Starting phenix.real_space_refine on Sat Jul 20 05:47:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9b_37363/07_2024/8w9b_37363_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9b_37363/07_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_37363/07_2024/8w9b_37363.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9b_37363/07_2024/8w9b_37363.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9b_37363/07_2024/8w9b_37363_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9b_37363/07_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-5388/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: 6.01, per 1000 atoms: 0.59 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: 3.78 Conformation dependent library (CDL) restraints added in 1.9 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: 1.30 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: 3.04 Time building geometry restraints manager: 4.06 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 2.440 nonbonded pdb=" O LEU B 347 " pdb=" NH1 ARG B 373 " model vdw 2.193 2.520 nonbonded pdb=" OD1 ASP A 155 " pdb=" OG SER A 158 " model vdw 2.198 2.440 nonbonded pdb=" NH2 ARG A 401 " pdb=" O PRO A 458 " model vdw 2.204 2.520 nonbonded pdb=" OH TYR A 641 " pdb=" N GLY A1007 " model vdw 2.208 2.520 ... (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 ========== 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: 1.350 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: 0.090 Process input model: 29.110 Find NCS groups from input model: 0.090 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:10.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.380 ------------------------------------------------------------------------------- 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 : 1.166 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: 1.3586 time to fit residues: 382.2959 Evaluate side-chains 145 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 1.180 ------------------------------------------------------------------------------- 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: 10.0000 chunk 93 optimal weight: 1.9990 chunk 51 optimal weight: 0.0270 chunk 31 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 96 optimal weight: 8.9990 chunk 37 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 111 optimal weight: 10.0000 overall best weight: 2.2046 ------------------------------------------------------------------------------- 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 444 ASN A 721 GLN A 738 GLN A 917 HIS A 920 ASN B 385 HIS B 478 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10460 Z= 0.258 Angle : 0.674 9.100 14112 Z= 0.357 Chirality : 0.047 0.172 1527 Planarity : 0.006 0.053 1811 Dihedral : 5.919 39.210 1369 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.27 % Favored : 93.65 % Rotamer: Outliers : 2.90 % Allowed : 11.53 % Favored : 85.56 % 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: -4.23 (0.20), residues: 1228 helix: -3.20 (0.17), residues: 529 sheet: -2.42 (0.38), residues: 157 loop : -2.33 (0.24), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 780 HIS 0.014 0.002 HIS A 917 PHE 0.027 0.003 PHE A 937 TYR 0.019 0.002 TYR A 392 ARG 0.004 0.001 ARG A 979 *********************** 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 187 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 154 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.6417 (OUTLIER) cc_final: 0.5765 (mmp) REVERT: A 76 GLU cc_start: 0.6791 (mt-10) cc_final: 0.6540 (mm-30) REVERT: A 211 ILE cc_start: 0.6314 (OUTLIER) cc_final: 0.5297 (pp) REVERT: A 852 ARG cc_start: 0.5916 (OUTLIER) cc_final: 0.5624 (mtt-85) REVERT: A 958 GLN cc_start: 0.6689 (OUTLIER) cc_final: 0.6292 (tt0) REVERT: A 975 ARG cc_start: 0.7209 (tmm160) cc_final: 0.6799 (tmm160) REVERT: A 977 PHE cc_start: 0.7432 (OUTLIER) cc_final: 0.6667 (p90) REVERT: B 326 MET cc_start: 0.6933 (mpm) cc_final: 0.6733 (mmm) REVERT: B 552 GLN cc_start: 0.7520 (OUTLIER) cc_final: 0.6932 (mt0) outliers start: 33 outliers final: 14 residues processed: 173 average time/residue: 1.3268 time to fit residues: 245.6122 Evaluate side-chains 148 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 128 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain A residue 358 THR 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 