Starting phenix.real_space_refine on Sat Aug 23 05:44:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w9b_37363/08_2025/8w9b_37363_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w9b_37363/08_2025/8w9b_37363.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8w9b_37363/08_2025/8w9b_37363_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w9b_37363/08_2025/8w9b_37363_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8w9b_37363/08_2025/8w9b_37363.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w9b_37363/08_2025/8w9b_37363.map" } resolution = 3.0 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 72 5.16 5 C 6526 2.51 5 N 1766 2.21 5 O 1880 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10245 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 966, 7886 Classifications: {'peptide': 966} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 920} Chain breaks: 5 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 2330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2330 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 271} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'UJ3': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.25, per 1000 atoms: 0.22 Number of scatterers: 10245 At special positions: 0 Unit cell: (88.8, 123.58, 119.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 F 1 9.00 O 1880 8.00 N 1766 7.00 C 6526 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: 0.75 Conformation dependent library (CDL) restraints added in 332.6 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2380 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 12 sheets defined 42.9% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 41 through 47 Processing helix chain 'A' and resid 48 through 53 Processing helix chain 'A' and resid 54 through 56 No H-bonds generated for 'chain 'A' and resid 54 through 56' Processing helix chain 'A' and resid 89 through 93 removed outlier: 3.820A pdb=" N ARG A 93 " --> pdb=" O CYS A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 121 removed outlier: 3.795A pdb=" N ARG A 115 " --> pdb=" O LYS A 111 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY A 118 " --> pdb=" O ASN A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 130 Processing helix chain 'A' and resid 133 through 143 removed outlier: 3.624A pdb=" N GLN A 137 " --> pdb=" O ASP A 133 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP A 138 " --> pdb=" O PRO A 134 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE A 139 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ARG A 141 " --> pdb=" O GLN A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 150 removed outlier: 3.598A pdb=" N ALA A 150 " --> pdb=" O VAL A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 167 removed outlier: 3.524A pdb=" N TYR A 165 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL A 166 " --> pdb=" O ARG A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 183 Processing helix chain 'A' and resid 216 through 229 removed outlier: 4.002A pdb=" N ILE A 221 " --> pdb=" O PRO A 217 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE A 225 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ARG A 226 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 270 removed outlier: 3.613A pdb=" N TYR A 270 " --> pdb=" O LEU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 280 removed outlier: 4.059A pdb=" N MET A 278 " --> pdb=" O ARG A 274 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 295 Processing helix chain 'A' and resid 305 through 309 removed outlier: 3.755A pdb=" N ARG A 309 " --> pdb=" O SER A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 330 removed outlier: 3.626A pdb=" N VAL A 329 " --> pdb=" O SER A 326 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE A 330 " --> pdb=" O LEU A 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 326 through 330' Processing helix chain 'A' and resid 392 through 396 Processing helix chain 'A' and resid 528 through 536 removed outlier: 3.507A pdb=" N LYS A 532 " --> pdb=" O LYS A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 554 removed outlier: 3.544A pdb=" N ASP A 549 " --> pdb=" O GLU A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 563 Proline residue: A 562 - end of helix Processing helix chain 'A' and resid 564 through 569 Processing helix chain 'A' and resid 578 through 588 removed outlier: 3.505A pdb=" N GLN A 582 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N CYS A 585 " --> pdb=" O ALA A 581 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 586 " --> pdb=" O GLN A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 603 removed outlier: 3.885A pdb=" N LEU A 602 " --> pdb=" O MET A 599 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP A 603 " --> pdb=" O GLU A 600 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 599 through 603' Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 624 through 631 Processing helix chain 'A' and resid 647 through 658 removed outlier: 3.787A pdb=" N ARG A 651 " --> pdb=" O ASN A 647 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE A 652 " --> pdb=" O LEU A 648 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS A 655 " --> pdb=" O ARG A 651 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA A 657 " --> pdb=" O LEU A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 673 removed outlier: 3.739A pdb=" N PHE A 666 " --> pdb=" O ARG A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 692 removed outlier: 3.654A pdb=" N SER A 690 " --> pdb=" O LEU A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 722 removed outlier: 3.559A pdb=" N ALA A 708 " --> pdb=" O ARG A 704 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 719 " --> pdb=" O LEU A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 740 removed outlier: 3.760A pdb=" N GLN A 731 " --> pdb=" O THR A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 748 removed outlier: 3.695A pdb=" N ALA A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU A 748 " --> pdb=" O PHE A 744 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 743 through 748' Processing helix chain 'A' and resid 807 through 828 removed outlier: 3.613A pdb=" N MET A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN A 815 " --> pdb=" O MET A 811 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN A 822 " --> pdb=" O ARG A 818 