Starting phenix.real_space_refine on Sun Aug 4 08:14:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9b_37363/08_2024/8w9b_37363_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9b_37363/08_2024/8w9b_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9b_37363/08_2024/8w9b_37363.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9b_37363/08_2024/8w9b_37363.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9b_37363/08_2024/8w9b_37363_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9b_37363/08_2024/8w9b_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 Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 5.97, per 1000 atoms: 0.58 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 - 3.50 Amino acid : False - 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: 3.60 Conformation dependent library (CDL) restraints added in 1.7 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: 1.18 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: 3.36 Time building geometry restraints manager: 3.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1717 1.31 - 1.43: 2708 1.43 - 1.56: 5923 1.56 - 1.68: 0 1.68 - 1.81: 112 Bond restraints: 10460 Sorted by residual: bond pdb=" C12 UJ3 A1101 " pdb=" N14 UJ3 A1101 " ideal model delta sigma weight residual 1.354 1.447 -0.093 2.00e-02 2.50e+03 2.14e+01 bond pdb=" C06 UJ3 A1101 " pdb=" N05 UJ3 A1101 " ideal model delta sigma weight residual 1.356 1.446 -0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" C06 UJ3 A1101 " pdb=" N07 UJ3 A1101 " ideal model delta sigma weight residual 1.376 1.442 -0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" C11 UJ3 A1101 " pdb=" C12 UJ3 A1101 " ideal model delta sigma weight residual 1.476 1.541 -0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" N LEU A 911 " pdb=" CA LEU A 911 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.16e-02 7.43e+03 8.48e+00 ... (remaining 10455 not shown) Histogram of bond angle deviations from ideal: 99.90 - 107.66: 396 107.66 - 115.42: 6258 115.42 - 123.18: 6969 123.18 - 130.94: 433 130.94 - 138.70: 56 Bond angle restraints: 14112 Sorted by residual: angle pdb=" C ARG A 740 " pdb=" N ARG A 741 " pdb=" CA ARG A 741 " ideal model delta sigma weight residual 120.65 131.45 -10.80 1.36e+00 5.41e-01 6.30e+01 angle pdb=" C GLU A 176 " pdb=" N LEU A 177 " pdb=" CA LEU A 177 " ideal model delta sigma weight residual 120.97 138.70 -17.73 2.84e+00 1.24e-01 3.90e+01 angle pdb=" N ILE A1019 " pdb=" CA ILE A1019 " pdb=" C ILE A1019 " ideal model delta sigma weight residual 111.91 106.78 5.13 8.90e-01 1.26e+00 3.33e+01 angle pdb=" N VAL A 636 " pdb=" CA VAL A 636 " pdb=" C VAL A 636 " ideal model delta sigma weight residual 113.43 107.71 5.72 1.09e+00 8.42e-01 2.75e+01 angle pdb=" N ILE A 894 " pdb=" CA ILE A 894 " pdb=" C ILE A 894 " ideal model delta sigma weight residual 112.96 108.24 4.72 1.00e+00 1.00e+00 2.23e+01 ... (remaining 14107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.59: 6043 15.59 - 31.19: 259 31.19 - 46.78: 70 46.78 - 62.37: 10 62.37 - 77.96: 10 Dihedral angle restraints: 6392 sinusoidal: 2726 harmonic: 3666 Sorted by residual: dihedral pdb=" CA VAL A 923 " pdb=" C VAL A 923 " pdb=" N LYS A 924 " pdb=" CA LYS A 924 " ideal model delta harmonic sigma weight residual -180.00 -155.74 -24.26 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA GLN B 591 " pdb=" C GLN B 591 " pdb=" N LYS B 592 " pdb=" CA LYS B 592 " ideal model delta harmonic sigma weight residual 180.00 157.26 22.74 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA PHE A 95 " pdb=" C PHE A 95 " pdb=" N GLN A 96 " pdb=" CA GLN A 96 " ideal model delta harmonic sigma weight residual 180.00 158.65 21.35 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 6389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 947 0.037 - 0.073: 426 0.073 - 0.110: 118 0.110 - 0.147: 31 0.147 - 0.184: 5 Chirality restraints: 1527 Sorted by residual: chirality pdb=" CA ILE A 913 " pdb=" N ILE A 913 " pdb=" C ILE A 913 " pdb=" CB ILE A 913 