) cc_final: 0.8096 (mm) REVERT: A 374 MET cc_start: 0.8454 (ttm) cc_final: 0.8174 (tpp) REVERT: A 486 ASP cc_start: 0.7284 (t70) cc_final: 0.7067 (t70) REVERT: A 492 ARG cc_start: 0.8316 (ttm-80) cc_final: 0.7964 (ttm170) REVERT: B 171 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.8815 (mp) REVERT: B 183 THR cc_start: 0.8725 (p) cc_final: 0.8468 (t) REVERT: B 189 LYS cc_start: 0.8052 (tttt) cc_final: 0.7814 (ttpp) REVERT: B 190 ARG cc_start: 0.8505 (mmm160) cc_final: 0.8260 (mmt180) REVERT: B 202 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7891 (tp40) REVERT: B 209 ARG cc_start: 0.7655 (mtm-85) cc_final: 0.7228 (mpt180) REVERT: B 384 ASP cc_start: 0.8461 (m-30) cc_final: 0.8251 (m-30) REVERT: B 571 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7572 (mmp-170) REVERT: B 633 HIS cc_start: 0.8143 (t-90) cc_final: 0.7845 (t-90) REVERT: B 704 THR cc_start: 0.9106 (p) cc_final: 0.8843 (m) REVERT: C 141 VAL cc_start: 0.8877 (OUTLIER) cc_final: 0.8641 (t) REVERT: C 171 GLU cc_start: 0.9025 (OUTLIER) cc_final: 0.7997 (mm-30) REVERT: C 195 ASN cc_start: 0.6829 (m-40) cc_final: 0.6548 (m110) REVERT: C 210 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8168 (tp30) REVERT: C 301 ASN cc_start: 0.5243 (OUTLIER) cc_final: 0.4823 (t0) REVERT: C 505 ARG cc_start: 0.4253 (OUTLIER) cc_final: 0.3001 (mtt90) REVERT: C 613 ILE cc_start: 0.7034 (mm) cc_final: 0.6577 (mp) REVERT: C 628 LEU cc_start: 0.5478 (OUTLIER) cc_final: 0.5144 (pt) REVERT: C 654 GLN cc_start: 0.7350 (pt0) cc_final: 0.6144 (mm110) outliers start: 87 outliers final: 33 residues processed: 352 average time/residue: 0.7196 time to fit residues: 281.5324 Evaluate side-chains 298 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 256 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 571 ARG Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 364 ASN Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 505 ARG Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 731 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 155 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 189 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 195 optimal weight: 0.0570 chunk 202 optimal weight: 0.0870 chunk 205 optimal weight: 4.9990 chunk 185 optimal weight: 30.0000 chunk 63 optimal weight: 5.9990 chunk 191 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.5876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 670 ASN B 629 ASN B 694 GLN C 13 ASN C 482 GLN C 614 GLN C 654 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.168357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.129227 restraints weight = 20135.295| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.45 r_work: 0.3135 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 18935 Z= 0.095 Angle : 0.472 8.663 25747 Z= 0.252 Chirality : 0.039 0.193 2867 Planarity : 0.004 0.050 3153 Dihedral : 12.066 88.022 3125 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.41 % Allowed : 16.58 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -0.68 (0.17), residues: 2171 helix: 0.64 (0.17), residues: 980 sheet: -0.74 (0.34), residues: 221 loop : -1.52 (0.18), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 75 TYR 0.023 0.001 TYR B 557 PHE 0.012 0.001 PHE B 333 TRP 0.014 0.001 TRP C 49 HIS 0.003 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00197 (18935) covalent geometry : angle 0.47177 (25747) hydrogen bonds : bond 0.03826 ( 858) hydrogen bonds : angle 4.26631 ( 2358) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 276 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 MET cc_start: 0.7458 (tpp) cc_final: 0.6896 (tpt) REVERT: A 100 ASN cc_start: 0.6770 (m-40) cc_final: 0.6084 (m-40) REVERT: A 147 ILE cc_start: 0.8400 (mm) cc_final: 0.8120 (mm) REVERT: A 321 THR cc_start: 0.8946 (p) cc_final: 0.8680 (p) REVERT: B 171 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.8823 (mp) REVERT: B 183 THR cc_start: 0.8544 (p) cc_final: 0.8326 (t) REVERT: B 189 LYS cc_start: 0.7962 (tttt) cc_final: 0.7699 (ttpp) REVERT: B 202 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7750 (tp-100) REVERT: B 209 ARG cc_start: 0.7662 (mtm-85) cc_final: 0.7186 (mpt180) REVERT: B 384 ASP cc_start: 0.8386 (m-30) cc_final: 0.8178 (m-30) REVERT: B 571 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7469 (mmp-170) REVERT: B 619 ASP cc_start: 0.7937 (p0) cc_final: 0.7728 (p0) REVERT: B 633 HIS cc_start: 0.8088 (t-90) cc_final: 0.7770 (t-90) REVERT: B 656 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7418 (mt-10) REVERT: B 704 THR