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN A 826 " --> pdb=" O ASN A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 864 removed outlier: 4.197A pdb=" N GLY A 864 " --> pdb=" O ILE A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 884 Processing helix chain 'A' and resid 894 through 899 Processing helix chain 'A' and resid 917 through 919 No H-bonds generated for 'chain 'A' and resid 917 through 919' Processing helix chain 'A' and resid 957 through 965 removed outlier: 3.700A pdb=" N VAL A 963 " --> pdb=" O ASP A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 979 removed outlier: 3.644A pdb=" N ARG A 979 " --> pdb=" O GLU A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 991 removed outlier: 3.564A pdb=" N LYS A 986 " --> pdb=" O GLU A 982 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 987 " --> pdb=" O MET A 983 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA A 990 " --> pdb=" O LYS A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1003 removed outlier: 3.764A pdb=" N PHE A 998 " --> pdb=" O HIS A 994 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A1001 " --> pdb=" O LEU A 997 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N PHE A1002 " --> pdb=" O PHE A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1009 removed outlier: 3.598A pdb=" N SER A1008 " --> pdb=" O MET A1005 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLY A1009 " --> pdb=" O LEU A1006 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1005 through 1009' Processing helix chain 'A' and resid 1015 through 1019 Processing helix chain 'A' and resid 1021 through 1026 Processing helix chain 'A' and resid 1031 through 1048 removed outlier: 3.556A pdb=" N GLU A1037 " --> pdb=" O GLN A1033 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N HIS A1048 " --> pdb=" O ASN A1044 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 344 removed outlier: 3.534A pdb=" N ASN B 344 " --> pdb=" O ARG B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 409 removed outlier: 3.604A pdb=" N TYR B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 416 Processing helix chain 'B' and resid 430 through 435 removed outlier: 3.641A pdb=" N ASP B 434 " --> pdb=" O LYS B 430 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN B 435 " --> pdb=" O TYR B 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 430 through 435' Processing helix chain 'B' and resid 441 through 446 removed outlier: 3.537A pdb=" N VAL B 445 " --> pdb=" O ASN B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 465 removed outlier: 4.075A pdb=" N TYR B 452 " --> pdb=" O LYS B 448 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR B 454 " --> pdb=" O HIS B 450 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLN B 455 " --> pdb=" O GLU B 451 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE B 456 " --> pdb=" O TYR B 452 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG B 461 " --> pdb=" O GLN B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 506 removed outlier: 3.720A pdb=" N GLN B 478 " --> pdb=" O SER B 474 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N MET B 479 " --> pdb=" O GLN B 475 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR B 482 " --> pdb=" O GLN B 478 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU B 485 " --> pdb=" O ARG B 481 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU B 489 " --> pdb=" O GLU B 485 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS B 492 " --> pdb=" O ASN B 488 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU B 496 " --> pdb=" O LYS B 492 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLN B 497 " --> pdb=" O ILE B 493 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN B 499 " --> pdb=" O GLU B 495 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR B 500 " --> pdb=" O GLU B 496 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG B 503 " --> pdb=" O GLN B 499 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR B 504 " --> pdb=" O THR B 500 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS B 506 " --> pdb=" O GLU B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 524 removed outlier: 3.511A pdb=" N GLN B 522 " --> pdb=" O GLU B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 565 removed outlier: 3.814A pdb=" N SER B 536 " --> pdb=" O LYS B 532 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU B 537 " --> pdb=" O SER B 533 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE B 539 " --> pdb=" O ILE B 535 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER B 541 " --> pdb=" O GLU B 537 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG B 544 " --> pdb=" O ASP B 540 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLU B 547 " --> pdb=" O ARG B 543 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ASP B 548 " --> pdb=" O ARG B 544 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU B 555 " --> pdb=" O LYS B 551 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG B 557 " --> pdb=" O ALA B 553 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET B 563 " --> pdb=" O ILE B 559 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASN B 564 " --> pdb=" O ASP B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 577 removed outlier: 3.691A pdb=" N LEU B 573 " --> pdb=" O ASP B 569 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ARG B 574 " --> pdb=" O LEU B 570 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS B 575 " --> pdb=" O ILE B 571 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 25 Processing sheet with id=AA2, first strand: chain 'A' and resid 70 through 73 removed outlier: 4.297A pdb=" N PHE A 70 " --> pdb=" O PHE A 82 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 209 through 211 removed outlier: 8.355A pdb=" N LEU A 285 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL A 193 " --> pdb=" O LEU A 285 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 259 through 261 removed outlier: 4.081A pdb=" N GLU A 259 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE A 261 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LEU A 252 " --> pdb=" O PHE A 261 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 325 Processing sheet with id=AA6, first strand: chain 'A' and resid 382 through 389 removed outlier: 6.820A pdb=" N TRP A 383 " --> pdb=" O CYS A 340 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N