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.43e-01 chirality pdb=" CA ASP A 258 " pdb=" N ASP A 258 " pdb=" C ASP A 258 " pdb=" CB ASP A 258 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.94e-01 chirality pdb=" CA ILE A 932 " pdb=" N ILE A 932 " pdb=" C ILE A 932 " pdb=" CB ILE A 932 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.28e-01 ... (remaining 1524 not shown) Planarity restraints: 1811 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 937 " -0.014 2.00e-02 2.50e+03 2.00e-02 6.99e+00 pdb=" CG PHE A 937 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE A 937 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE A 937 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE A 937 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 937 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 937 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 96 " -0.033 5.00e-02 4.00e+02 5.05e-02 4.09e+00 pdb=" N PRO A 97 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 97 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 97 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 538 " 0.033 5.00e-02 4.00e+02 5.00e-02 4.01e+00 pdb=" N PRO A 539 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 539 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 539 " 0.028 5.00e-02 4.00e+02 ... (remaining 1808 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 140 2.64 - 3.21: 9658 3.21 - 3.77: 14183 3.77 - 4.34: 21997 4.34 - 4.90: 34432 Nonbonded interactions: 80410 Sorted by model distance: nonbonded pdb=" OD1 ASN B 325 " pdb=" OG SER B 400 " model vdw 2.078 3.040 nonbonded pdb=" O LEU B 347 " pdb=" NH1 ARG B 373 " model vdw 2.193 3.120 nonbonded pdb=" OD1 ASP A 155 " pdb=" OG SER A 158 " model vdw 2.198 3.040 nonbonded pdb=" NH2 ARG A 401 " pdb=" O PRO A 458 " model vdw 2.204 3.120 nonbonded pdb=" OH TYR A 641 " pdb=" N GLY A1007 " model vdw 2.208 3.120 ... (remaining 80405 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.370 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: 0.000 Extract box with map and model: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 29.190 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.330 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 4 poor density : 262 time to evaluate : 1.182 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: 1.3911 time to fit residues: 391.2118 Evaluate side-chains 145 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 1.168 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 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 fitting. rotamer outliers: 27 poor density : 165 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.6797 (mt-10) cc_final: 0.6546 (mm-30) REVERT: A 211 ILE cc_start: 0.6240 (OUTLIER) cc_final: 0.5216 (pp) REVERT: A 438 SER cc_start: 0.8355 (p) cc_final: 0.7984 (p) REVERT: A 852 ARG cc_start: 0.5879 (OUTLIER) cc_final: 0.5519 (mtt-85) REVERT: A 975 ARG cc_start: 0.7170 (tmm160) cc_final: 0.6770 (tmm160) REVERT: A 977 PHE cc_start: 0.7370 (OUTLIER) cc_final: 0.6588 (p90) REVERT: B 552 GLN cc_start: 0.7508 (OUTLIER) cc_final: 0.6983 (mt0) REVERT: B 562 ARG cc_start: 0.6126 (mtp180) cc_final: 0.5890 (mtt-85) outliers start: 27 outliers final: 9 residues processed: 180 average time/residue: 1.3505 time to fit residues: 259.9142 Evaluate side-chains 144 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 131 time to evaluate : 1.153 ------------------------------------------------------------------------------- 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 552 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 6.9990 chunk 34 optimal weight: 0.6980 chunk 92 optimal weight: 0.3980 chunk 76 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 111 optimal weight: 9.9990 chunk 120 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 110 optimal weight: 9.9990 chunk 38 optimal weight: 0.0770 chunk 89 optimal weight: 4.9990 overall best weight: 2.