Starting phenix.real_space_refine on Fri Feb 14 10:05:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w9b_37363/02_2025/8w9b_37363_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w9b_37363/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8w9b_37363/02_2025/8w9b_37363.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w9b_37363/02_2025/8w9b_37363.map" model { file = "/net/cci-nas-00/data/ceres_data/8w9b_37363/02_2025/8w9b_37363_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w9b_37363/02_2025/8w9b_37363_trim.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLU:plan': 1, 'ASP:plan': 2} 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: 5.86, per 1000 atoms: 0.57 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: 2.59 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.32 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: 2.95 Time building geometry restraints manager: 2.97 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: 0.910 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 25.070 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.270 ------------------------------------------------------------------------------- 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= 0.269 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 : 21.63 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.027 0.003 TRP A 880 HIS 0.009 0.002 HIS A 759 PHE 0.045 0.003 PHE A 937 TYR 0.019 0.002 TYR A 392 ARG 0.005 0.001 ARG A 992 *********************** 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 : 1.152 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: 1.4864 time to fit residues: 418.2360 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 : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 51 optimal weight: 0.0370 chunk 31 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 96 optimal weight: 20.0000 chunk 37 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 overall best weight: 1.3864 ------------------------------------------------------------------------------- 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 = 0.4318 r_free = 0.4318 target = 0.192106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.149408 restraints weight = 11244.629| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 2.02 r_work: 0.3778 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3650 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2615 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= 0.214 Angle : 0.647 9.390 14112 Z= 0.344 Chirality : 0.045 0.165 1527 Planarity : 0.005 0.052 1811 Dihedral : 5.740 37.264 1369 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.21 % Favored : 94.71 % Rotamer: Outliers : 2.38 % Allowed : 11.36 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.07 (0.20), residues: 1228 helix: -3.10 (0.17), residues: 525 sheet: -2.36 (0.38), residues: 157 loop : -2.21 (0.24), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 780 HIS 0.014 0.002 HIS A 917 PHE 0.026 0.002 PHE A 744 TYR 0.019 0.002 TYR A 392 ARG 0.005 0.001 ARG A 154 *********************** 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 192 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 165 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.6982 (mt-10) cc_final: 0.6397 (mm-30) REVERT: A 187 LYS cc_start: 0.7321 (mtpm) cc_final: 0.7040 (tptp) REVERT: A 211 ILE cc_start: 0.6129 (OUTLIER) cc_final: 0.5085 (pp) REVERT: A 384 ASN cc_start: 0.8027 (t0) cc_final: 0.7786 (t160) REVERT: A 438 SER cc_start: 0.8632 (p) cc_final: 0.8342 (p) REVERT: A 745 MET cc_start: 0.8514 (tpp) cc_final: 0.8173 (mpp) REVERT: A 852 ARG cc_start: 0.5831 (OUTLIER) cc_final: 0.5476 (mtt-85) REVERT: A 975 ARG cc_start: 0.7473 (tmm160) cc_final: 0.6897 (tmm160) REVERT: A 977 PHE cc_start: 0.7642 (OUTLIER) cc_final: 0.6887 (p90) REVERT: B 326 MET cc_start: 0.6331 (mpm) cc_final: 0.6114 (mmm) REVERT: B 451 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.7217 (tt0) REVERT: B 552 GLN cc_start: 0.7467 (OUTLIER) cc_final: 0.6883 (mt0) REVERT: B 562 ARG cc_start: 0.5970 (mtp180) cc_final: 0.5393 (mtt-85) outliers start: 27 outliers final: 9 residues processed: 180 average time/residue: 