576 SER Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 810 ASP Chi-restraints excluded: chain A residue 852 ARG Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 958 GLN 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: 6.9990 chunk 92 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 chunk 111 optimal weight: 10.0000 chunk 120 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 110 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN A 497 ASN 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: 0.7535 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 10460 Z= 0.391 Angle : 0.751 8.852 14112 Z= 0.393 Chirality : 0.051 0.189 1527 Planarity : 0.006 0.058 1811 Dihedral : 6.149 39.772 1369 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.17 % Favored : 92.75 % Rotamer: Outliers : 4.40 % Allowed : 12.24 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.80 (0.20), residues: 1228 helix: -2.77 (0.18), residues: 530 sheet: -1.88 (0.40), residues: 150 loop : -2.30 (0.23), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 590 HIS 0.013 0.002 HIS A 759 PHE 0.030 0.003 PHE A 667 TYR 0.019 0.002 TYR A 392 ARG 0.005 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 188 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 138 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.6168 (OUTLIER) cc_final: 0.5589 (mmp) REVERT: A 211 ILE cc_start: 0.6343 (OUTLIER) cc_final: 0.5479 (pp) REVERT: A 431 ASP cc_start: 0.6694 (t0) cc_final: 0.6274 (t70) REVERT: A 852 ARG cc_start: 0.5954 (OUTLIER) cc_final: 0.5732 (mtt-85) REVERT: A 920 ASN cc_start: 0.7380 (OUTLIER) cc_final: 0.7048 (p0) REVERT: A 975 ARG cc_start: 0.7211 (tmm160) cc_final: 0.6777 (tmm160) REVERT: A 977 PHE cc_start: 0.7585 (OUTLIER) cc_final: 0.6564 (p90) REVERT: B 389 LYS cc_start: 0.7495 (OUTLIER) cc_final: 0.6713 (mmtt) outliers start: 50 outliers final: 19 residues processed: 171 average time/residue: 1.2932 time to fit residues: 237.4352 Evaluate side-chains 144 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 119 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET 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 358 THR Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 426 ASN Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 810 ASP 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 10.0000 chunk 84 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 106 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 chunk 99 optimal weight: 8.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 ASN A 917 HIS A 920 ASN ** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.3311 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= 0.186 Angle : 0.578 8.194 14112 Z= 0.306 Chirality : 0.044 0.174 1527 Planarity : 0.004 0.048 1811 Dihedral : 5.379 32.755 1369 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.13 % Favored : 94.79 % Rotamer: Outliers : 3.52 % Allowed : 13.82 % 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: -3.08 (0.21), residues: 1228 helix: -2.05 (0.20), residues: 527 sheet: -1.66 (0.39), residues: 157 loop : -2.00 (0.24), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 669 HIS 0.007 0.001 HIS A 450 PHE 0.027 0.002 PHE A 734 TYR 0.015 0.001 TYR A 392 ARG 0.004 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 180 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 140 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.6813 (mt-10) cc_final: 0.6599 (mm-30) REVERT: A 211 ILE cc_start: 0.6211 (OUTLIER) cc_final: 0.5292 (pp) REVERT: A 959 ASP cc_start: 0.7660 (OUTLIER) cc_final: 0.7401 (p0) REVERT: A 975 ARG cc_start: 0.7106 (tmm160) cc_final: 0.6844 (tmm160) REVERT: A 977 PHE cc_start: 0.7385 (OUTLIER) cc_final: 0.6332 (p90) REVERT: B 472 ARG cc_start: 0.6492 (tmm-80) cc_final: 0.6185 (tpt170) REVERT: B 479 MET cc_start: 0.7235 (mtm) cc_final: 0.6985 (mmt) outliers start: 40 outliers final: 14 residues processed: 168 average time/residue: 1.2309 time to fit residues: 222.2325 Evaluate side-chains 140 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 123 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 810 ASP Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 959 ASP 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 0.0000 chunk 1 optimal weight: 20.0000 chunk 88 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 