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN A 428 ASN ** A 917 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10460 Z= 0.231 Angle : 0.622 8.662 14112 Z= 0.330 Chirality : 0.046 0.172 1527 Planarity : 0.005 0.055 1811 Dihedral : 5.555 37.449 1369 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.54 % Favored : 94.38 % Rotamer: Outliers : 2.64 % Allowed : 13.91 % Favored : 83.45 % 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: -3.42 (0.21), residues: 1228 helix: -2.42 (0.19), residues: 525 sheet: -1.85 (0.40), residues: 157 loop : -2.08 (0.24), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 552 HIS 0.008 0.001 HIS A 759 PHE 0.022 0.002 PHE A 930 TYR 0.017 0.001 TYR A 392 ARG 0.006 0.000 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 167 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 137 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 ILE cc_start: 0.6062 (OUTLIER) cc_final: 0.5150 (pp) REVERT: A 304 MET cc_start: 0.6533 (mpt) cc_final: 0.6313 (mpt) REVERT: A 540 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.7984 (mp) REVERT: A 779 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8681 (mt) REVERT: A 852 ARG cc_start: 0.5935 (OUTLIER) cc_final: 0.5579 (mtt-85) REVERT: A 975 ARG cc_start: 0.7032 (tmm160) cc_final: 0.6728 (tmm160) REVERT: B 472 ARG cc_start: 0.6548 (tmm-80) cc_final: 0.6320 (tpt170) REVERT: B 552 GLN cc_start: 0.7444 (OUTLIER) cc_final: 0.6885 (mt0) REVERT: B 562 ARG cc_start: 0.6072 (mtp180) cc_final: 0.5851 (mtt-85) outliers start: 30 outliers final: 13 residues processed: 157 average time/residue: 1.2298 time to fit residues: 207.3020 Evaluate side-chains 141 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 123 time to evaluate : 1.168 ------------------------------------------------------------------------------- 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 491 VAL Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 610 MET 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 1014 GLN Chi-restraints excluded: chain A residue 1037 GLU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 552 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 9.9990 chunk 84 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 112 optimal weight: 10.0000 chunk 118 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 99 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN A 450 HIS A 825 GLN A 917 HIS A 920 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 10460 Z= 0.429 Angle : 0.761 8.008 14112 Z= 0.395 Chirality : 0.052 0.190 1527 Planarity : 0.006 0.058 1811 Dihedral : 6.056 39.427 1369 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.49 % Favored : 92.43 % Rotamer: Outliers : 4.05 % Allowed : 13.56 % Favored : 82.39 % 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: -3.35 (0.21), residues: 1228 helix: -2.38 (0.19), residues: 525 sheet: -1.58 (0.41), residues: 150 loop : -2.12 (0.24), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 590 HIS 0.012 0.002 HIS A 759 PHE 0.032 0.003 PHE A 930 TYR 0.016 0.002 TYR A 392 ARG 0.004 0.001 ARG A 808 *********************** 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 178 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 132 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 ILE cc_start: 0.6372 (OUTLIER) cc_final: 0.5589 (pp) REVERT: A 431 ASP cc_start: 0.6774 (t0) cc_final: 0.6503 (t70) REVERT: A 474 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6967 (mm-30) REVERT: A 779 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8505 (mp) REVERT: A 852 ARG cc_start: 0.5999 (OUTLIER) cc_final: 0.5740 (mtt-85) REVERT: A 975 ARG cc_start: 0.7086 (tmm160) cc_final: 0.6844 (tmm160) REVERT: A 977 PHE cc_start: 0.7685 (OUTLIER) cc_final: 0.6863 (p90) REVERT: A 1005 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.7182 (mtm) REVERT: B 435 GLN cc_start: 0.5411 (pp30) cc_final: 0.5129 (pt0) REVERT: B 562 ARG cc_start: 0.6178 (mtp180) cc_final: 0.5904 (mtt-85) outliers start: 46 outliers final: 17 residues processed: 163 average