1.4469 time to fit residues: 278.2473 Evaluate side-chains 145 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 427 ILE Chi-restraints excluded: chain A residue 461 VAL 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 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 451 GLU 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 54 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 chunk 96 optimal weight: 30.0000 chunk 40 optimal weight: 10.0000 chunk 50 optimal weight: 0.2980 chunk 92 optimal weight: 0.0370 chunk 101 optimal weight: 10.0000 chunk 93 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 overall best weight: 2.6664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 ASN ** A 917 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.189237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.146278 restraints weight = 11302.749| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 2.19 r_work: 0.3547 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10460 Z= 0.278 Angle : 0.648 8.466 14112 Z= 0.343 Chirality : 0.047 0.176 1527 Planarity : 0.005 0.055 1811 Dihedral : 5.713 38.270 1369 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.27 % Favored : 93.65 % Rotamer: Outliers : 3.17 % Allowed : 13.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.21), residues: 1228 helix: -2.50 (0.19), residues: 531 sheet: -1.90 (0.39), residues: 157 loop : -2.16 (0.24), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 590 HIS 0.010 0.001 HIS A 759 PHE 0.025 0.003 PHE A 930 TYR 0.017 0.002 TYR A 392 ARG 0.006 0.001 ARG A 979 *********************** 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 173 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 LYS cc_start: 0.7422 (mtpm) cc_final: 0.7128 (tptp) REVERT: A 211 ILE cc_start: 0.6168 (OUTLIER) cc_final: 0.5180 (pp) REVERT: A 218 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7706 (tm-30) REVERT: A 384 ASN cc_start: 0.8041 (t0) cc_final: 0.7811 (t160) REVERT: A 474 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7486 (mm-30) REVERT: A 540 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8109 (mp) REVERT: A 745 MET cc_start: 0.8718 (tpp) cc_final: 0.8345 (mpp) REVERT: A 779 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8763 (mt) REVERT: A 852 ARG cc_start: 0.5933 (OUTLIER) cc_final: 0.5576 (mtt-85) REVERT: A 975 ARG cc_start: 0.7421 (tmm160) cc_final: 0.6885 (tmm160) REVERT: A 977 PHE cc_start: 0.7701 (OUTLIER) cc_final: 0.6656 (p90) REVERT: B 326 MET cc_start: 0.6482 (mpm) cc_final: 0.6234 (mmm) REVERT: B 472 ARG cc_start: 0.6856 (tmm-80) cc_final: 0.6169 (tpt170) REVERT: B 562 ARG cc_start: 0.6095 (mtp180) cc_final: 0.5506 (mtt-85) outliers start: 36 outliers final: 14 residues processed: 161 average time/residue: 1.2997 time to fit residues: 224.4061 Evaluate side-chains 142 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 1.136 ------------------------------------------------------------------------------- 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 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 474 GLU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 540 LEU 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 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 104 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 122 optimal weight: 20.0000 chunk 57 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 99 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN A 738 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 = 0.4279 r_free = 0.4279 target = 0.188604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.145538 restraints weight = 11235.559| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 2.12 r_work: 0.3543 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10460 Z= 0.263 Angle : 0.621 7.936 14112 Z= 0.327 Chirality : 0.046 0.176 1527 Planarity : 0.005 0.048 1811 Dihedral : 5.538 36.360 1369 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.86 % Favored : 94.06 % Rotamer: Outliers : 3.26 % Allowed : 14.08 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.21), residues: 1228 helix: -2.06 (0.20), residues: 526 sheet: -1.52 (0.41), residues: 