cc_start: 0.9096 (p) cc_final: 0.8893 (m) REVERT: B 730 LEU cc_start: 0.8715 (tp) cc_final: 0.8478 (tt) REVERT: C 18 GLU cc_start: 0.7914 (tp30) cc_final: 0.7707 (tp30) REVERT: C 141 VAL cc_start: 0.8864 (OUTLIER) cc_final: 0.8660 (t) REVERT: C 195 ASN cc_start: 0.6770 (m-40) cc_final: 0.6455 (m110) REVERT: C 249 GLU cc_start: 0.6347 (OUTLIER) cc_final: 0.5282 (mp0) REVERT: C 301 ASN cc_start: 0.5373 (OUTLIER) cc_final: 0.5072 (t0) REVERT: C 354 MET cc_start: 0.3580 (OUTLIER) cc_final: 0.3315 (mmm) REVERT: C 394 ILE cc_start: 0.1548 (OUTLIER) cc_final: 0.1077 (mt) REVERT: C 482 GLN cc_start: 0.2357 (OUTLIER) cc_final: 0.1875 (pt0) REVERT: C 505 ARG cc_start: 0.4225 (OUTLIER) cc_final: 0.3151 (mtt90) REVERT: C 555 LYS cc_start: 0.7324 (OUTLIER) cc_final: 0.6578 (ttmt) REVERT: C 613 ILE cc_start: 0.6974 (mm) cc_final: 0.6511 (mp) REVERT: C 654 GLN cc_start: 0.7348 (pt0) cc_final: 0.6135 (mm110) outliers start: 66 outliers final: 29 residues processed: 321 average time/residue: 0.7634 time to fit residues: 271.0617 Evaluate side-chains 292 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 252 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 571 ARG Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain C residue 364 ASN Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain C residue 482 GLN Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 505 ARG Chi-restraints excluded: chain C residue 555 LYS Chi-restraints excluded: chain C residue 637 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 91 optimal weight: 2.9990 chunk 54 optimal weight: 20.0000 chunk 41 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 165 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 171 optimal weight: 10.0000 chunk 172 optimal weight: 10.0000 chunk 175 optimal weight: 5.9990 chunk 169 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 670 ASN ** B 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 694 GLN C 301 ASN C 439 GLN C 551 HIS C 614 GLN C 639 ASN C 723 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.163898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.125739 restraints weight = 20052.330| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.43 r_work: 0.3049 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 18935 Z= 0.218 Angle : 0.571 8.534 25747 Z= 0.303 Chirality : 0.044 0.206 2867 Planarity : 0.004 0.062 3153 Dihedral : 12.134 89.363 3112 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.27 % Favored : 96.68 % Rotamer: Outliers : 4.13 % Allowed : 17.67 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -0.61 (0.17), residues: 2171 helix: 0.70 (0.17), residues: 981 sheet: -0.67 (0.34), residues: 221 loop : -1.50 (0.18), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 734 TYR 0.027 0.002 TYR B 557 PHE 0.020 0.002 PHE A 211 TRP 0.015 0.002 TRP C 49 HIS 0.005 0.001 HIS A 52 Details of bonding type rmsd covalent geometry : bond 0.00499 (18935) covalent geometry : angle 0.57147 (25747) hydrogen bonds : bond 0.05061 ( 858) hydrogen bonds : angle 4.36681 ( 2358) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 261 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4399 (OUTLIER) cc_final: 0.3922 (mmt) REVERT: A 42 MET cc_start: 0.7343 (tpp) cc_final: 0.6666 (tpt) REVERT: A 100 ASN cc_start: 0.6762 (m-40) cc_final: 0.6037 (m-40) REVERT: A 124 ARG cc_start: 0.6196 (OUTLIER) cc_final: 0.5475 (mtt180) REVERT: A 174 ARG cc_start: 0.7586 (tmt170) cc_final: 0.6590 (tmt170) REVERT: A 321 THR cc_start: 0.9001 (p) cc_final: 0.8688 (p) REVERT: A 492 ARG cc_start: 0.8302 (ttm-80) cc_final: 0.7858 (ttp-170) REVERT: B 171 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.8811 (mp) REVERT: B 183 THR cc_start: 0.8722 (p) cc_final: 0.8451 (t) REVERT: B 189 LYS cc_start: 0.8102 (tttt) cc_final: 0.7863 (ttpp) REVERT: B 209 ARG cc_start: 0.7700 (mtm-85) cc_final: 0.7204 (mpt180) REVERT: B 296 GLU cc_start: 0.7867 (pt0) cc_final: 0.7537 (pt0) REVERT: B 384 ASP cc_start: 0.8501 (m-30) cc_final: 0.8299 (m-30) REVERT: B 571 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7601 (mmp-170) REVERT: B 619 ASP cc_start: 0.8048 (p0) cc_final: 0.7794 (p0) REVERT: B 633 HIS cc_start: 0.8215 (t-90) cc_final: 0.7853 (t-90) REVERT: B 656 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7508 (mt-10) REVERT: B 672 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.7873 (mtm-85) REVERT: B 704 THR cc_start: 0.9136 (p) cc_final: 0.8904 (m) REVERT: B 730 LEU cc_start: 0.8714 (tp) cc_final: 0.8490 (tt) REVERT: C 138 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.7125 (mp10) REVERT: C 141 VAL cc_start: 0.8910 (OUTLIER) cc_final: 0.8664 (t) REVERT: C 195 ASN cc_start: 0.6871 (m-40) cc_final: 0.6546 (m110) REVERT: C 249 GLU cc_start: 0.6402 (OUTLIER) cc_final: 0.5406 (mp0) REVERT: C 332 ARG cc_start: 0.5031 (OUTLIER) cc_final: 0.3753 (tpt170) REVERT: C 354 MET cc_start: 0.3832 (OUTLIER) cc_final: 0.3477 (mmm) REVERT: C 394 ILE cc_start: 0.1363 (OUTLIER) cc_final: 0.1043 (mt) REVERT: C 429 ASN cc_start: 0.2044 (OUTLIER) cc_final: 0.1348 (m-40) REVERT: C 505 ARG cc_start: 0.4338 (OUTLIER) cc_final: 0.3146 (mtt90) REVERT: C 613 ILE cc_start: 0.6959 (mm) cc_final: 0.6523 (mp) REVERT: C 654 GLN cc_start: 0.7248 (pt0) cc_final: 0.6141 (mm110) outliers start: 80 outliers final: 42 residues processed: 316 average time/residue: 0.7508 time to fit residues: 261.6007 Evaluate side-chains 303 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 248 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 571 ARG Chi-restraints excluded: chain B residue 672 ARG Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 332 ARG Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain C residue 364 ASN Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 429 ASN Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 505 ARG Chi-restraints excluded: chain C residue 637 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 171 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 chunk 178 optimal weight: 6.9990 chunk 138 optimal weight: 4.9990 chunk 198 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 130 optimal weight: 0.7980 chunk 179 optimal weight: 8.9990 chunk 97 optimal weight: 1.9990 chunk 136 optimal weight: 9.9990 chunk 26 optimal weight: 0.7980 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 670 ASN B 629 ASN ** B 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.164520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.125556 restraints weight = 19840.925| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.50 r_work: 0.3050 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 18935 Z= 0.182 Angle : 0.538 8.683 25747 Z= 0.287 Chirality : 0.042 0.206 2867 Planarity : 0.004 0.050 3153 Dihedral : 11.963 89.532 3109 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.39 % Allowed : 18.13 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -0.42 (0.17), residues: 2171 helix: 0.87 (0.17), residues: 982 sheet: -0.58 (0.34), residues: 220 loop : -1.41 (0.18), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 734 TYR 0.026 0.002 TYR B 557 PHE 0.018 0.002 PHE A 211 TRP 0.016 0.002 TRP C 49 HIS 0.004 0.001 HIS A 52 Details of bonding type rmsd covalent geometry : bond 0.00416 (18935) covalent geometry : angle 0.53830 (25747) hydrogen bonds : bond 0.04660 ( 858) hydrogen bonds : angle 4.30182 ( 2358) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 255 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4358 (OUTLIER) cc_final: 0.3798 (mmt) REVERT: A 42 MET cc_start: 0.7289 (tpp) cc_final: 0.6582 (tpt) REVERT: A 100 ASN cc_start: 0.6714 (m-40) cc_final: 0.5983 (m-40) REVERT: A 124 ARG cc_start: 0.6146 (OUTLIER) cc_final: 0.5430 (mtt180) REVERT: A 125 ARG cc_start: 0.6032 (mmt90) cc_final: 0.5413 (ppt-90) REVERT: A 147 ILE cc_start: 0.8456 (mm) cc_final: 0.8199 (mm) REVERT: A 321 THR cc_start: 0.9023 (p) cc_final: 0.8704 (p) REVERT: A 395 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8582 (mmtt) REVERT: A 492 ARG cc_start: 0.8332 (ttm-80) cc_final: 0.7876 (ttp-170) REVERT: B 120 ASP cc_start: 0.8489 (p0) cc_final: 0.8273 (p0) REVERT: B 171 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.8820 (mp) REVERT: B 183 THR cc_start: 0.8699 (p) cc_final: 0.8428 (t) REVERT: B 187 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.7510 (mttt) REVERT: B 189 LYS cc_start: 0.8041 (tttt) cc_final: 0.7785 (ttpp) REVERT: B 209 ARG cc_start: 0.7683 (mtm-85) cc_final: 0.7126 (mpt180) REVERT: B 296 GLU cc_start: 0.7963 (pt0) cc_final: 0.7616 (pt0) REVERT: B 384 ASP cc_start: 0.8534 (m-30) cc_final: 0.8326 (m-30) REVERT: B 571 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7522 (mmp-170) REVERT: B 619 ASP cc_start: 0.8052 (p0) cc_final: 0.7777 (p0) REVERT: B 633 HIS cc_start: 0.8164 (t-90) cc_final: 0.7822 (t-90) REVERT: B 656 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7512 (mt-10) REVERT: B 672 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.7856 (mtm-85) REVERT: B 704 THR cc_start: 0.9116 (p) cc_final: 0.8880 (m) REVERT: B 730 LEU cc_start: 0.8716 (tp) cc_final: 0.8505 (tt) REVERT: C 171 