time/residue: 1.2586 time to fit residues: 220.2190 Evaluate side-chains 145 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 122 time to evaluate : 1.201 ------------------------------------------------------------------------------- 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 576 SER Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 852 ARG Chi-restraints excluded: chain A residue 920 ASN 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 571 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 88 optimal weight: 0.2980 chunk 49 optimal weight: 0.6980 chunk 101 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 ASN A 384 ASN ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 825 GLN A 917 HIS A 920 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10460 Z= 0.243 Angle : 0.625 7.728 14112 Z= 0.330 Chirality : 0.046 0.176 1527 Planarity : 0.005 0.047 1811 Dihedral : 5.565 33.735 1369 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.29 % Favored : 94.63 % Rotamer: Outliers : 3.61 % Allowed : 14.61 % 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: -2.88 (0.22), residues: 1228 helix: -1.94 (0.20), residues: 525 sheet: -1.35 (0.41), residues: 148 loop : -1.92 (0.24), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 590 HIS 0.006 0.001 HIS A 759 PHE 0.023 0.002 PHE A 930 TYR 0.015 0.001 TYR A 392 ARG 0.004 0.000 ARG A 154 *********************** 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 173 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 132 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 ILE cc_start: 0.6231 (OUTLIER) cc_final: 0.5453 (pp) REVERT: A 391 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7617 (tp) REVERT: A 474 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6940 (mm-30) REVERT: A 540 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8062 (mp) REVERT: A 745 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7582 (mmm) REVERT: A 779 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8687 (mt) REVERT: A 852 ARG cc_start: 0.6020 (OUTLIER) cc_final: 0.5764 (mtt-85) REVERT: A 977 PHE cc_start: 0.7514 (OUTLIER) cc_final: 0.6738 (p90) REVERT: A 1005 MET cc_start: 0.7682 (OUTLIER) cc_final: 0.7212 (mtm) REVERT: B 389 LYS cc_start: 0.7448 (OUTLIER) cc_final: 0.6609 (mmpt) REVERT: B 431 TYR cc_start: 0.6336 (m-10) cc_final: 0.5811 (m-80) REVERT: B 435 GLN cc_start: 0.5374 (pp30) cc_final: 0.5116 (pt0) REVERT: B 472 ARG cc_start: 0.6526 (tmm-80) cc_final: 0.6312 (tpt170) REVERT: B 479 MET cc_start: 0.7267 (mtm) cc_final: 0.6959 (mmt) REVERT: B 562 ARG cc_start: 0.6075 (mtp180) cc_final: 0.5830 (mtt-85) outliers start: 41 outliers final: 18 residues processed: 161 average time/residue: 1.2753 time to fit residues: 220.7942 Evaluate side-chains 146 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 118 time to evaluate : 1.132 ------------------------------------------------------------------------------- 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 391 ILE 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 493 GLU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 745 MET 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 389 LYS Chi-restraints excluded: chain B residue 422 VAL 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 107 optimal weight: 20.0000 chunk 23 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 119 optimal weight: 10.0000 chunk 98 optimal weight: 0.7980 chunk 55 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 114 optimal weight: 20.0000 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 825 GLN ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 455 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10460 Z= 0.334 Angle : 0.688 7.391 14112 Z= 0.359 Chirality : 0.049 0.184 1527 Planarity : 0.005 0.048 1811 Dihedral : 5.696 35.488 1369 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.00 % Favored : 92.92 % Rotamer: Outliers : 3.79 % Allowed : 15.67 % Favored : 80.55 % 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: -2.84 (0.22), residues: 1228 helix: -1.90 (0.20), residues: 527 sheet: -1.18 (0.41), residues: 148 loop : -1.95 (0.24), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 590 HIS 0.008 0.001 HIS A 759 PHE 0.026 0.003 PHE A 930 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 164 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 121 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 ILE cc_start: 0.6305 (OUTLIER) cc_final: 0.5565 (pp) REVERT: A 474 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6954 (mm-30) REVERT: A 779 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8632 (mt) REVERT: A 852 ARG cc_start: 0.5966 (OUTLIER) cc_final: 0.5734 (mtt-85) REVERT: A 858 MET cc_start: 0.7323 (OUTLIER) cc_final: 0.6366 (tmm) REVERT: A 977 PHE cc_start: 0.7606 (OUTLIER) cc_final: 0.6829 (p90) REVERT: B 389 LYS cc_start: 0.7478 (OUTLIER) cc_final: 0.6585 (mmpt) REVERT: B 431 TYR cc_start: 0.6340 (m-10) cc_final: 0.5835 (m-80) REVERT: B 435 GLN cc_start: 0.5348 (pp30) cc_final: 0.5109 (pt0) REVERT: B 472 ARG cc_start: 0.6547 (tmm-80) cc_final: 0.6301 (tpt170) REVERT: B 562 ARG cc_start: 0.6067 (mtp180) cc_final: 0.5809 (mtm-85) outliers start: 43 outliers final: 20 residues processed: 152 average time/residue: 1.2311 time to fit residues: 201.2890 Evaluate side-chains 145 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 118 time to evaluate : 1.265 ------------------------------------------------------------------------------- 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 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 610 MET 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 858 MET 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 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 13 optimal weight: 9.9990 chunk 67 optimal weight: 0.0970 chunk 86 optimal weight: 0.0040 chunk 100 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 118 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 920 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.3912 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= 0.153 Angle : 0.553 7.603 14112 Z= 0.293 Chirality : 0.042 0.166 1527 Planarity : 0.004 0.040 1811 Dihedral : 4.904 28.829 1369 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.64 % Favored : 95.28 % Rotamer: Outliers : 2.73 % Allowed : 16.81 % Favored : 80.46 % 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: -2.12 (0.23), residues: 1228 helix: -1.21 (0.22), residues: 525 sheet: -1.07 (0.39), residues: 154 loop : -1.58 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 669 HIS 0.004 0.001 HIS A 450 PHE 0.023 0.001 PHE A 930 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 175 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 144 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 ILE cc_start: 0.6251 (OUTLIER) cc_final: 0.5496 (pp) REVERT: A 391 ILE cc_start: 0.8069 (OUTLIER) cc_final: 0.7669 (tp) REVERT: A 745 MET cc_start: 0.7626 (mpp) cc_final: 0.7367 (mmm) REVERT: A 811 MET cc_start: 0.8108 (mtp) cc_final: 0.7788 (mtp) REVERT: A 852 ARG cc_start: 0.5956 (OUTLIER) cc_final: 0.5728 (mtt-85) REVERT: A 858 MET cc_start: 0.7193 (tmm) cc_final: 0.6976 (tmt) REVERT: A 937 PHE cc_start: 0.6643 (OUTLIER) cc_final: 0.6294 (t80) REVERT: A 977 PHE cc_start: 0.7355 (OUTLIER) cc_final: 0.6593 (p90) REVERT: B 431 TYR cc_start: 0.6283 (m-10) cc_final: 0.5791 (m-80) REVERT: B 479 MET cc_start: 0.7230 (mtm) cc_final: 0.6830 (mmt) REVERT: B 562 ARG cc_start: 0.5919 (mtp180) cc_final: 0.5683 (mtt-85) outliers start: 31 outliers final: 15 residues processed: 165 average time/residue: 1.1362 time to fit residues: 202.7067 Evaluate side-chains 144 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 124 time to evaluate : 1.083 ------------------------------------------------------------------------------- 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 576 SER Chi-restraints excluded: chain A residue 718 ILE 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 929 