106 optimal weight: 0.0770 chunk 30 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 overall best weight: 3.0148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 HIS A 384 ASN A 825 GLN A 917 HIS B 455 GLN ** B 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.3453 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= 0.294 Angle : 0.647 7.895 14112 Z= 0.336 Chirality : 0.047 0.182 1527 Planarity : 0.005 0.045 1811 Dihedral : 5.609 35.873 1369 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.68 % Favored : 93.24 % Rotamer: Outliers : 4.31 % Allowed : 15.14 % 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: -2.93 (0.22), residues: 1228 helix: -1.94 (0.20), residues: 530 sheet: -1.33 (0.40), residues: 150 loop : -1.99 (0.24), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 590 HIS 0.007 0.001 HIS A 759 PHE 0.032 0.003 PHE A 937 TYR 0.015 0.002 TYR A 392 ARG 0.005 0.001 ARG A 852 *********************** 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 174 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 125 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 ILE cc_start: 0.6303 (OUTLIER) cc_final: 0.5501 (pp) REVERT: A 459 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.8131 (tt) REVERT: A 745 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.7599 (mmm) REVERT: A 959 ASP cc_start: 0.7738 (OUTLIER) cc_final: 0.7388 (p0) REVERT: A 977 PHE cc_start: 0.7615 (OUTLIER) cc_final: 0.6718 (p90) REVERT: B 389 LYS cc_start: 0.7336 (OUTLIER) cc_final: 0.6493 (mmtt) REVERT: B 426 TYR cc_start: 0.6932 (OUTLIER) cc_final: 0.6705 (m-80) REVERT: B 472 ARG cc_start: 0.6547 (tmm-80) cc_final: 0.6340 (tpt170) outliers start: 49 outliers final: 25 residues processed: 160 average time/residue: 1.2815 time to fit residues: 220.9969 Evaluate side-chains 147 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 115 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL 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 358 THR Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 390 ASP 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 459 ILE Chi-restraints excluded: chain A residue 461 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 610 MET Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 810 ASP Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain A residue 977 PHE Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1014 GLN Chi-restraints excluded: chain A residue 1037 GLU Chi-restraints excluded: chain B residue 389 LYS Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 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: 0.9980 chunk 69 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 119 optimal weight: 10.0000 chunk 98 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 114 optimal weight: 10.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 10460 Z= 0.362 Angle : 0.705 7.637 14112 Z= 0.365 Chirality : 0.049 0.184 1527 Planarity : 0.005 0.048 1811 Dihedral : 5.770 35.419 1369 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.25 % Favored : 92.67 % Rotamer: Outliers : 5.11 % Allowed : 15.49 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.93 (0.22), residues: 1228 helix: -1.95 (0.20), residues: 529 sheet: -1.18 (0.41), residues: 150 loop : -2.05 (0.24), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 590 HIS 0.007 0.001 HIS A 759 PHE 0.029 0.003 PHE A 937 TYR 0.015 0.002 TYR A 392 ARG 0.005 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 187 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 129 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 ILE cc_start: 0.6326 (OUTLIER) cc_final: 0.5543 (pp) REVERT: A 384 ASN cc_start: 0.7675 (t0) cc_final: 0.7472 (t0) REVERT: A 391 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7631 (tp) REVERT: A 459 ILE cc_start: 0.8459 (OUTLIER) cc_final: 0.8132 (tt) REVERT: A 474 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6996 (mm-30) REVERT: A 858 MET cc_start: 0.7330 (OUTLIER) cc_final: 0.6321 (tmm) REVERT: A 959 ASP cc_start: 0.7854 (OUTLIER) cc_final: 0.7464 (p0) REVERT: A 977 PHE cc_start: 0.7707 (OUTLIER) cc_final: 0.6795 (p90) REVERT: B 389 LYS cc_start: 0.7392 (OUTLIER) cc_final: 0.6559 (mmtt) REVERT: B 426 TYR cc_start: 0.6956 (OUTLIER) cc_final: 0.6750 (m-80) REVERT: B 431 TYR cc_start: 0.6348 (m-10) cc_final: 