CYS A 340 " --> pdb=" O TRP A 383 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU A 334 " --> pdb=" O TYR A 389 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU A 476 " --> pdb=" O LYS A 337 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N GLU A 474 " --> pdb=" O LEU A 339 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET A 441 " --> pdb=" O LEU A 475 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 376 through 377 removed outlier: 3.926A pdb=" N LYS A 353 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU A 402 " --> pdb=" O ASN A 426 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASN A 426 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N LEU A 404 " --> pdb=" O TRP A 424 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N TRP A 424 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE A 406 " --> pdb=" O LEU A 422 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 3.841A pdb=" N GLU A 365 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 770 through 771 removed outlier: 3.505A pdb=" N ARG A 770 " --> pdb=" O TRP A 780 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN A 797 " --> pdb=" O TRP A 783 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 855 through 856 Processing sheet with id=AB2, first strand: chain 'B' and resid 334 through 336 removed outlier: 4.301A pdb=" N THR B 354 " --> pdb=" O ARG B 373 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU B 356 " --> pdb=" O THR B 371 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASN B 377 " --> pdb=" O LYS B 374 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 334 through 336 294 hydrogen bonds defined for protein. 807 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.59 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1717 1.31 - 1.43: 2708 1.43 - 1.56: 5923 1.56 - 1.68: 0 1.68 - 1.81: 112 Bond restraints: 10460 Sorted by residual: bond pdb=" C12 UJ3 A1101 " pdb=" N14 UJ3 A1101 " ideal model delta sigma weight residual 1.354 1.447 -0.093 2.00e-02 2.50e+03 2.14e+01 bond pdb=" C06 UJ3 A1101 " pdb=" N05 UJ3 A1101 " ideal model delta sigma weight residual 1.356 1.446 -0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" C06 UJ3 A1101 " pdb=" N07 UJ3 A1101 " ideal model delta sigma weight residual 1.376 1.442 -0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" C11 UJ3 A1101 " pdb=" C12 UJ3 A1101 " ideal model delta sigma weight residual 1.476 1.541 -0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" N LEU A 911 " pdb=" CA LEU A 911 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.16e-02 7.43e+03 8.48e+00 ... (remaining 10455 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.55: 14045 3.55 - 7.09: 62 7.09 - 10.64: 2 10.64 - 14.18: 2 14.18 - 17.73: 1 Bond angle restraints: 14112 Sorted by residual: angle pdb=" C ARG A 740 " pdb=" N ARG A 741 " pdb=" CA ARG A 741 " ideal model delta sigma weight residual 120.65 131.45 -10.80 1.36e+00 5.41e-01 6.30e+01 angle pdb=" C GLU A 176 " pdb=" N LEU A 177 " pdb=" CA LEU A 177 " ideal model delta sigma weight residual 120.97 138.70 -17.73 2.84e+00 1.24e-01 3.90e+01 angle pdb=" N ILE A1019 " pdb=" CA ILE A1019 " pdb=" C ILE A1019 " ideal model delta sigma weight residual 111.91 106.78 5.13 8.90e-01 1.26e+00 3.33e+01 angle pdb=" N VAL A 636 " pdb=" CA VAL A 636 " pdb=" C VAL A 636 " ideal model delta sigma weight residual 113.43 107.71 5.72 1.09e+00 8.42e-01 2.75e+01 angle pdb=" N ILE A 894 " pdb=" CA ILE A 894 " pdb=" C ILE A 894 " ideal model delta sigma weight residual 112.96 108.24 4.72 1.00e+00 1.00e+00 2.23e+01 ... (remaining 14107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.59: 6043 15.59 - 31.19: 259 31.19 - 46.78: 70 46.78 - 62.37: 10 62.37 - 77.96: 10 Dihedral angle restraints: 6392 sinusoidal: 2726 harmonic: 3666 Sorted by residual: dihedral pdb=" CA VAL A 923 " pdb=" C VAL A 923 " pdb=" N LYS A 924 " pdb=" CA LYS A 924 " ideal model delta harmonic sigma weight residual -180.00 -155.74 -24.26 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA GLN B 591 " pdb=" C GLN B 591 " pdb=" N LYS B 592 " pdb=" CA LYS B 592 " ideal model delta harmonic sigma weight residual 180.00 157.26 22.74 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA PHE A 95 " pdb=" C PHE A 95 " pdb=" N GLN A 96 " pdb=" CA GLN A 96 " ideal model delta harmonic sigma weight residual 180.00 158.65 21.35 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 6389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 947 0.037 - 0.073: 426 0.073 - 0.110: 118 0.110 - 0.147: 31 0.147 - 0.184: 5 Chirality restraints: 1527 Sorted by residual: chirality pdb=" CA ILE A 913 " pdb=" N ILE A 913 " pdb=" C ILE A 913 " pdb=" CB ILE A 913 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.43e-01 chirality pdb=" CA ASP A 258 " pdb=" N ASP A 258 " pdb=" C ASP A 258 " pdb=" CB ASP A 258 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.94e-01 chirality pdb=" CA ILE A 932 " pdb=" N ILE A 932 " pdb=" C ILE A 932 " pdb=" CB ILE A 932 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.28e-01 ... (remaining 1524 not shown) Planarity restraints: 1811 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 937 " -0.014 2.00e-02 2.50e+03 2.00e-02 6.99e+00 pdb=" CG PHE A 937 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE A 937 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE A 937 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE A 937 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 937 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 937 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 96 " -0.033 5.00e-02 4.00e+02 5.05e-02 4.09e+00 pdb=" N PRO A 97 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 97 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 97 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 538 " 0.033 5.00e-02 4.00e+02 5.00e-02 4.01e+00 pdb=" N PRO A 539 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 539 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 539 " 0.028 5.00e-02 4.00e+02 ... (remaining 1808 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 140 2.64 - 3.21: 9658 3.21 - 3.77: 14183 3.77 - 4.34: 21997 4.34 - 4.90: 34432 Nonbonded interactions: 80410 Sorted by model distance: nonbonded pdb=" OD1 ASN B 325 " pdb=" OG SER B 400 " model vdw 2.078 3.040 nonbonded pdb=" O LEU B 347 " pdb=" NH1 ARG B 373 " model vdw 2.193 3.120 nonbonded pdb=" OD1 ASP A 155 " pdb=" OG SER A 158 " model vdw 2.198 3.040 nonbonded pdb=" NH2 ARG A 401 " pdb=" O PRO A 458 " model vdw 2.204 3.120 nonbonded pdb=" OH TYR A 641 " pdb=" N GLY A1007 " model vdw 2.208 3.120 ... (remaining 80405 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: 1.520 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: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.580 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 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 : 0.004 0.093 10460 Z= 0.215 Angle : 0.761 17.731 14112 Z= 0.457 Chirality : 0.045 0.184 1527 Planarity : 0.005 0.051 1811 Dihedral : 10.610 77.962 4012 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 21.