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.7835 (mm-30) REVERT: C 195 ASN cc_start: 0.6971 (m-40) cc_final: 0.6609 (m110) REVERT: C 249 GLU cc_start: 0.6308 (OUTLIER) cc_final: 0.5396 (mp0) REVERT: C 332 ARG cc_start: 0.5079 (OUTLIER) cc_final: 0.3811 (tpt170) REVERT: C 354 MET cc_start: 0.3734 (OUTLIER) cc_final: 0.3470 (mmm) REVERT: C 394 ILE cc_start: 0.1409 (OUTLIER) cc_final: 0.1070 (mt) REVERT: C 429 ASN cc_start: 0.2014 (OUTLIER) cc_final: 0.1322 (m-40) REVERT: C 505 ARG cc_start: 0.4250 (OUTLIER) cc_final: 0.3071 (mtt90) REVERT: C 613 ILE cc_start: 0.6843 (mm) cc_final: 0.6416 (mp) REVERT: C 654 GLN cc_start: 0.7214 (pt0) cc_final: 0.6124 (mm110) outliers start: 85 outliers final: 44 residues processed: 315 average time/residue: 0.7222 time to fit residues: 251.8810 Evaluate side-chains 302 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 244 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 395 LYS Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 571 ARG Chi-restraints excluded: chain B residue 672 ARG Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 332 ARG Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain C residue 364 ASN Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 429 ASN Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 505 ARG Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 731 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 175 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 136 optimal weight: 7.9990 chunk 154 optimal weight: 3.9990 chunk 216 optimal weight: 20.0000 chunk 125 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 181 optimal weight: 30.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 670 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.164125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.124186 restraints weight = 19828.879| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.49 r_work: 0.3049 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 18935 Z= 0.196 Angle : 0.554 9.329 25747 Z= 0.295 Chirality : 0.043 0.208 2867 Planarity : 0.004 0.045 3153 Dihedral : 11.962 89.543 3107 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.32 % Favored : 96.64 % Rotamer: Outliers : 4.70 % Allowed : 18.18 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.18), residues: 2171 helix: 0.90 (0.17), residues: 983 sheet: -0.59 (0.34), residues: 215 loop : -1.36 (0.18), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 734 TYR 0.026 0.002 TYR B 557 PHE 0.018 0.002 PHE A 211 TRP 0.016 0.002 TRP C 49 HIS 0.004 0.001 HIS A 52 Details of bonding type rmsd covalent geometry : bond 0.00451 (18935) covalent geometry : angle 0.55386 (25747) hydrogen bonds : bond 0.04788 ( 858) hydrogen bonds : angle 4.31373 ( 2358) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 250 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4399 (OUTLIER) cc_final: 0.3838 (mmt) REVERT: A 42 MET cc_start: 0.7332 (tpp) cc_final: 0.6608 (tpt) REVERT: A 43 GLU cc_start: 0.7468 (tm-30) cc_final: 0.6866 (tm-30) REVERT: A 100 ASN cc_start: 0.6803 (m-40) cc_final: 0.6067 (m-40) REVERT: A 124 ARG cc_start: 0.6173 (OUTLIER) cc_final: 0.5480 (mtt180) REVERT: A 125 ARG cc_start: 0.5986 (mmt90) cc_final: 0.5388 (ppt-90) REVERT: A 147 ILE cc_start: 0.8464 (mm) cc_final: 0.8241 (mm) REVERT: A 192 ARG cc_start: 0.6528 (OUTLIER) cc_final: 0.6207 (ptm-80) REVERT: A 321 THR cc_start: 0.9016 (p) cc_final: 0.8701 (p) REVERT: A 492 ARG cc_start: 0.8304 (ttm-80) cc_final: 0.7893 (ttp-170) REVERT: B 171 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.8834 (mp) REVERT: B 183 THR cc_start: 0.8715 (p) cc_final: 0.8450 (t) REVERT: B 189 LYS cc_start: 0.8044 (tttt) cc_final: 0.7804 (ttpp) REVERT: B 209 ARG cc_start: 0.7676 (mtm-85) cc_final: 0.7183 (mpt180) REVERT: B 296 GLU cc_start: 0.7911 (pt0) cc_final: 0.7578 (pt0) REVERT: B 371 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7815 (pt0) REVERT: B 384 ASP cc_start: 0.8514 (m-30) cc_final: 0.8310 (m-30) REVERT: B 571 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7556 (mmp-170) REVERT: B 619 ASP cc_start: 0.8081 (p0) cc_final: 0.7790 (p0) REVERT: B 633 HIS cc_start: 0.8193 (t-90) cc_final: 0.7853 (t-90) REVERT: B 656 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7500 (mt-10) REVERT: B 672 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.7865 (mtm-85) REVERT: B 704 THR cc_start: 0.9108 (p) cc_final: 0.8879 (m) REVERT: B 730 LEU cc_start: 0.8717 (tp) cc_final: 0.8501 (tt) REVERT: C 138 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.7003 (mp10) REVERT: C 141 VAL