0.5881 (m-80) REVERT: B 472 ARG cc_start: 0.6629 (tmm-80) cc_final: 0.6383 (tpt170) outliers start: 58 outliers final: 31 residues processed: 172 average time/residue: 1.2144 time to fit residues: 224.9120 Evaluate side-chains 159 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 119 time to evaluate : 1.141 ------------------------------------------------------------------------------- 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 358 THR Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 390 ASP 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 459 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 526 ASN 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 727 THR Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 810 ASP Chi-restraints excluded: chain A residue 858 MET Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 959 ASP 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 337 ASP Chi-restraints excluded: chain B residue 389 LYS Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 441 ASN Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain B residue 552 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 100 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 825 GLN A 917 HIS B 455 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10460 Z= 0.216 Angle : 0.590 7.370 14112 Z= 0.311 Chirality : 0.044 0.175 1527 Planarity : 0.004 0.047 1811 Dihedral : 5.309 31.200 1369 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.70 % Favored : 94.22 % Rotamer: Outliers : 4.49 % Allowed : 17.25 % Favored : 78.26 % 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: -2.48 (0.22), residues: 1228 helix: -1.55 (0.21), residues: 529 sheet: -0.96 (0.41), residues: 148 loop : -1.82 (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 0.023 0.002 PHE A 937 TYR 0.013 0.001 TYR A 392 ARG 0.009 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 182 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 131 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.7651 (OUTLIER) cc_final: 0.7407 (mmt) REVERT: A 211 ILE cc_start: 0.6295 (OUTLIER) cc_final: 0.5538 (pp) REVERT: A 391 ILE cc_start: 0.8066 (OUTLIER) cc_final: 0.7595 (tp) REVERT: A 459 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.8119 (tt) REVERT: A 745 MET cc_start: 0.7781 (mpp) cc_final: 0.7480 (mmm) REVERT: A 852 ARG cc_start: 0.6028 (OUTLIER) cc_final: 0.5827 (mtt-85) REVERT: A 977 PHE cc_start: 0.7506 (OUTLIER) cc_final: 0.6653 (p90) REVERT: B 389 LYS cc_start: 0.7365 (OUTLIER) cc_final: 0.6465 (mmtt) REVERT: B 426 TYR cc_start: 0.6925 (OUTLIER) cc_final: 0.6721 (m-80) REVERT: B 431 TYR cc_start: 0.6341 (m-10) cc_final: 0.5901 (m-80) REVERT: B 479 MET cc_start: 0.7294 (mtm) cc_final: 0.6924 (mmt) outliers start: 51 outliers final: 29 residues processed: 168 average time/residue: 1.1298 time to fit residues: 205.1002 Evaluate side-chains 154 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 117 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 390 ASP 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 459 ILE Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 700 LYS Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 810 ASP Chi-restraints excluded: chain A residue 852 ARG Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 959 ASP 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 337 ASP Chi-restraints excluded: chain B residue 389 LYS Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 441 ASN 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: 7.9990 chunk 35 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 22 optimal weight: 0.1980 chunk 75 optimal weight: 0.0270 chunk 80 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 107 optimal weight: 20.0000 chunk 113 optimal weight: 10.0000 overall best weight: 1.6444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 917 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10460 Z= 0.205 Angle : 0.582 7.327 14112 Z= 0.306 Chirality : 0.044 0.172 1527 Planarity : 0.004 0.041 1811 Dihedral : 5.112 31.188 1369 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.70 % Favored : 94.22 % Rotamer: Outliers : 4.40 % Allowed : 17.61 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.22 (0.23), residues: 1228 helix: -1.31 (0.21), residues: 529 sheet: -0.89 (0.41), residues: 150 loop : -1.69 (0.25), residues: 