LEU Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 977 PHE 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 70 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 113 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN A 825 GLN B 435 GLN B 527 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 10460 Z= 0.431 Angle : 0.754 7.841 14112 Z= 0.389 Chirality : 0.052 0.236 1527 Planarity : 0.006 0.057 1811 Dihedral : 5.717 37.090 1369 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.57 % Favored : 92.35 % Rotamer: Outliers : 3.43 % Allowed : 17.78 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.63 (0.22), residues: 1228 helix: -1.73 (0.20), residues: 528 sheet: -1.08 (0.40), residues: 157 loop : -1.83 (0.25), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 590 HIS 0.009 0.002 HIS A 759 PHE 0.026 0.003 PHE B 355 TYR 0.015 0.002 TYR A 392 ARG 0.008 0.001 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 152 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 113 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 211 ILE cc_start: 0.6318 (OUTLIER) cc_final: 0.5586 (pp) REVERT: A 278 MET cc_start: 0.7002 (ttp) cc_final: 0.6770 (ttt) REVERT: A 391 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7651 (tp) REVERT: A 745 MET cc_start: 0.7931 (mpp) cc_final: 0.7596 (mmm) REVERT: A 852 ARG cc_start: 0.5965 (OUTLIER) cc_final: 0.5727 (mtt-85) REVERT: A 858 MET cc_start: 0.7340 (OUTLIER) cc_final: 0.6351 (tmm) REVERT: A 954 PHE cc_start: 0.7048 (OUTLIER) cc_final: 0.6362 (m-80) REVERT: A 977 PHE cc_start: 0.7644 (OUTLIER) cc_final: 0.6926 (p90) REVERT: B 389 LYS cc_start: 0.7464 (OUTLIER) cc_final: 0.6553 (mmpt) REVERT: B 431 TYR cc_start: 0.6407 (m-10) cc_final: 0.5642 (m-80) REVERT: B 562 ARG cc_start: 0.5879 (mtp180) cc_final: 0.5665 (mtt-85) outliers start: 39 outliers final: 16 residues processed: 142 average time/residue: 1.1459 time to fit residues: 175.8829 Evaluate side-chains 132 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 109 time to evaluate : 1.190 ------------------------------------------------------------------------------- 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 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 937 PHE Chi-restraints excluded: chain A residue 954 PHE Chi-restraints excluded: chain A residue 977 PHE Chi-restraints excluded: chain A residue 989 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.8980 chunk 110 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 825 GLN B 415 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10460 Z= 0.234 Angle : 0.628 7.697 14112 Z= 0.331 Chirality : 0.045 0.175 1527 Planarity : 0.004 0.042 1811 Dihedral : 5.299 31.222 1369 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.21 % Favored : 94.71 % Rotamer: Outliers : 2.55 % Allowed : 18.84 % Favored : 78.61 % 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: -2.27 (0.23), residues: 1228 helix: -1.38 (0.21), residues: 529 sheet: -0.94 (0.40), residues: 155 loop : -1.67 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 590 HIS 0.004 0.001 HIS A 759 PHE 0.035 0.002 PHE B 355 TYR 0.013 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 148 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 119 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7707 (mp) REVERT: A 211 ILE cc_start: 0.6335 (OUTLIER) cc_final: 0.5598 (pp) REVERT: A 391 ILE cc_start: 0.8108 (OUTLIER) cc_final: 0.7649 (tp) REVERT: A 745 MET cc_start: 0.7785 (mpp) cc_final: 0.7493 (mmm) REVERT: A 852 ARG cc_start: 0.5988 (OUTLIER) cc_final: 0.5737 (mtt-85) REVERT: A 954 PHE cc_start: 0.6964 (OUTLIER) cc_final: 0.6464 (m-80) REVERT: A 977 PHE cc_start: 0.7512 (OUTLIER) cc_final: 0.6826 (p90) REVERT: B 431 TYR cc_start: 0.6220 (m-10) cc_final: 0.5719 (m-80) REVERT: B 479 MET cc_start: 0.7282 (mtm) cc_final: 0.6926 (mmt) REVERT: B 562 ARG cc_start: 0.5856 (mtp180) cc_final: 0.5572 (mtt-85) outliers start: 29 outliers final: 17 residues processed: 137 average time/residue: 1.3564 time to fit residues: 