cc_start: 0.8877 (OUTLIER) cc_final: 0.8673 (t) REVERT: C 171 GLU cc_start: 0.8989 (OUTLIER) cc_final: 0.7860 (mm-30) REVERT: C 249 GLU cc_start: 0.6359 (OUTLIER) cc_final: 0.5435 (mp0) REVERT: C 332 ARG cc_start: 0.5121 (OUTLIER) cc_final: 0.3352 (tmm-80) REVERT: C 354 MET cc_start: 0.3550 (OUTLIER) cc_final: 0.3293 (mmm) REVERT: C 394 ILE cc_start: 0.1610 (OUTLIER) cc_final: 0.1294 (tp) REVERT: C 429 ASN cc_start: 0.2036 (OUTLIER) cc_final: 0.1323 (m-40) REVERT: C 505 ARG cc_start: 0.4357 (OUTLIER) cc_final: 0.3171 (mtt90) REVERT: C 628 LEU cc_start: 0.5515 (OUTLIER) cc_final: 0.5141 (pt) REVERT: C 654 GLN cc_start: 0.7207 (pt0) cc_final: 0.6135 (mm110) outliers start: 91 outliers final: 53 residues processed: 313 average time/residue: 0.7093 time to fit residues: 245.9967 Evaluate side-chains 313 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 243 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 571 ARG Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 672 ARG Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 687 ARG Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 332 ARG Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain C residue 364 ASN Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 429 ASN Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 505 ARG Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 731 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 32 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 168 optimal weight: 0.7980 chunk 105 optimal weight: 6.9990 chunk 80 optimal weight: 0.6980 chunk 210 optimal weight: 2.9990 chunk 207 optimal weight: 10.0000 chunk 185 optimal weight: 20.0000 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 670 ASN B 629 ASN C 663 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.165514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.125831 restraints weight = 20005.105| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.46 r_work: 0.3068 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18935 Z= 0.143 Angle : 0.511 9.296 25747 Z= 0.272 Chirality : 0.041 0.200 2867 Planarity : 0.004 0.044 3153 Dihedral : 11.828 89.090 3107 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.87 % Allowed : 19.27 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.18), residues: 2171 helix: 1.10 (0.17), residues: 983 sheet: -0.49 (0.35), residues: 215 loop : -1.30 (0.18), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 734 TYR 0.024 0.001 TYR B 557 PHE 0.016 0.001 PHE A 211 TRP 0.017 0.001 TRP C 49 HIS 0.004 0.001 HIS A 52 Details of bonding type rmsd covalent geometry : bond 0.00320 (18935) covalent geometry : angle 0.51103 (25747) hydrogen bonds : bond 0.04237 ( 858) hydrogen bonds : angle 4.20461 ( 2358) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 252 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4277 (OUTLIER) cc_final: 0.3748 (mmt) REVERT: A 42 MET cc_start: 0.7320 (tpp) cc_final: 0.6588 (tpt) REVERT: A 43 GLU cc_start: 0.7462 (tm-30) cc_final: 0.6850 (tm-30) REVERT: A 100 ASN cc_start: 0.6726 (m-40) cc_final: 0.6025 (m-40) REVERT: A 124 ARG cc_start: 0.6160 (OUTLIER) cc_final: 0.5437 (mtt180) REVERT: A 125 ARG cc_start: 0.5986 (mmt90) cc_final: 0.5462 (ppt-90) REVERT: A 147 ILE cc_start: 0.8440 (mm) cc_final: 0.8213 (mm) REVERT: A 174 ARG cc_start: 0.7678 (tmt170) cc_final: 0.7437 (tmt170) REVERT: A 187 LEU cc_start: 0.6946 (OUTLIER) cc_final: 0.6557 (pp) REVERT: A 321 THR cc_start: 0.8999 (p) cc_final: 0.8686 (p) REVERT: A 492 ARG cc_start: 0.8300 (ttm-80) cc_final: 0.7878 (ttp-170) REVERT: B 171 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.8785 (mp) REVERT: B 183 THR cc_start: 0.8591 (p) cc_final: 0.8356 (t) REVERT: B 189 LYS cc_start: 0.7946 (tttt) cc_final: 0.7691 (ttpp) REVERT: B 209 ARG cc_start: 0.7631 (mtm-85) cc_final: 0.7149 (mpt180) REVERT: B 296 GLU cc_start: 0.7967 (pt0) cc_final: 0.7603 (pt0) REVERT: B 371 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7756 (pt0) REVERT: B 384 ASP cc_start: 0.8510 (m-30) cc_final: 0.8300 (m-30) REVERT: B 571 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7398 (mmp80) REVERT: B 619 ASP cc_start: 0.8019 (p0) cc_final: 0.7722 (p0) REVERT: B 633 HIS cc_start: 0.8154 (t-90) cc_final: 0.7824 (t-90) REVERT: B 656 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7417 (mt-10) REVERT: B 704 THR cc_start: 0.9090 (p) cc_final: 0.8868 (m) REVERT: B 730 LEU cc_start: 0.8712 (tp) cc_final: 0.8502 (tt) REVERT: C 171 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.7843 (mm-30) REVERT: C 249 GLU cc_start: 