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.76 % Favored : 93.16 % Rotamer: Outliers : 0.35 % Allowed : 1.41 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -5.57 (0.18), residues: 1228 helix: -4.54 (0.11), residues: 510 sheet: -3.03 (0.36), residues: 165 loop : -2.89 (0.23), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 992 TYR 0.019 0.002 TYR A 392 PHE 0.045 0.003 PHE A 937 TRP 0.027 0.003 TRP A 880 HIS 0.009 0.002 HIS A 759 Details of bonding type rmsd covalent geometry : bond 0.00431 (10460) covalent geometry : angle 0.76139 (14112) hydrogen bonds : bond 0.33558 ( 293) hydrogen bonds : angle 10.06782 ( 807) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 262 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 ILE cc_start: 0.7572 (tt) cc_final: 0.6937 (tp) REVERT: B 562 ARG cc_start: 0.6108 (mtp180) cc_final: 0.5700 (mtt90) outliers start: 4 outliers final: 0 residues processed: 264 average time/residue: 0.6086 time to fit residues: 170.9140 Evaluate side-chains 145 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.0070 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.0980 chunk 117 optimal weight: 3.9990 overall best weight: 0.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 HIS A 201 ASN A 219 GLN A 370 ASN A 372 ASN A 738 GLN ** A 917 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 385 HIS B 478 GLN ** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.193459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.151041 restraints weight = 11231.913| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 2.01 r_work: 0.3795 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3667 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10460 Z= 0.138 Angle : 0.634 9.598 14112 Z= 0.337 Chirality : 0.045 0.165 1527 Planarity : 0.005 0.051 1811 Dihedral : 5.648 36.782 1369 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.80 % Favored : 95.11 % Rotamer: Outliers : 2.29 % Allowed : 11.36 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -4.02 (0.20), residues: 1228 helix: -3.06 (0.17), residues: 524 sheet: -2.33 (0.39), residues: 156 loop : -2.18 (0.24), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 979 TYR 0.018 0.001 TYR A 392 PHE 0.025 0.002 PHE A 937 TRP 0.015 0.001 TRP A 780 HIS 0.015 0.001 HIS A 917 Details of bonding type rmsd covalent geometry : bond 0.00294 (10460) covalent geometry : angle 0.63352 (14112) hydrogen bonds : bond 0.06592 ( 293) hydrogen bonds : angle 5.41650 ( 807) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 168 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.6967 (mt-10) cc_final: 0.6373 (mm-30) REVERT: A 187 LYS cc_start: 0.7316 (mtpm) cc_final: 0.7041 (tptp) REVERT: A 211 ILE cc_start: 0.6026 (OUTLIER) cc_final: 0.4988 (pp) REVERT: A 384 ASN cc_start: 0.7975 (t0) cc_final: 0.7734 (t160) REVERT: A 438 SER cc_start: 0.8666 (p) cc_final: 0.8374 (p) REVERT: A 745 MET cc_start: 0.8522 (tpp) cc_final: 0.8185 (mpp) REVERT: A 852 ARG cc_start: 0.5807 (OUTLIER) cc_final: 0.5474 (mtt-85) REVERT: A 929 LEU cc_start: 0.5910 (OUTLIER) cc_final: 0.5638 (tm) REVERT: A 975 ARG cc_start: 0.7483 (tmm160) cc_final: 0.6900 (tmm160) REVERT: A 977 PHE cc_start: 0.7574 (OUTLIER) cc_final: 0.6842 (p90) REVERT: B 326 MET cc_start: 0.6363 (mpm) cc_final: 0.6141 (mmm) REVERT: B 552 GLN cc_start: 0.7469 (OUTLIER) cc_final: 0.6907 (mt0) REVERT: B 562 ARG cc_start: 0.5974 (mtp180) cc_final: 0.5411 (mtt-85) outliers start: 26 outliers final: 7 residues processed: 181 average time/residue: 0.5954 time to fit residues: 114.8356 Evaluate side-chains 146 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 852 ARG Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 977 PHE Chi-restraints excluded: chain A residue 1014 GLN Chi-restraints excluded: chain A residue 1037 GLU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 552 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 77 optimal weight: 0.4980 chunk 103 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 44 optimal weight: 8.9990 chunk 39 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 112 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 overall best weight: 3.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 ASN A 825 GLN A 917 HIS A 920 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.186903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.143684 restraints weight = 11359.252| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.28 r_work: 0.3520 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 10460 Z= 0.235 Angle : 0.721 8.760 14112 Z= 0.379 Chirality : 0.050 0.184 1527 Planarity : 0.006 0.058 1811 Dihedral : 6.003 40.230 1369 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.25 % Favored : 92.67 % Rotamer: Outliers : 3.70 % Allowed : 13.20 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -3.66 (0.21), residues: 1228 helix: -2.67 (0.18), residues: 531 sheet: -1.76 (0.41), residues: 150 loop : -2.22 (0.23), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 704 TYR 0.018 0.002 TYR A 392 PHE 0.031 0.003 PHE A 667 TRP 0.018 0.002 TRP A 590 HIS 0.013 0.002 HIS A 759 Details of bonding type rmsd covalent geometry : bond 0.00563 (10460) covalent geometry : angle 0.72120 (14112) hydrogen bonds : bond 0.06470 ( 293) hydrogen bonds : angle 5.14067 ( 807) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 140 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 LYS cc_start: 0.7353 (mtpm) cc_final: 0.7025 (tptp) REVERT: A 211 ILE cc_start: 0.6134 (OUTLIER) cc_final: 0.5217 (pp) REVERT: A 218 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7665 (tm-30) REVERT: A 