150 loop : -1.99 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 590 HIS 0.008 0.001 HIS A 759 PHE 0.027 0.003 PHE A 734 TYR 0.015 0.002 TYR A 392 ARG 0.003 0.000 ARG A 777 *********************** 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: 37 poor density : 137 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.7089 (mt-10) cc_final: 0.6574 (mm-30) REVERT: A 187 LYS cc_start: 0.7359 (mtpm) cc_final: 0.7088 (tptp) REVERT: A 211 ILE cc_start: 0.6255 (OUTLIER) cc_final: 0.5353 (pp) REVERT: A 384 ASN cc_start: 0.8050 (t0) cc_final: 0.7829 (t160) REVERT: A 745 MET cc_start: 0.8633 (tpp) cc_final: 0.8230 (mpp) REVERT: A 779 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8771 (mt) REVERT: A 852 ARG cc_start: 0.5951 (OUTLIER) cc_final: 0.5607 (mtt-85) REVERT: A 975 ARG cc_start: 0.7447 (tmm160) cc_final: 0.7062 (tmm160) REVERT: A 977 PHE cc_start: 0.7724 (OUTLIER) cc_final: 0.6839 (p90) REVERT: A 1005 MET cc_start: 0.7972 (OUTLIER) cc_final: 0.7515 (mtm) REVERT: B 326 MET cc_start: 0.6486 (mpm) cc_final: 0.6201 (mmm) REVERT: B 472 ARG cc_start: 0.6852 (tmm-80) cc_final: 0.6181 (tpt170) REVERT: B 479 MET cc_start: 0.7964 (mtm) cc_final: 0.7015 (mmt) REVERT: B 562 ARG cc_start: 0.6043 (mtp180) cc_final: 0.5475 (mtt-85) outliers start: 37 outliers final: 18 residues processed: 161 average time/residue: 1.3481 time to fit residues: 233.2922 Evaluate side-chains 145 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 1.127 ------------------------------------------------------------------------------- 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 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 461 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 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 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 Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain B residue 582 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 48 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 chunk 104 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 76 optimal weight: 0.0870 chunk 41 optimal weight: 9.9990 chunk 94 optimal weight: 0.0060 chunk 63 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 ASN A 677 ASN A 917 HIS A 920 ASN B 455 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.192669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.149770 restraints weight = 11153.149| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 2.24 r_work: 0.3752 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3621 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10460 Z= 0.149 Angle : 0.527 7.454 14112 Z= 0.280 Chirality : 0.042 0.164 1527 Planarity : 0.004 0.044 1811 Dihedral : 4.898 32.753 1369 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.23 % Favored : 95.68 % Rotamer: Outliers : 2.73 % Allowed : 15.49 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.22), residues: 1228 helix: -1.37 (0.21), residues: 523 sheet: -1.25 (0.40), residues: 154 loop : -1.64 (0.25), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 669 HIS 0.006 0.001 HIS A 450 PHE 0.025 0.002 PHE A 930 TYR 0.013 0.001 TYR A 392 ARG 0.004 0.000 ARG A 777 *********************** 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 172 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.6867 (mt-10) cc_final: 0.6391 (mm-30) REVERT: A 83 PHE cc_start: 0.6643 (m-10) cc_final: 0.6388 (m-10) REVERT: A 187 LYS cc_start: 0.7243 (mtpm) cc_final: 0.7006 (tptp) REVERT: A 211 ILE cc_start: 0.6061 (OUTLIER) cc_final: 0.5201 (pp) REVERT: A 304 MET cc_start: 0.7359 (mpt) cc_final: 0.6935 (mpt) REVERT: A 384 ASN cc_start: 0.7821 (t0) cc_final: 0.7548 (t160) REVERT: A 745 MET cc_start: 0.8424 (tpp) cc_final: 0.8173 (mpp) REVERT: A 811 MET cc_start: 0.8359 (mtp) cc_final: 0.8133 (mtp) REVERT: A 852 ARG cc_start: 0.5926 (OUTLIER) cc_final: 0.5620 (mtt-85) REVERT: A 929 LEU cc_start: 0.5964 (OUTLIER) cc_final: 0.5753 (tm) REVERT: A 975 ARG cc_start: 0.7322 (tmm160) cc_final: 0.6940 (tmm160) REVERT: A 977 PHE cc_start: 0.7457 (OUTLIER) cc_final: 0.6558 (p90) REVERT: B 326 MET cc_start: 0.6477 (mpm) cc_final: 0.6181 (mmm) REVERT: B 389 LYS cc_start: 0.6473 (OUTLIER) cc_final: 