0.6270 (OUTLIER) cc_final: 0.5362 (mp0) REVERT: C 394 ILE cc_start: 0.1473 (OUTLIER) cc_final: 0.1202 (tp) REVERT: C 429 ASN cc_start: 0.1996 (OUTLIER) cc_final: 0.1299 (m-40) REVERT: C 654 GLN cc_start: 0.7144 (pt0) cc_final: 0.6193 (mm110) outliers start: 75 outliers final: 44 residues processed: 303 average time/residue: 0.7674 time to fit residues: 257.4880 Evaluate side-chains 299 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 245 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 571 ARG Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 687 ARG Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 364 ASN Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 429 ASN Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 731 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 154 optimal weight: 0.3980 chunk 64 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 chunk 200 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 152 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 chunk 206 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 582 GLN A 670 ASN B 634 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.168656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.129247 restraints weight = 19930.160| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.47 r_work: 0.3130 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 18935 Z= 0.097 Angle : 0.469 10.174 25747 Z= 0.249 Chirality : 0.039 0.192 2867 Planarity : 0.003 0.044 3153 Dihedral : 11.549 87.651 3100 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.79 % Allowed : 20.56 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.18), residues: 2171 helix: 1.38 (0.17), residues: 978 sheet: -0.25 (0.35), residues: 215 loop : -1.19 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 104 TYR 0.021 0.001 TYR B 557 PHE 0.011 0.001 PHE A 211 TRP 0.017 0.001 TRP C 49 HIS 0.004 0.001 HIS A 52 Details of bonding type rmsd covalent geometry : bond 0.00209 (18935) covalent geometry : angle 0.46937 (25747) hydrogen bonds : bond 0.03464 ( 858) hydrogen bonds : angle 4.03577 ( 2358) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 267 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4079 (OUTLIER) cc_final: 0.3598 (mmt) REVERT: A 42 MET cc_start: 0.7284 (tpp) cc_final: 0.6607 (tpt) REVERT: A 43 GLU cc_start: 0.7426 (tm-30) cc_final: 0.6848 (tm-30) REVERT: A 100 ASN cc_start: 0.6561 (m-40) cc_final: 0.5926 (m-40) REVERT: A 124 ARG cc_start: 0.6140 (OUTLIER) cc_final: 0.5411 (mtt180) REVERT: A 164 ASP cc_start: 0.6844 (p0) cc_final: 0.6559 (p0) REVERT: A 187 LEU cc_start: 0.6877 (OUTLIER) cc_final: 0.6580 (pp) REVERT: A 321 THR cc_start: 0.8900 (p) cc_final: 0.8665 (p) REVERT: A 492 ARG cc_start: 0.8354 (ttm-80) cc_final: 0.8018 (ttp-170) REVERT: B 120 ASP cc_start: 0.8426 (p0) cc_final: 0.8201 (p0) REVERT: B 171 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.8798 (mp) REVERT: B 189 LYS cc_start: 0.7915 (tttt) cc_final: 0.7332 (mttt) REVERT: B 209 ARG cc_start: 0.7609 (mtm-85) cc_final: 0.7165 (mpt180) REVERT: B 296 GLU cc_start: 0.7944 (pt0) cc_final: 0.7547 (pt0) REVERT: B 384 ASP cc_start: 0.8448 (m-30) cc_final: 0.8234 (m-30) REVERT: B 571 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7326 (mmp80) REVERT: B 619 ASP cc_start: 0.7992 (p0) cc_final: 0.7747 (p0) REVERT: B 633 HIS cc_start: 0.8105 (t-90) cc_final: 0.7799 (t-90) REVERT: B 656 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7377 (mt-10) REVERT: C 301 ASN cc_start: 0.5365 (OUTLIER) cc_final: 0.4775 (t0) REVERT: C 398 MET cc_start: 0.2041 (mmm) cc_final: 0.1536 (ptm) REVERT: C 429 ASN cc_start: 0.1869 (OUTLIER) cc_final: 0.1209 (m-40) REVERT: C 530 ASN cc_start: 0.7057 (m-40) cc_final: 0.6825 (m110) REVERT: C 654 GLN cc_start: 0.7111 (pt0) cc_final: 0.6206 (mm110) outliers start: 54 outliers final: 28 residues processed: 305 average time/residue: 0.7059 time to fit residues: 238.5436 Evaluate side-chains 278 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 243 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 571 ARG Chi-restraints excluded: chain B residue 687 ARG Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 364 ASN Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 429 ASN Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain C residue 684 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 147 optimal weight: 4.9990 chunk 145 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 153 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 211 optimal weight: 0.1980 chunk 207 optimal weight: 