549 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 0.022 0.002 PHE A 937 TYR 0.013 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 180 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 130 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.7585 (OUTLIER) cc_final: 0.7341 (mmt) REVERT: A 211 ILE cc_start: 0.6307 (OUTLIER) cc_final: 0.5537 (pp) REVERT: A 391 ILE cc_start: 0.8065 (OUTLIER) cc_final: 0.7573 (tp) REVERT: A 459 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.8104 (tt) REVERT: A 745 MET cc_start: 0.7754 (mpp) cc_final: 0.7450 (mmm) REVERT: A 852 ARG cc_start: 0.6017 (OUTLIER) cc_final: 0.5814 (mtt-85) REVERT: A 954 PHE cc_start: 0.6876 (OUTLIER) cc_final: 0.6523 (m-80) REVERT: A 977 PHE cc_start: 0.7448 (OUTLIER) cc_final: 0.6586 (p90) REVERT: A 993 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.7678 (mt0) REVERT: B 389 LYS cc_start: 0.7318 (OUTLIER) cc_final: 0.6437 (mmtt) REVERT: B 431 TYR cc_start: 0.6328 (m-10) cc_final: 0.5901 (m-80) REVERT: B 455 GLN cc_start: 0.7294 (mm-40) cc_final: 0.6896 (mm-40) REVERT: B 479 MET cc_start: 0.7302 (mtm) cc_final: 0.6845 (mmt) outliers start: 50 outliers final: 29 residues processed: 167 average time/residue: 1.1686 time to fit residues: 210.3234 Evaluate side-chains 162 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 124 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 390 ASP 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 459 ILE Chi-restraints excluded: chain A residue 461 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 610 MET Chi-restraints excluded: chain A residue 700 LYS Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 810 ASP Chi-restraints excluded: chain A residue 852 ARG Chi-restraints excluded: chain A residue 920 ASN Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 954 PHE Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain A residue 977 PHE Chi-restraints excluded: chain A residue 993 GLN Chi-restraints excluded: chain A residue 1014 GLN Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 389 LYS Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 441 ASN 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: 5.9990 chunk 110 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 48 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 33 optimal weight: 0.0980 chunk 99 optimal weight: 7.9990 chunk 104 optimal weight: 6.9990 chunk 72 optimal weight: 0.2980 chunk 116 optimal weight: 8.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 825 GLN A 917 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10460 Z= 0.210 Angle : 0.585 7.278 14112 Z= 0.306 Chirality : 0.044 0.170 1527 Planarity : 0.004 0.038 1811 Dihedral : 5.062 31.595 1369 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.70 % Favored : 94.22 % Rotamer: Outliers : 3.70 % Allowed : 18.75 % Favored : 77.55 % 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: -1.97 (0.23), residues: 1228 helix: -1.08 (0.22), residues: 524 sheet: -0.73 (0.42), residues: 148 loop : -1.60 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 669 HIS 0.005 0.001 HIS A 450 PHE 0.022 0.002 PHE A 937 TYR 0.013 0.001 TYR A 392 ARG 0.008 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 169 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 127 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.7574 (OUTLIER) cc_final: 0.7358 (mmm) REVERT: A 211 ILE cc_start: 0.6329 (OUTLIER) cc_final: 0.5607 (pp) REVERT: A 391 ILE cc_start: 0.8050 (OUTLIER) cc_final: 0.7562 (tp) REVERT: A 459 ILE cc_start: 0.8401 (OUTLIER) cc_final: 0.8076 (tt) REVERT: A 745 MET cc_start: 0.7784 (mpp) cc_final: 0.7479 (mmm) REVERT: A 852 ARG cc_start: 0.6069 (OUTLIER) cc_final: 0.5857 (mtt-85) REVERT: A 954 PHE cc_start: 0.6890 (OUTLIER) cc_final: 0.6548 (m-80) REVERT: A 977 PHE cc_start: 0.7440 (OUTLIER) cc_final: 0.6630 (p90) REVERT: A 993 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7669 (mt0) REVERT: B 389 LYS cc_start: 0.7220 (OUTLIER) cc_final: 0.6344 (mmtt) REVERT: B 431 TYR cc_start: 0.6327 (m-10) cc_final: 0.5931 (m-80) REVERT: B 479 MET cc_start: 0.7312 (mtm) cc_final: 0.6835 (mmt) outliers start: 42 outliers final: 30 residues processed: 158 average time/residue: 1.1862 time to fit residues: 202.8827 Evaluate side-chains 163 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 124 