0.5813 (mmpt) REVERT: B 479 MET cc_start: 0.7736 (mtm) cc_final: 0.6745 (mmt) REVERT: B 537 GLU cc_start: 0.6809 (tt0) cc_final: 0.6557 (tt0) REVERT: B 562 ARG cc_start: 0.5800 (mtp180) cc_final: 0.5327 (mtt-85) outliers start: 31 outliers final: 12 residues processed: 159 average time/residue: 1.3828 time to fit residues: 236.0838 Evaluate side-chains 139 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 365 GLU 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 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 389 LYS Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain B residue 552 GLN Chi-restraints excluded: chain B residue 571 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 20 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 118 optimal weight: 7.9990 chunk 94 optimal weight: 6.9990 chunk 110 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 HIS A 825 GLN A 917 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.184074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.140354 restraints weight = 11290.525| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.60 r_work: 0.3446 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 10460 Z= 0.453 Angle : 0.759 7.707 14112 Z= 0.391 Chirality : 0.053 0.242 1527 Planarity : 0.006 0.060 1811 Dihedral : 5.811 39.929 1369 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.49 % Favored : 92.43 % Rotamer: Outliers : 3.79 % Allowed : 15.49 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.22), residues: 1228 helix: -1.90 (0.20), residues: 533 sheet: -1.20 (0.41), residues: 150 loop : -1.96 (0.24), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 590 HIS 0.011 0.002 HIS A 759 PHE 0.033 0.003 PHE B 355 TYR 0.015 0.002 TYR A 392 ARG 0.006 0.001 ARG B 503 *********************** 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 168 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 125 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.6992 (mt-10) cc_final: 0.6485 (mm-30) REVERT: A 83 PHE cc_start: 0.6723 (m-10) cc_final: 0.6466 (m-10) REVERT: A 187 LYS cc_start: 0.7322 (mtpm) cc_final: 0.6971 (tptp) REVERT: A 211 ILE cc_start: 0.6263 (OUTLIER) cc_final: 0.5473 (pp) REVERT: A 391 ILE cc_start: 0.8478 (OUTLIER) cc_final: 0.7948 (tp) REVERT: A 474 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7580 (mm-30) REVERT: A 745 MET cc_start: 0.8762 (tpp) cc_final: 0.8361 (mpp) REVERT: A 852 ARG cc_start: 0.5965 (OUTLIER) cc_final: 0.5711 (mtt-85) REVERT: A 975 ARG cc_start: 0.7333 (tmm160) cc_final: 0.6899 (tmm160) REVERT: A 977 PHE cc_start: 0.7861 (OUTLIER) cc_final: 0.7090 (p90) REVERT: A 1034 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7801 (tm-30) REVERT: B 326 MET cc_start: 0.6481 (mpm) cc_final: 0.6180 (mmm) REVERT: B 389 LYS cc_start: 0.6440 (OUTLIER) cc_final: 0.5771 (mmpt) REVERT: B 431 TYR cc_start: 0.7030 (m-10) cc_final: 0.6022 (m-80) REVERT: B 435 GLN cc_start: 0.4467 (pp30) cc_final: 0.4168 (pt0) REVERT: B 537 GLU cc_start: 0.6931 (tt0) cc_final: 0.6664 (tt0) REVERT: B 562 ARG cc_start: 0.5933 (mtp180) cc_final: 0.5365 (mtt-85) outliers start: 43 outliers final: 22 residues processed: 153 average time/residue: 1.3669 time to fit residues: 224.3322 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 : 1.138 ------------------------------------------------------------------------------- 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 211 ILE Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 391 ILE 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 474 GLU 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 716 THR 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 543 ARG 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 92 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 120 optimal weight: 7.9990 chunk 56 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 3 optimal weight: 0.0980 chunk 104 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 917 HIS B 415 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.190829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.147752 restraints weight = 11383.048| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 2.52 