2.9990 chunk 61 optimal weight: 0.0870 chunk 180 optimal weight: 20.0000 chunk 2 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 overall best weight: 2.4564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 670 ASN A 691 ASN B 186 GLN B 629 ASN C 13 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.165416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.125727 restraints weight = 19792.744| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.49 r_work: 0.3077 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 18935 Z= 0.169 Angle : 0.528 8.822 25747 Z= 0.280 Chirality : 0.042 0.195 2867 Planarity : 0.004 0.044 3153 Dihedral : 11.650 88.748 3096 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.94 % Allowed : 21.33 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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 (0.18), residues: 2171 helix: 1.29 (0.17), residues: 978 sheet: -0.23 (0.36), residues: 203 loop : -1.23 (0.18), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 104 TYR 0.025 0.002 TYR B 557 PHE 0.017 0.002 PHE A 211 TRP 0.015 0.002 TRP B 438 HIS 0.003 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00389 (18935) covalent geometry : angle 0.52771 (25747) hydrogen bonds : bond 0.04350 ( 858) hydrogen bonds : angle 4.17442 ( 2358) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 247 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4184 (OUTLIER) cc_final: 0.3688 (mmt) REVERT: A 42 MET cc_start: 0.7317 (tpp) cc_final: 0.6568 (tpt) REVERT: A 43 GLU cc_start: 0.7431 (tm-30) cc_final: 0.6826 (tm-30) REVERT: A 100 ASN cc_start: 0.6620 (m-40) cc_final: 0.5992 (m-40) REVERT: A 124 ARG cc_start: 0.6179 (OUTLIER) cc_final: 0.5447 (mtt180) REVERT: A 125 ARG cc_start: 0.5933 (mmt90) cc_final: 0.5531 (ppt-90) REVERT: A 187 LEU cc_start: 0.6950 (OUTLIER) cc_final: 0.6671 (pp) REVERT: A 192 ARG cc_start: 0.6493 (OUTLIER) cc_final: 0.6166 (ptm-80) REVERT: A 321 THR cc_start: 0.9020 (p) cc_final: 0.8702 (p) REVERT: A 492 ARG cc_start: 0.8327 (ttm-80) cc_final: 0.7997 (ttp-170) REVERT: B 60 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.7788 (mp0) REVERT: B 120 ASP cc_start: 0.8478 (p0) cc_final: 0.8235 (p0) REVERT: B 171 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.8796 (mp) REVERT: B 189 LYS cc_start: 0.7981 (tttt) cc_final: 0.7721 (ttpp) REVERT: B 209 ARG cc_start: 0.7660 (mtm-85) cc_final: 0.7164 (mpt180) REVERT: B 296 GLU cc_start: 0.7945 (pt0) cc_final: 0.7546 (pt0) REVERT: B 384 ASP cc_start: 0.8459 (m-30) cc_final: 0.8240 (m-30) REVERT: B 571 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7430 (mmp80) REVERT: B 619 ASP cc_start: 0.8037 (p0) cc_final: 0.7722 (p0) REVERT: B 633 HIS cc_start: 0.8166 (t-90) cc_final: 0.7828 (t-90) REVERT: B 656 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7471 (mt-10) REVERT: C 301 ASN cc_start: 0.5342 (OUTLIER) cc_final: 0.4761 (t0) REVERT: C 429 ASN cc_start: 0.1906 (OUTLIER) cc_final: 0.1243 (m-40) REVERT: C 517 GLU cc_start: 0.6388 (OUTLIER) cc_final: 0.5673 (mt-10) REVERT: C 654 GLN cc_start: 0.7187 (pt0) cc_final: 0.6245 (mm110) outliers start: 57 outliers final: 32 residues processed: 289 average time/residue: 0.7618 time to fit residues: 243.3970 Evaluate side-chains 280 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 238 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 571 ARG Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 687 ARG Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 364 ASN Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 429 ASN Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain C residue 517 GLU Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain C residue 684 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 146 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 202 optimal weight: 0.9980 chunk 187 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 150 optimal weight: 10.0000 chunk 113 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 670 ASN B 629 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.166865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.127039 restraints weight = 19758.637| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.49 r_work: 0.3105 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18935 Z= 0.120 Angle : 0.495 8.488 25747 Z= 0.263 Chirality : 0.040 0.193 2867 Planarity : 0.004 0.043 3153 Dihedral : 11.586 88.572 3096 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.32 % Allowed : 22.21 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.18), residues: 