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 700 LYS Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 810 ASP Chi-restraints excluded: chain A residue 852 ARG Chi-restraints excluded: chain A residue 920 ASN Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 954 PHE Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain A residue 977 PHE Chi-restraints excluded: chain A residue 993 GLN 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 441 ASN 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: 1.9990 chunk 55 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 122 optimal weight: 0.9990 chunk 112 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 75 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 ASN ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 917 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10460 Z= 0.221 Angle : 0.597 7.378 14112 Z= 0.313 Chirality : 0.045 0.170 1527 Planarity : 0.004 0.040 1811 Dihedral : 5.057 31.765 1369 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.62 % Favored : 94.30 % Rotamer: Outliers : 3.70 % Allowed : 18.93 % Favored : 77.38 % 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: 525 sheet: -0.77 (0.40), residues: 155 loop : -1.59 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 386 HIS 0.005 0.001 HIS A 450 PHE 0.023 0.002 PHE A 937 TYR 0.013 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 166 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 124 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.7558 (OUTLIER) cc_final: 0.7348 (mmm) REVERT: A 211 ILE cc_start: 0.6354 (OUTLIER) cc_final: 0.5626 (pp) REVERT: A 391 ILE cc_start: 0.8041 (OUTLIER) cc_final: 0.7561 (tp) REVERT: A 459 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.8074 (tt) REVERT: A 745 MET cc_start: 0.7779 (mpp) cc_final: 0.7473 (mmm) REVERT: A 852 ARG cc_start: 0.6078 (OUTLIER) cc_final: 0.5867 (mtt-85) REVERT: A 954 PHE cc_start: 0.6903 (OUTLIER) cc_final: 0.6563 (m-80) REVERT: A 977 PHE cc_start: 0.7441 (OUTLIER) cc_final: 0.6636 (p90) REVERT: A 993 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.7647 (mt0) REVERT: B 389 LYS cc_start: 0.7212 (OUTLIER) cc_final: 0.6334 (mmtt) REVERT: B 431 TYR cc_start: 0.6345 (m-10) cc_final: 0.5901 (m-80) REVERT: B 479 MET cc_start: 0.7317 (mtm) cc_final: 0.6852 (mmt) outliers start: 42 outliers final: 29 residues processed: 154 average time/residue: 1.1779 time to fit residues: 195.8498 Evaluate side-chains 158 residues out of total 1142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 120 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 461 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 610 MET Chi-restraints excluded: chain A residue 700 LYS Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 810 ASP Chi-restraints excluded: chain A residue 852 ARG Chi-restraints excluded: chain A residue 920 ASN Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 954 PHE Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain A residue 977 PHE Chi-restraints excluded: chain A residue 993 GLN 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 441 ASN 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: 7.9990 chunk 89 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 85 optimal weight: 0.8980 chunk 5 optimal weight: 0.1980 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4243 r_free = 0.4243 target = 0.185879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.143546 restraints weight = 11238.721| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.22 r_work: 0.3473 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 10460 Z= 0.308 Angle : 0.662 7.439 14112 Z= 0.345 Chirality : 0.048 0.180 1527 Planarity : 0.005 0.038 1811 Dihedral : 5.367 34.100 1369 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.84 % Favored : 93.08 % Rotamer: Outliers : 3.79 % Allowed : 18.84 % Favored : 77.38 % 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: -2.19 (0.23), residues: 1228 helix: -1.34 (0.21), residues: 530 sheet: -0.73 (0.41), residues: 155 loop : -1.67 (0.25), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 590 HIS 0.006 0.001 HIS A 759 PHE 0.027 0.002 PHE A 937 TYR 0.014 0.002 TYR A 392 ARG 0.007 0.001 ARG B 503 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4235.67 seconds wall clock time: 74 minutes 36.31 seconds (4476.31 seconds total)