384 ASN cc_start: 0.8127 (t0) cc_final: 0.7902 (t160) REVERT: A 453 GLU cc_start: 0.7501 (mt-10) cc_final: 0.7268 (mm-30) REVERT: A 474 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7460 (mm-30) REVERT: A 745 MET cc_start: 0.8784 (tpp) cc_final: 0.8298 (mpp) REVERT: A 779 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8596 (mp) REVERT: A 852 ARG cc_start: 0.5896 (OUTLIER) cc_final: 0.5590 (mtt-85) REVERT: A 975 ARG cc_start: 0.7422 (tmm160) cc_final: 0.6834 (tmm160) REVERT: A 977 PHE cc_start: 0.7826 (OUTLIER) cc_final: 0.6796 (p90) REVERT: B 326 MET cc_start: 0.6403 (mpm) cc_final: 0.6142 (mmm) REVERT: B 562 ARG cc_start: 0.6078 (mtp180) cc_final: 0.5453 (mtt-85) outliers start: 42 outliers final: 16 residues processed: 170 average time/residue: 0.5674 time to fit residues: 103.2995 Evaluate side-chains 148 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 852 ARG Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 977 PHE Chi-restraints excluded: chain A residue 1014 GLN Chi-restraints excluded: chain A residue 1037 GLU Chi-restraints excluded: chain B residue 422 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 1 optimal weight: 10.0000 chunk 74 optimal weight: 0.9990 chunk 114 optimal weight: 8.9990 chunk 57 optimal weight: 0.9990 chunk 30 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 78 optimal weight: 0.0060 chunk 58 optimal weight: 0.6980 chunk 110 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 ASN A 917 HIS A 920 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.193093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.149704 restraints weight = 11357.415| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 2.16 r_work: 0.3783 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3655 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10460 Z= 0.110 Angle : 0.546 7.802 14112 Z= 0.290 Chirality : 0.043 0.167 1527 Planarity : 0.004 0.045 1811 Dihedral : 5.141 32.621 1369 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.56 % Favored : 95.36 % Rotamer: Outliers : 2.64 % Allowed : 14.26 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -2.82 (0.22), residues: 1228 helix: -1.86 (0.20), residues: 525 sheet: -1.60 (0.39), residues: 157 loop : -1.82 (0.25), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 777 TYR 0.014 0.001 TYR A 392 PHE 0.026 0.002 PHE A 734 TRP 0.011 0.001 TRP A 669 HIS 0.006 0.001 HIS A 450 Details of bonding type rmsd covalent geometry : bond 0.00232 (10460) covalent geometry : angle 0.54605 (14112) hydrogen bonds : bond 0.04689 ( 293) hydrogen bonds : angle 4.45905 ( 807) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.6985 (mt-10) cc_final: 0.6460 (mm-30) REVERT: A 83 PHE cc_start: 0.6703 (m-10) cc_final: 0.6367 (m-10) REVERT: A 187 LYS cc_start: 0.7367 (mtpm) cc_final: 0.7097 (tptp) REVERT: A 211 ILE cc_start: 0.6075 (OUTLIER) cc_final: 0.5164 (pp) REVERT: A 218 GLU cc_start: 0.7656 (tm-30) cc_final: 0.7456 (tm-30) REVERT: A 304 MET cc_start: 0.7383 (mpt) cc_final: 0.6955 (mpt) REVERT: A 384 ASN cc_start: 0.7907 (t0) cc_final: 0.7699 (t160) REVERT: A 745 MET cc_start: 0.8423 (tpp) cc_final: 0.8131 (mpp) REVERT: A 779 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8747 (mt) REVERT: A 787 ASP cc_start: 0.7639 (OUTLIER) cc_final: 0.7427 (t0) REVERT: A 852 ARG cc_start: 0.5938 (OUTLIER) cc_final: 0.5579 (mtt-85) REVERT: A 929 LEU cc_start: 0.6070 (OUTLIER) cc_final: 0.5826 (tm) REVERT: A 975 ARG cc_start: 0.7372 (tmm160) cc_final: 0.6996 (tmm160) REVERT: A 977 PHE cc_start: 0.7540 (OUTLIER) cc_final: 0.6498 (p90) REVERT: A 1005 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7555 (mtm) REVERT: B 326 MET cc_start: 0.6451 (mpm) cc_final: 0.6155 (mmm) REVERT: B 472 ARG cc_start: 0.6776 (tmm-80) cc_final: 0.6164 (tpt170) REVERT: B 479 MET cc_start: 0.7846 (mtm) cc_final: 0.6914 (mmt) REVERT: B 562 ARG cc_start: 0.5884 (mtp180) cc_final: 0.5391 (mtt-85) outliers start: 30 outliers final: 12 residues processed: 162 average time/residue: 0.5827 time to fit residues: 100.6992 Evaluate side-chains 138 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 700 LYS Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 787 ASP Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 852 ARG Chi-restraints excluded: chain A residue 920 ASN Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 977 PHE Chi-restraints excluded: chain A residue 1005 MET Chi-restraints excluded: chain A residue 1014 GLN Chi-restraints excluded: chain A residue 1037 GLU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 552 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 26 optimal weight: 0.8980 chunk 111 optimal weight: 10.0000 chunk 109 optimal weight: 0.9990 chunk 105 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 87 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 113 optimal weight: 9.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.191668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.148154 restraints weight = 11292.962| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 2.32 r_work: 0.3582 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3452 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10460 Z= 0.129 Angle : 0.559 7.841 14112 Z= 0.295 Chirality : 0.044 0.168 1527 Planarity : 0.004 0.043 1811 Dihedral : 5.105 34.775 1369 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.13 % Favored : 94.79 % Rotamer: Outliers : 3.08 % Allowed : 15.23 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -2.49 (0.22), residues: 1228 helix: -1.52 (0.21), residues: 527 sheet: -1.39 (0.39), residues: 157 loop : -1.73 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 777 TYR 0.012 0.001 TYR A 392 PHE 0.034 0.002 PHE B 355 TRP 0.010 0.001 TRP A 552 HIS 0.005 0.001 HIS A 450 Details of bonding type rmsd covalent geometry : bond 0.00292 (10460) covalent geometry : angle 0.55902 (14112) hydrogen bonds : bond 0.04597 ( 293) hydrogen bonds : angle 4.32690 ( 807) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 127 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.7074 (mt-10) cc_final: 0.6506 (mm-30) REVERT: A 83 PHE cc_start: 0.6756 (m-10) cc_final: 0.6553 (m-10) REVERT: A 187 LYS cc_start: 0.7312 (mtpm) cc_final: 0.7048 (tptp) REVERT: A 211 ILE cc_start: 0.6088 (OUTLIER) cc_final: 0.5214 (pp) REVERT: A 218 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7466 (tm-30) REVERT: A 304 MET cc_start: 0.7485 (mpt) cc_final: 0.7031 (mpt) REVERT: A 745 MET cc_start: 0.8558 (tpp) cc_final: 0.8206 (mpp) REVERT: A 779 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8784 (mt) REVERT: A 787 ASP cc_start: 0.7711 (OUTLIER) cc_final: 0.7479 (t0) REVERT: A 811 MET cc_start: 0.8187 (mtp) cc_final: 0.7911 (mtp) REVERT: A 852 ARG cc_start: 0.5956 (OUTLIER) cc_final: 0.5605 (mtt-85) REVERT: A 975 ARG cc_start: 0.7419 (tmm160) cc_final: 0.6935 (tmm160) REVERT: A 977 PHE cc_start: 0.7586 (OUTLIER) cc_final: 0.6693 (p90) REVERT: B 326 MET cc_start: 0.6483 (mpm) cc_final: 0.6190 (mmm) REVERT: B 389 LYS cc_start: 0.6481 (OUTLIER) cc_final: 0.5828 (mmpt) REVERT: B 472 ARG cc_start: 0.6788 (tmm-80) cc_final: 0.6584 (ttm110) REVERT: B 479 MET cc_start: 0.7877 (mtm) cc_final: 0.6837 (mmt) REVERT: B 537 GLU cc_start: 0.6855 (tt0) cc_final: 0.6595 (tt0) REVERT: B 562 ARG cc_start: 0.5933 (mtp180) cc_final: 0.5415 (mtt-85) outliers start: 35 outliers final: 14 residues processed: 153 average time/residue: 0.6297 time to fit residues: 102.9724 Evaluate side-chains 140 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 700 LYS Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 787 ASP Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 852 ARG Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 977 PHE Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1014 GLN Chi-restraints excluded: chain A residue 1037 GLU Chi-restraints excluded: chain B residue 389 LYS Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 552 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 114 optimal weight: 7.9990 chunk 90 optimal weight: 8.9990 chunk 121 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 chunk 79 optimal weight: 9.9990 chunk 44 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN A 825 GLN ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.185580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.142518 restraints weight = 11466.874| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 2.24 r_work: 0.3487 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10460 Z= 0.223 Angle : 0.685 7.773 14112 Z= 0.356 Chirality : 0.049 0.191 1527 Planarity : 0.005 0.047 1811 Dihedral : 5.580 37.883 1369 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.51 % Favored : 93.40 % Rotamer: Outliers : 4.23 % Allowed : 14.79 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -2.65 (0.22), residues: 1228 helix: -1.70 (0.20), residues: 527 sheet: -1.22 (0.40), residues: 150 loop : -1.85 (0.24), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 503 TYR 0.013 0.002 TYR A 392 PHE 0.031 0.003 PHE B 355 TRP 0.015 0.002 TRP A 590 HIS 0.009 0.001 HIS A 759 Details of bonding type rmsd covalent geometry : bond 0.00537 (10460) covalent geometry : angle 0.68469 (14112) hydrogen bonds : bond 0.05396 ( 293) hydrogen bonds : angle 4.63275 ( 807) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 125 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.6929 (mt-10) cc_final: 0.6438 (mm-30) REVERT: A 187 LYS cc_start: 0.7382 (mtpm) cc_final: 0.7071 (tptp) REVERT: A 211 ILE cc_start: 0.6188 (OUTLIER) cc_final: 0.5370 (pp) REVERT: A 718 ILE cc_start: 0.7478 (mp) cc_final: 0.7261 (mm) REVERT: A 745 MET cc_start: 0.8695 (tpp) cc_final: 0.8343 (mpp) REVERT: A 779 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8724 (mt) REVERT: A 852 ARG cc_start: 0.5969 (OUTLIER) cc_final: 0.5703 (mtt-85) REVERT: A 975 ARG cc_start: 0.7355 (tmm160) cc_final: 0.7011 (tmm160) REVERT: A 977 PHE cc_start: 0.7812 (OUTLIER) cc_final: 0.7034 (p90) REVERT: A 1034 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7691 (tm-30) REVERT: B 326 MET cc_start: 0.6502 (mpm) cc_final: 0.6170 (mmm) REVERT: B 389 LYS cc_start: 0.6554 (OUTLIER) cc_final: 0.5848 (mmpt) REVERT: B 426 TYR cc_start: 0.7548 (OUTLIER) cc_final: 0.7228 (m-80) REVERT: B 431 TYR cc_start: 0.6934 (m-10) cc_final: 0.5966 (m-80) REVERT: B 435 GLN cc_start: 0.4486 (pp30) cc_final: 0.4181 (pt0) REVERT: B 472 ARG cc_start: 0.6868 (tmm-80) cc_final: 0.6661 (ttm110) REVERT: B 479 MET cc_start: 0.7847 (mtm) cc_final: 0.6833 (mmt) REVERT: B 537 GLU cc_start: 0.6935 (tt0) cc_final: 0.6683 (tt0) REVERT: B 562 ARG cc_start: 0.6002 (mtp180) cc_final: 0.5447 (mtt-85) outliers start: 48 outliers final: 22 residues processed: 159 average time/residue: 0.5647 time to fit residues: 96.1876 Evaluate side-chains 145 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 700 LYS Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 852 ARG Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 977 PHE Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1014 GLN Chi-restraints excluded: chain A residue 1037 GLU Chi-restraints excluded: chain B residue 389 LYS Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 498 CYS Chi-restraints excluded: chain B residue 552 GLN Chi-restraints excluded: chain B residue 571 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 90 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 118 optimal weight: 8.9990 chunk 80 optimal weight: 7.9990 chunk 84 optimal weight: 0.0970 chunk 95 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 14 optimal weight: 7.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.190212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.147482 restraints weight = 11283.999| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 2.23 r_work: 0.3540 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10460 Z= 0.116 Angle : 0.559 7.407 14112 Z= 0.295 Chirality : 0.043 0.180 1527 Planarity : 0.004 0.041 1811 Dihedral : 5.012 31.997 1369 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.13 % Favored : 94.79 % Rotamer: Outliers : 3.17 % Allowed : 16.55 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -2.18 (0.23), residues: 1228 helix: -1.26 (0.21), residues: 527 sheet: -1.13 (0.39), residues: 157 loop : -1.59 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 503 TYR 0.011 0.001 TYR A 392 PHE 0.024 0.002 PHE B 355 TRP 0.011 0.001 TRP A 669 HIS 0.006 0.001 HIS A 450 Details of bonding type rmsd covalent geometry : bond 0.00259 (10460) covalent geometry : angle 0.55926 (14112) hydrogen bonds : bond 0.04297 ( 293) hydrogen bonds : angle 4.21462 ( 807) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 129 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.6955 (mt-10) cc_final: 