2171 helix: 1.36 (0.17), residues: 983 sheet: -0.20 (0.36), residues: 203 loop : -1.18 (0.18), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 104 TYR 0.024 0.001 TYR B 557 PHE 0.014 0.001 PHE A 211 TRP 0.017 0.001 TRP C 49 HIS 0.005 0.001 HIS A 52 Details of bonding type rmsd covalent geometry : bond 0.00269 (18935) covalent geometry : angle 0.49520 (25747) hydrogen bonds : bond 0.03874 ( 858) hydrogen bonds : angle 4.11746 ( 2358) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 241 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4257 (OUTLIER) cc_final: 0.3641 (mmt) REVERT: A 42 MET cc_start: 0.7278 (tpp) cc_final: 0.6596 (tpt) REVERT: A 43 GLU cc_start: 0.7376 (tm-30) cc_final: 0.6854 (tm-30) REVERT: A 100 ASN cc_start: 0.6564 (m-40) cc_final: 0.5963 (m-40) REVERT: A 124 ARG cc_start: 0.6141 (OUTLIER) cc_final: 0.5412 (mtt180) REVERT: A 125 ARG cc_start: 0.6000 (mmt90) cc_final: 0.5545 (ppt-90) REVERT: A 187 LEU cc_start: 0.6906 (OUTLIER) cc_final: 0.6624 (pp) REVERT: A 192 ARG cc_start: 0.6508 (OUTLIER) cc_final: 0.6178 (ptm-80) REVERT: A 321 THR cc_start: 0.8975 (p) cc_final: 0.8699 (p) REVERT: A 492 ARG cc_start: 0.8372 (ttm-80) cc_final: 0.8039 (ttp-170) REVERT: B 60 GLU cc_start: 0.8901 (OUTLIER) cc_final: 0.7800 (mp0) REVERT: B 120 ASP cc_start: 0.8462 (p0) cc_final: 0.8222 (p0) REVERT: B 171 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.8785 (mp) REVERT: B 189 LYS cc_start: 0.7986 (tttt) cc_final: 0.7731 (ttpp) REVERT: B 209 ARG cc_start: 0.7656 (mtm-85) cc_final: 0.7137 (mpt180) REVERT: B 296 GLU cc_start: 0.7948 (pt0) cc_final: 0.7571 (pt0) REVERT: B 384 ASP cc_start: 0.8448 (m-30) cc_final: 0.8233 (m-30) REVERT: B 571 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7358 (mmp80) REVERT: B 619 ASP cc_start: 0.8005 (p0) cc_final: 0.7718 (p0) REVERT: B 633 HIS cc_start: 0.8129 (t-90) cc_final: 0.7805 (t-90) REVERT: B 656 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7433 (mt-10) REVERT: B 730 LEU cc_start: 0.8664 (tp) cc_final: 0.8451 (tt) REVERT: C 398 MET cc_start: 0.2268 (mmm) cc_final: 0.1659 (ptm) REVERT: C 429 ASN cc_start: 0.1901 (OUTLIER) cc_final: 0.1252 (m-40) REVERT: C 517 GLU cc_start: 0.6349 (OUTLIER) cc_final: 0.5632 (mt-10) REVERT: C 654 GLN cc_start: 0.7147 (pt0) cc_final: 0.6221 (mm110) outliers start: 45 outliers final: 29 residues processed: 274 average time/residue: 0.8092 time to fit residues: 244.2967 Evaluate side-chains 274 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 236 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 571 ARG Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 687 ARG Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 364 ASN Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 429 ASN Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain C residue 517 GLU Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain C residue 684 SER Chi-restraints excluded: chain C residue 731 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 93 optimal weight: 3.9990 chunk 205 optimal weight: 9.9990 chunk 37 optimal weight: 0.8980 chunk 218 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 187 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 69 optimal weight: 0.7980 chunk 216 optimal weight: 8.9990 chunk 18 optimal weight: 9.9990 chunk 182 optimal weight: 30.0000 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 670 ASN B 629 ASN C 348 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.164390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.124544 restraints weight = 19947.452| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.50 r_work: 0.3048 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 18935 Z= 0.204 Angle : 0.564 8.543 25747 Z= 0.299 Chirality : 0.043 0.207 2867 Planarity : 0.004 0.044 3153 Dihedral : 11.709 89.244 3095 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.41 % Favored : 96.55 % Rotamer: Outliers : 2.79 % Allowed : 22.06 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.18), residues: 2171 helix: 1.13 (0.17), residues: 989 sheet: -0.25 (0.36), residues: 203 loop : -1.28 (0.18), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 734 TYR 0.026 0.002 TYR B 557 PHE 0.019 0.002 PHE A 211 TRP 0.016 0.002 TRP B 438 HIS 0.003 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00472 (18935) covalent geometry : angle 0.56367 (25747) hydrogen bonds : bond 0.04715 ( 858) hydrogen bonds : angle 4.26474 ( 2358) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8188.25 seconds wall clock time: 139 minutes 59.58 seconds (8399.58 seconds total)