r_work: 0.3534 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 10460 Z= 0.161 Angle : 0.552 7.518 14112 Z= 0.292 Chirality : 0.043 0.171 1527 Planarity : 0.004 0.041 1811 Dihedral : 4.963 31.036 1369 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.56 % Favored : 95.36 % Rotamer: Outliers : 2.73 % Allowed : 16.90 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.23), residues: 1228 helix: -1.23 (0.21), residues: 529 sheet: -1.09 (0.39), residues: 157 loop : -1.57 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 669 HIS 0.003 0.001 HIS B 407 PHE 0.031 0.002 PHE B 355 TYR 0.011 0.001 TYR A 392 ARG 0.010 0.000 ARG B 503 *********************** 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 162 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 PHE cc_start: 0.6641 (m-10) cc_final: 0.6438 (m-10) REVERT: A 187 LYS cc_start: 0.7280 (mtpm) cc_final: 0.6970 (tptp) REVERT: A 211 ILE cc_start: 0.6130 (OUTLIER) cc_final: 0.5339 (pp) REVERT: A 384 ASN cc_start: 0.7851 (t0) cc_final: 0.7573 (t160) REVERT: A 391 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.7944 (tp) REVERT: A 787 ASP cc_start: 0.7715 (OUTLIER) cc_final: 0.7447 (t0) REVERT: A 811 MET cc_start: 0.8382 (mtp) cc_final: 0.8097 (mtp) REVERT: A 852 ARG cc_start: 0.5975 (OUTLIER) cc_final: 0.5704 (mtt-85) REVERT: A 975 ARG cc_start: 0.7325 (tmm160) cc_final: 0.6981 (tmm160) REVERT: A 977 PHE cc_start: 0.7583 (OUTLIER) cc_final: 0.6758 (p90) REVERT: A 1034 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7827 (tm-30) REVERT: B 326 MET cc_start: 0.6374 (mpm) cc_final: 0.6060 (mmm) REVERT: B 431 TYR cc_start: 0.6930 (m-10) cc_final: 0.5966 (m-80) REVERT: B 435 GLN cc_start: 0.4612 (pp30) cc_final: 0.4319 (pt0) REVERT: B 479 MET cc_start: 0.7830 (mtm) cc_final: 0.6747 (mmt) REVERT: B 521 ILE cc_start: 0.8095 (mp) cc_final: 0.7834 (pt) REVERT: B 537 GLU cc_start: 0.6860 (tt0) cc_final: 0.6545 (tt0) REVERT: B 562 ARG cc_start: 0.5785 (mtp180) cc_final: 0.5265 (mtt-85) outliers start: 31 outliers final: 12 residues processed: 153 average time/residue: 1.2665 time to fit residues: 208.2396 Evaluate side-chains 133 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 211 ILE 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 787 ASP Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 852 ARG 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 543 ARG Chi-restraints excluded: chain B residue 552 GLN Chi-restraints excluded: chain B residue 571 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 38 optimal weight: 7.9990 chunk 121 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 122 optimal weight: 0.0570 chunk 92 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 overall best weight: 2.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 825 GLN A 917 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 = 0.4266 r_free = 0.4266 target = 0.188043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.146161 restraints weight = 11265.481| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 2.36 r_work: 0.3512 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10460 Z= 0.235 Angle : 0.600 7.512 14112 Z= 0.314 Chirality : 0.046 0.173 1527 Planarity : 0.004 0.040 1811 Dihedral : 5.101 33.756 1369 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.94 % Favored : 93.97 % Rotamer: Outliers : 2.38 % Allowed : 17.52 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.23), residues: 1228 helix: -1.20 (0.21), residues: 530 sheet: -0.95 (0.39), residues: 157 loop : -1.56 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 590 HIS 0.005 0.001 HIS A 759 PHE 0.028 0.002 PHE B 355 TYR 0.012 0.001 TYR A 392 ARG 0.009 0.000 ARG B 503 *********************** 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 148 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.7004 (mt-10) cc_final: 0.6491 (mm-30) REVERT: A 187 LYS cc_start: 0.7333 (mtpm) cc_final: 0.6881 (tptp) REVERT: A 211 ILE cc_start: 0.6241 (OUTLIER) cc_final: 0.5467 (pp) REVERT: A 384 ASN cc_start: 0.7943 (t0) cc_final: 0.7640 (t0) REVERT: A 391 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.7931 (tp) REVERT: A 852 ARG cc_start: 0.5979 (OUTLIER) cc_final: 