0.6450 (mm-30) REVERT: A 83 PHE cc_start: 0.6605 (m-10) cc_final: 0.6369 (m-10) REVERT: A 187 LYS cc_start: 0.7284 (mtpm) cc_final: 0.7013 (tptp) REVERT: A 211 ILE cc_start: 0.6147 (OUTLIER) cc_final: 0.5360 (pp) REVERT: A 384 ASN cc_start: 0.7884 (t0) cc_final: 0.7597 (t160) REVERT: A 391 ILE cc_start: 0.8421 (OUTLIER) cc_final: 0.7964 (tp) REVERT: A 779 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8763 (mt) REVERT: A 787 ASP cc_start: 0.7668 (OUTLIER) cc_final: 0.7431 (t0) REVERT: A 852 ARG cc_start: 0.6001 (OUTLIER) cc_final: 0.5739 (mtt-85) REVERT: A 920 ASN cc_start: 0.7597 (OUTLIER) cc_final: 0.7388 (p0) REVERT: A 975 ARG cc_start: 0.7314 (tmm160) cc_final: 0.6989 (tmm160) REVERT: A 977 PHE cc_start: 0.7636 (OUTLIER) cc_final: 0.6874 (p90) REVERT: A 1034 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7745 (tm-30) REVERT: B 326 MET cc_start: 0.6379 (mpm) cc_final: 0.6084 (mmm) REVERT: B 431 TYR cc_start: 0.6945 (m-10) cc_final: 0.5957 (m-80) REVERT: B 435 GLN cc_start: 0.4641 (pp30) cc_final: 0.4323 (pt0) REVERT: B 472 ARG cc_start: 0.6762 (tmm-80) cc_final: 0.6109 (tpt170) REVERT: B 479 MET cc_start: 0.7800 (mtm) cc_final: 0.6788 (mmt) REVERT: B 521 ILE cc_start: 0.8025 (mp) cc_final: 0.7768 (pt) REVERT: B 537 GLU cc_start: 0.6864 (tt0) cc_final: 0.6555 (tt0) REVERT: B 562 ARG cc_start: 0.5854 (mtp180) cc_final: 0.5333 (mtt-85) outliers start: 36 outliers final: 14 residues processed: 155 average time/residue: 0.5189 time to fit residues: 86.2497 Evaluate side-chains 139 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 700 LYS Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 787 ASP Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 852 ARG Chi-restraints excluded: chain A residue 920 ASN Chi-restraints excluded: chain A residue 977 PHE Chi-restraints excluded: chain A residue 1014 GLN Chi-restraints excluded: chain A residue 1037 GLU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 552 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 101 optimal weight: 10.0000 chunk 73 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 36 optimal weight: 0.1980 chunk 122 optimal weight: 0.0000 chunk 89 optimal weight: 0.9980 chunk 121 optimal weight: 6.9990 chunk 116 optimal weight: 20.0000 chunk 68 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.192379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.151198 restraints weight = 11220.680| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 2.07 r_work: 0.3583 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 10460 Z= 0.108 Angle : 0.546 7.311 14112 Z= 0.288 Chirality : 0.043 0.163 1527 Planarity : 0.004 0.042 1811 Dihedral : 4.704 30.589 1369 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.05 % Favored : 94.87 % Rotamer: Outliers : 2.20 % Allowed : 17.61 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.71 (0.23), residues: 1228 helix: -0.83 (0.22), residues: 528 sheet: -0.76 (0.40), residues: 151 loop : -1.44 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 503 TYR 0.011 0.001 TYR A 392 PHE 0.022 0.002 PHE A 734 TRP 0.010 0.001 TRP A 669 HIS 0.005 0.001 HIS A 450 Details of bonding type rmsd covalent geometry : bond 0.00239 (10460) covalent geometry : angle 0.54603 (14112) hydrogen bonds : bond 0.03972 ( 293) hydrogen bonds : angle 4.15743 ( 807) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.6959 (mt-10) cc_final: 0.6433 (mm-30) REVERT: A 83 PHE cc_start: 0.6552 (m-10) cc_final: 0.6346 (m-10) REVERT: A 187 LYS cc_start: 0.7230 (mtpm) cc_final: 0.6907 (tptp) REVERT: A 211 ILE cc_start: 0.6125 (OUTLIER) cc_final: 0.5406 (pp) REVERT: A 384 ASN cc_start: 0.7800 (t0) cc_final: 0.7506 (t0) REVERT: A 391 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.7923 (tp) REVERT: A 779 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8726 (mt) REVERT: A 811 MET cc_start: 0.8352 (mtp) cc_final: 0.8074 (mtp) REVERT: A 853 ASN cc_start: 0.6803 (m110) cc_final: 0.6468 (p0) REVERT: A 884 LYS cc_start: 0.7966 (mmmm) cc_final: 0.7402 (mmmt) REVERT: A 920 ASN cc_start: 0.7384 (OUTLIER) cc_final: 0.7184 (p0) REVERT: A 975 ARG cc_start: 0.7343 (tmm160) cc_final: 0.6968 (tmm160) REVERT: A 977 PHE cc_start: 0.7519 (OUTLIER) cc_final: 0.6764 (p90) REVERT: A 1034 GLU cc_start: 0.7991 (tm-30) cc_final: 0.7694 (tm-30) REVERT: B 326 MET cc_start: 0.6408 (mpm) cc_final: 0.6078 (mmm) REVERT: B 382 LYS cc_start: 0.6660 (tptm) cc_final: 0.6363 (tppt) REVERT: B 431 TYR cc_start: 0.6964 (m-10) cc_final: 0.5982 (m-80) REVERT: B 435 GLN cc_start: 0.4615 (pp30) cc_final: 0.4301 (pt0) REVERT: B 479 MET cc_start: 0.7779 (mtm) cc_final: 0.6692 (mmt) REVERT: B 521 ILE cc_start: 0.8085 (mp) cc_final: 0.7832 (pt) REVERT: B 562 ARG cc_start: 0.5763 (mtp180) cc_final: 0.5274 (mtt-85) outliers start: 25 outliers final: 10 residues processed: 152 average time/residue: 0.5225 time to fit residues: 85.4708 Evaluate side-chains 131 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 920 ASN Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 977 PHE Chi-restraints excluded: chain A residue 1014 GLN Chi-restraints excluded: chain A residue 1037 GLU Chi-restraints excluded: chain B residue 571 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 39 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 78 optimal weight: 0.0370 chunk 79 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 83 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 overall best weight: 2.1262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 825 GLN ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 GLN ** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.189175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.147249 restraints weight = 11181.561| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 2.36 r_work: 0.3520 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10460 Z= 0.149 Angle : 0.598 9.798 14112 Z= 0.312 Chirality : 0.045 0.167 1527 Planarity : 0.004 0.038 1811 Dihedral : 4.940 32.925 1369 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.78 % Favored : 94.14 % Rotamer: Outliers : 2.02 % Allowed : 18.57 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.75 (0.23), residues: 1228 helix: -0.90 (0.22), residues: 531 sheet: -0.73 (0.40), residues: 155 loop : -1.43 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 503 TYR 0.012 0.001 TYR A 392 PHE 0.030 0.002 PHE A 937 TRP 0.010 0.001 