201.6597 Evaluate side-chains 134 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 111 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 852 ARG Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 112 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 10 optimal weight: 0.5980 chunk 75 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 chunk 77 optimal weight: 0.3980 chunk 103 optimal weight: 0.7980 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN A 419 HIS A 825 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10460 Z= 0.210 Angle : 0.611 7.855 14112 Z= 0.321 Chirality : 0.044 0.167 1527 Planarity : 0.004 0.037 1811 Dihedral : 5.083 31.038 1369 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.62 % Favored : 94.30 % Rotamer: Outliers : 2.38 % Allowed : 19.19 % Favored : 78.43 % 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: -1.97 (0.23), residues: 1228 helix: -1.08 (0.22), residues: 529 sheet: -0.82 (0.40), 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 0.004 0.001 HIS A 450 PHE 0.034 0.002 PHE B 355 TYR 0.012 0.001 TYR A 392 ARG 0.007 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 147 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 120 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 LYS cc_start: 0.7495 (tttt) cc_final: 0.7090 (tptt) REVERT: A 211 ILE cc_start: 0.6306 (OUTLIER) cc_final: 0.5569 (pp) REVERT: A 391 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7616 (tp) REVERT: A 745 MET cc_start: 0.7728 (mpp) cc_final: 0.7433 (mmm) REVERT: A 852 ARG cc_start: 0.6005 (OUTLIER) cc_final: 0.5733 (mtt-85) REVERT: A 937 PHE cc_start: 0.6882 (OUTLIER) cc_final: 0.6499 (t80) REVERT: A 954 PHE cc_start: 0.6885 (OUTLIER) cc_final: 0.6508 (m-80) REVERT: A 975 ARG cc_start: 0.6983 (tmm160) cc_final: 0.6777 (tmm160) REVERT: A 977 PHE cc_start: 0.7433 (OUTLIER) cc_final: 0.6828 (p90) REVERT: B 431 TYR cc_start: 0.6275 (m-10) cc_final: 0.5812 (m-80) REVERT: B 479 MET cc_start: 0.7315 (mtm) cc_final: 0.6942 (mmt) REVERT: B 562 ARG cc_start: 0.5787 (mtp180) cc_final: 0.5500 (mtt-85) outliers start: 27 outliers final: 16 residues processed: 139 average time/residue: 1.3069 time to fit residues: 196.1242 Evaluate side-chains 135 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 113 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 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 937 PHE Chi-restraints excluded: chain A residue 954 PHE Chi-restraints excluded: chain A residue 977 PHE Chi-restraints excluded: chain A residue 1014 GLN Chi-restraints excluded: chain 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 10.0000 chunk 89 optimal weight: 0.8980 chunk 14 optimal weight: 8.9990 chunk 27 optimal weight: 8.9990 chunk 97 optimal weight: 9.9990 chunk 40 optimal weight: 8.9990 chunk 100 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.0370 chunk 85 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 overall best weight: 2.5864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 825 GLN B 415 GLN B 526 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.186845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.143852 restraints weight = 11253.220| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 2.50 r_work: 0.3485 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10460 Z= 0.273 Angle : 0.650 7.769 14112 Z= 0.340 Chirality : 0.047 0.171 1527 Planarity : 0.005 0.038 1811 Dihedral : 5.268 33.385 1369 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.60 % Favored : 93.32 % Rotamer: Outliers : 2.29 % Allowed : 19.19 % Favored : 78.52 % 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: -2.03 (0.23), residues: 1228 helix: -1.16 (0.22), residues: 530 sheet: -0.74 (0.41), residues: 157 loop : -1.61 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 590 HIS 0.005 0.001 HIS A 759 PHE 0.034 0.002 PHE B 355 TYR 0.014 0.002 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: 4152.79 seconds wall clock time: 73 minutes 12.25 seconds (4392.25 seconds total)