0.5715 (mtt-85) REVERT: A 975 ARG cc_start: 0.7348 (tmm160) cc_final: 0.6980 (tmm160) REVERT: A 977 PHE cc_start: 0.7662 (OUTLIER) cc_final: 0.6874 (p90) REVERT: A 1034 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7703 (tm-30) REVERT: B 326 MET cc_start: 0.6444 (mpm) cc_final: 0.6131 (mmm) REVERT: B 431 TYR cc_start: 0.6931 (m-10) cc_final: 0.5969 (m-80) REVERT: B 435 GLN cc_start: 0.4629 (pp30) cc_final: 0.4313 (pt0) REVERT: B 479 MET cc_start: 0.7815 (mtm) cc_final: 0.6811 (mmt) REVERT: B 521 ILE cc_start: 0.8084 (mp) cc_final: 0.7829 (pt) REVERT: B 537 GLU cc_start: 0.6841 (tt0) cc_final: 0.6526 (tt0) REVERT: B 562 ARG cc_start: 0.5815 (mtp180) cc_final: 0.5286 (mtt-85) outliers start: 27 outliers final: 12 residues processed: 140 average time/residue: 1.3137 time to fit residues: 197.8887 Evaluate side-chains 135 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 793 LEU Chi-restraints excluded: chain A residue 852 ARG 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 543 ARG 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 86 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 46 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 825 GLN A 917 HIS B 527 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.188456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.146548 restraints weight = 11343.929| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 2.41 r_work: 0.3518 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10460 Z= 0.222 Angle : 0.594 7.352 14112 Z= 0.314 Chirality : 0.045 0.169 1527 Planarity : 0.004 0.038 1811 Dihedral : 5.019 32.624 1369 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.21 % Favored : 94.71 % Rotamer: Outliers : 2.38 % Allowed : 17.61 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.23), residues: 1228 helix: -1.08 (0.21), residues: 529 sheet: -0.83 (0.40), residues: 157 loop : -1.54 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 669 HIS 0.005 0.001 HIS A 759 PHE 0.027 0.002 PHE B 355 TYR 0.012 0.001 TYR A 392 ARG 0.007 0.000 ARG B 503 *********************** 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 145 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 1.203 Fit side-chains revert: symmetry clash REVERT: A 76 GLU cc_start: 0.7014 (mt-10) cc_final: 0.6490 (mm-30) REVERT: A 187 LYS cc_start: 0.7337 (mtpm) cc_final: 0.6899 (tptp) REVERT: A 211 ILE cc_start: 0.6236 (OUTLIER) cc_final: 0.5464 (pp) REVERT: A 384 ASN cc_start: 0.7926 (t0) cc_final: 0.7624 (t0) REVERT: A 391 ILE cc_start: 0.8427 (OUTLIER) cc_final: 0.7909 (tp) REVERT: A 852 ARG cc_start: 0.5969 (OUTLIER) cc_final: 0.5700 (mtt-85) REVERT: A 954 PHE cc_start: 0.7605 (OUTLIER) cc_final: 0.7012 (m-80) REVERT: A 975 ARG cc_start: 0.7393 (tmm160) cc_final: 0.6976 (tmm160) REVERT: A 977 PHE cc_start: 0.7672 (OUTLIER) cc_final: 0.6936 (p90) REVERT: A 1034 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7723 (tm-30) REVERT: B 389 LYS cc_start: 0.6446 (OUTLIER) cc_final: 0.5638 (mmpt) REVERT: B 431 TYR cc_start: 0.6916 (m-10) cc_final: 0.5949 (m-80) REVERT: B 435 GLN cc_start: 0.4590 (pp30) cc_final: 0.4272 (pt0) REVERT: B 479 MET cc_start: 0.7812 (mtm) cc_final: 0.6781 (mmt) REVERT: B 521 ILE cc_start: 0.8065 (mp) cc_final: 0.7816 (pt) REVERT: B 537 GLU cc_start: 0.6897 (tt0) cc_final: 0.6595 (tt0) REVERT: B 562 ARG cc_start: 0.5708 (mtp180) cc_final: 0.5146 (mtt-85) outliers start: 27 outliers final: 13 residues processed: 138 average time/residue: 1.4064 time to fit residues: 208.4035 Evaluate side-chains 134 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 365 GLU Chi-restraints excluded: chain A residue 391 ILE 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 491 VAL 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 954 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 389 LYS Chi-restraints excluded: chain B residue 543 ARG 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 46 optimal weight: 9.9990 chunk 116 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 119 optimal weight: 9.9990 chunk 104 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 917 HIS B 415 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.187700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.145228 