TRP A 552 HIS 0.005 0.001 HIS A 759 Details of bonding type rmsd covalent geometry : bond 0.00350 (10460) covalent geometry : angle 0.59772 (14112) hydrogen bonds : bond 0.04385 ( 293) hydrogen bonds : angle 4.24259 ( 807) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: A 76 GLU cc_start: 0.7064 (mt-10) cc_final: 0.6548 (mm-30) REVERT: A 83 PHE cc_start: 0.6594 (m-10) cc_final: 0.6354 (m-10) REVERT: A 187 LYS cc_start: 0.7316 (mtpm) cc_final: 0.6901 (tptp) REVERT: A 211 ILE cc_start: 0.6253 (OUTLIER) cc_final: 0.5478 (pp) REVERT: A 384 ASN cc_start: 0.7926 (t0) cc_final: 0.7602 (t0) REVERT: A 391 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.7892 (tp) REVERT: A 745 MET cc_start: 0.8737 (mmm) cc_final: 0.8207 (mpp) REVERT: A 779 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8718 (mt) REVERT: A 920 ASN cc_start: 0.7530 (OUTLIER) cc_final: 0.7296 (p0) REVERT: A 975 ARG cc_start: 0.7403 (tmm160) cc_final: 0.7007 (tmm160) REVERT: A 977 PHE cc_start: 0.7684 (OUTLIER) cc_final: 0.6902 (p90) REVERT: A 1034 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7776 (tm-30) REVERT: B 326 MET cc_start: 0.6434 (mpm) cc_final: 0.6092 (mmm) REVERT: B 431 TYR cc_start: 0.6988 (m-10) cc_final: 0.5978 (m-80) REVERT: B 435 GLN cc_start: 0.4584 (pp30) cc_final: 0.4265 (pt0) REVERT: B 479 MET cc_start: 0.7862 (mtm) cc_final: 0.6821 (mmt) REVERT: B 521 ILE cc_start: 0.8069 (mp) cc_final: 0.7820 (pt) REVERT: B 562 ARG cc_start: 0.5750 (mtp180) cc_final: 0.5221 (mtt-85) outliers start: 23 outliers final: 12 residues processed: 134 average time/residue: 0.5648 time to fit residues: 81.0350 Evaluate side-chains 131 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 920 ASN Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 977 PHE Chi-restraints excluded: chain A residue 1014 GLN Chi-restraints excluded: chain A residue 1037 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 7.9990 chunk 8 optimal weight: 0.0470 chunk 18 optimal weight: 0.0670 chunk 80 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 52 optimal weight: 0.8980 chunk 82 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 overall best weight: 0.7818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.192293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.149769 restraints weight = 11252.366| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 2.28 r_work: 0.3743 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3613 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10460 Z= 0.109 Angle : 0.554 10.068 14112 Z= 0.290 Chirality : 0.043 0.162 1527 Planarity : 0.004 0.035 1811 Dihedral : 4.665 30.405 1369 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.89 % Favored : 95.03 % Rotamer: Outliers : 1.67 % Allowed : 19.19 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.37 (0.23), residues: 1228 helix: -0.51 (0.22), residues: 528 sheet: -0.43 (0.41), residues: 146 loop : -1.34 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 503 TYR 0.011 0.001 TYR A 392 PHE 0.018 0.002 PHE A 937 TRP 0.011 0.001 TRP A 669 HIS 0.005 0.001 HIS A 450 Details of bonding type rmsd covalent geometry : bond 0.00240 (10460) covalent geometry : angle 0.55390 (14112) hydrogen bonds : bond 0.03855 ( 293) hydrogen bonds : angle 4.02580 ( 807) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.405 Fit side-chains REVERT: A 76 GLU cc_start: 0.7018 (mt-10) cc_final: 0.6522 (mm-30) REVERT: A 83 PHE cc_start: 0.6550 (m-10) cc_final: 0.6212 (m-10) REVERT: A 187 LYS cc_start: 0.7290 (mtpm) cc_final: 0.6974 (tptp) REVERT: A 211 ILE cc_start: 0.6185 (OUTLIER) cc_final: 0.5428 (pp) REVERT: A 384 ASN cc_start: 0.7829 (t0) cc_final: 0.7473 (t0) REVERT: A 391 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.7862 (tp) REVERT: A 779 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8715 (mt) REVERT: A 884 LYS cc_start: 0.7967 (mmmm) cc_final: 0.7403 (mmmt) REVERT: A 954 PHE cc_start: 0.7386 (OUTLIER) cc_final: 0.7065 (m-80) REVERT: A 975 ARG cc_start: 0.7326 (tmm160) cc_final: 0.7020 (tmm160) REVERT: A 977 PHE cc_start: 0.7552 (OUTLIER) cc_final: 0.6832 (p90) REVERT: A 1034 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7710 (tm-30) REVERT: B 326 MET cc_start: 0.6432 (mpm) cc_final: 0.6108 (mmm) REVERT: B 431 TYR cc_start: 0.6950 (m-10) cc_final: 0.5990 (m-80) REVERT: B 435 GLN cc_start: 0.4491 (pp30) cc_final: 0.4193 (pt0) REVERT: B 479 MET cc_start: 0.7803 (mtm) cc_final: 0.6710 (mmt) REVERT: B 521 ILE cc_start: 0.8111 (mp) cc_final: 0.7862 (pt) REVERT: B 562 ARG cc_start: 0.5793 (mtp180) cc_final: 0.5302 (mtt-85) outliers start: 19 outliers final: 10 residues processed: 138 average time/residue: 0.5778 time to fit residues: 85.6718 Evaluate side-chains 130 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 954 PHE Chi-restraints excluded: chain A residue 977 PHE Chi-restraints excluded: chain A residue 1014 GLN Chi-restraints excluded: chain B residue 571 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 38 optimal weight: 0.9990 chunk 28 optimal weight: 9.9990 chunk 95 optimal weight: 0.7980 chunk 120 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 107 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 415 GLN B 526 HIS ** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.188811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.146898 restraints weight = 11236.120| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 2.42 r_work: 0.3527 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10460 Z= 0.151 Angle : 0.607 9.897 14112 Z= 0.315 Chirality : 0.046 0.164 1527 Planarity : 0.004 0.034 1811 Dihedral : 4.925 33.110 1369 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.86 % Favored : 94.06 % Rotamer: Outliers : 1.76 % Allowed : 19.45 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.55 (0.23), residues: 1228 helix: -0.68 (0.22), residues: 529 sheet: -0.62 (0.41), residues: 155 loop : -1.38 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 503 TYR 0.012 0.001 TYR A 392 PHE 0.030 0.002 PHE A 937 TRP 0.011 0.001 TRP A 590 HIS 0.005 0.001 HIS A 450 Details of bonding type rmsd covalent geometry : bond 0.00356 (10460) covalent geometry : angle 0.60732 (14112) hydrogen bonds : bond 0.04365 ( 293) hydrogen bonds : angle 4.15847 ( 807) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3713.40 seconds wall clock time: 64 minutes 0.71 seconds (3840.71 seconds total)