restraints weight = 11298.920| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 2.46 r_work: 0.3510 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10460 Z= 0.247 Angle : 0.616 7.466 14112 Z= 0.322 Chirality : 0.046 0.168 1527 Planarity : 0.004 0.036 1811 Dihedral : 5.111 33.268 1369 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.35 % Favored : 93.57 % Rotamer: Outliers : 2.46 % Allowed : 17.61 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.23), residues: 1228 helix: -1.07 (0.21), residues: 529 sheet: -0.77 (0.40), residues: 157 loop : -1.54 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 590 HIS 0.006 0.001 HIS A 759 PHE 0.034 0.002 PHE A 937 TYR 0.012 0.001 TYR A 392 ARG 0.008 0.000 ARG B 503 ********************** 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 146 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 1.119 Fit side-chains REVERT: A 76 GLU cc_start: 0.7013 (mt-10) cc_final: 0.6503 (mm-30) REVERT: A 187 LYS cc_start: 0.7347 (mtpm) cc_final: 0.6900 (tptp) REVERT: A 211 ILE cc_start: 0.6229 (OUTLIER) cc_final: 0.5461 (pp) REVERT: A 384 ASN cc_start: 0.7956 (t0) cc_final: 0.7666 (t0) REVERT: A 391 ILE cc_start: 0.8432 (OUTLIER) cc_final: 0.7897 (tp) REVERT: A 420 CYS cc_start: 0.6418 (t) cc_final: 0.6077 (p) REVERT: A 852 ARG cc_start: 0.5940 (OUTLIER) cc_final: 0.5673 (mtt-85) REVERT: A 858 MET cc_start: 0.7587 (OUTLIER) cc_final: 0.6706 (tmt) REVERT: A 954 PHE cc_start: 0.7645 (OUTLIER) cc_final: 0.6962 (m-80) REVERT: A 975 ARG cc_start: 0.7369 (tmm160) cc_final: 0.6951 (tmm160) REVERT: A 977 PHE cc_start: 0.7697 (OUTLIER) cc_final: 0.6999 (p90) REVERT: A 1034 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7748 (tm-30) REVERT: B 326 MET cc_start: 0.6206 (OUTLIER) cc_final: 0.5993 (mmm) REVERT: B 389 LYS cc_start: 0.6393 (OUTLIER) cc_final: 0.5641 (mmpt) REVERT: B 431 TYR cc_start: 0.6915 (m-10) cc_final: 0.5951 (m-80) REVERT: B 435 GLN cc_start: 0.4577 (pp30) cc_final: 0.4263 (pt0) REVERT: B 479 MET cc_start: 0.7851 (mtm) cc_final: 0.6785 (mmt) REVERT: B 521 ILE cc_start: 0.8134 (mp) cc_final: 0.7903 (pt) REVERT: B 537 GLU cc_start: 0.6880 (tt0) cc_final: 0.6619 (tt0) REVERT: B 562 ARG cc_start: 0.5654 (mtp180) cc_final: 0.5070 (mtt-85) outliers start: 28 outliers final: 14 residues processed: 137 average time/residue: 1.3520 time to fit residues: 198.5755 Evaluate side-chains 138 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 365 GLU Chi-restraints excluded: chain A residue 391 ILE 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 491 VAL Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 852 ARG Chi-restraints excluded: chain A residue 858 MET Chi-restraints excluded: chain A residue 929 LEU 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 326 MET Chi-restraints excluded: chain B residue 389 LYS Chi-restraints excluded: chain B residue 543 ARG 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 39 optimal weight: 1.9990 chunk 115 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 chunk 42 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 95 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 917 HIS B 415 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.188367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.146623 restraints weight = 11235.267| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 2.44 r_work: 0.3517 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10460 Z= 0.221 Angle : 0.597 7.446 14112 Z= 0.313 Chirality : 0.045 0.168 1527 Planarity : 0.004 0.035 1811 Dihedral : 5.008 32.248 1369 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.37 % Favored : 94.54 % Rotamer: Outliers : 2.55 % Allowed : 17.96 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.23), residues: 1228 helix: -0.94 (0.22), residues: 529 sheet: -0.70 (0.40), residues: 157 loop : -1.48 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 669 HIS 0.005 0.001 HIS A 759 PHE 0.031 0.002 PHE A 937 TYR 0.012 0.001 TYR A 392 ARG 0.007 0.000 ARG B 503 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8183.20 seconds wall clock time: 144 minutes 53.08 seconds (8693.08 seconds total)