Starting phenix.real_space_refine on Fri Feb 16 05:33:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olx_16964/02_2024/8olx_16964_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olx_16964/02_2024/8olx_16964.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olx_16964/02_2024/8olx_16964.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olx_16964/02_2024/8olx_16964.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olx_16964/02_2024/8olx_16964_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olx_16964/02_2024/8olx_16964_updated.pdb" } resolution = 3.1 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= 0.001 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 47 5.49 5 Mg 1 5.21 5 S 65 5.16 5 C 9068 2.51 5 N 2488 2.21 5 O 2823 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 56": "OE1" <-> "OE2" Residue "A GLU 226": "OE1" <-> "OE2" Residue "A GLU 290": "OE1" <-> "OE2" Residue "A GLU 452": "OE1" <-> "OE2" Residue "A GLU 768": "OE1" <-> "OE2" Residue "A GLU 850": "OE1" <-> "OE2" Residue "B GLU 233": "OE1" <-> "OE2" Residue "B GLU 251": "OE1" <-> "OE2" Residue "B GLU 373": "OE1" <-> "OE2" Residue "B GLU 425": "OE1" <-> "OE2" Residue "B GLU 523": "OE1" <-> "OE2" Residue "B GLU 718": "OE1" <-> "OE2" Residue "B GLU 812": "OE1" <-> "OE2" Residue "B GLU 886": "OE1" <-> "OE2" Residue "B GLU 889": "OE1" <-> "OE2" Residue "B GLU 1092": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14492 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 863, 6832 Classifications: {'peptide': 863} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 836} Chain breaks: 6 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 6709 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 836, 6706 Classifications: {'peptide': 836} Link IDs: {'PTRANS': 25, 'TRANS': 810} Chain breaks: 5 Conformer: "B" Number of residues, atoms: 836, 6706 Classifications: {'peptide': 836} Link IDs: {'PTRANS': 25, 'TRANS': 810} Chain breaks: 5 bond proxies already assigned to first conformer: 6825 Chain: "C" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 408 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain breaks: 1 Chain: "D" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 515 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain breaks: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.39, per 1000 atoms: 0.72 Number of scatterers: 14492 At special positions: 0 Unit cell: (93.2484, 118.846, 169.127, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 65 16.00 P 47 15.00 Mg 1 11.99 O 2823 8.00 N 2488 7.00 C 9068 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: 5.96 Conformation dependent library (CDL) restraints added in 3.5 seconds 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3230 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 68 helices and 11 sheets defined 47.0% alpha, 10.6% beta 18 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 6.36 Creating SS restraints... Processing helix chain 'A' and resid 17 through 25 Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'A' and resid 82 through 93 Processing helix chain 'A' and resid 185 through 194 Processing helix chain 'A' and resid 208 through 220 removed outlier: 3.805A pdb=" N GLY A 220 " --> pdb=" O ILE A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'A' and resid 237 through 242 Processing helix chain 'A' and resid 255 through 257 No H-bonds generated for 'chain 'A' and resid 255 through 257' Processing helix chain 'A' and resid 259 through 261 No H-bonds generated for 'chain 'A' and resid 259 through 261' Processing helix chain 'A' and resid 264 through 277 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 298 No H-bonds generated for 'chain 'A' and resid 296 through 298' Processing helix chain 'A' and resid 304 through 309 Processing helix chain 'A' and resid 326 through 329 No H-bonds generated for 'chain 'A' and resid 326 through 329' Processing helix chain 'A' and resid 336 through 347 Processing helix chain 'A' and resid 353 through 368 Processing helix chain 'A' and resid 370 through 377 Processing helix chain 'A' and resid 381 through 383 No H-bonds generated for 'chain 'A' and resid 381 through 383' Processing helix chain 'A' and resid 387 through 395 Processing helix chain 'A' and resid 401 through 421 Proline residue: A 415 - end of helix Processing helix chain 'A' and resid 430 through 444 removed outlier: 3.601A pdb=" N VAL A 435 " --> pdb=" O LEU A 431 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE A 436 " --> pdb=" O LEU A 432 " (cutoff:3.500A) Proline residue: A 439 - end of helix Processing helix chain 'A' and resid 448 through 456 Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 476 through 503 Processing helix chain 'A' and resid 527 through 533 removed outlier: 3.752A pdb=" N GLU A 530 " --> pdb=" O CYS A 527 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS A 531 " --> pdb=" O LYS A 528 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU A 533 " --> pdb=" O GLU A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 586 removed outlier: 3.651A pdb=" N THR A 568 " --> pdb=" O THR A 564 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU A 569 " --> pdb=" O LYS A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 613 Processing helix chain 'A' and resid 642 through 644 No H-bonds generated for 'chain 'A' and resid 642 through 644' Processing helix chain 'A' and resid 676 through 691 Processing helix chain 'A' and resid 725 through 738 Processing helix chain 'A' and resid 756 through 772 Processing helix chain 'A' and resid 785 through 792 removed outlier: 3.954A pdb=" N ALA A 789 " --> pdb=" O GLU A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 833 Processing helix chain 'A' and resid 838 through 851 Processing helix chain 'A' and resid 881 through 892 Processing helix chain 'A' and resid 901 through 921 removed outlier: 4.110A pdb=" N GLU A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL A 915 " --> pdb=" O LEU A 911 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ASN A 920 " --> pdb=" O ILE A 916 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N SER A 921 " --> pdb=" O ALA A 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 242 removed outlier: 3.922A pdb=" N GLN B 242 " --> pdb=" O GLU B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 270 removed outlier: 4.061A pdb=" N GLU B 269 " --> pdb=" O ALA B 266 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU B 270 " --> pdb=" O ALA B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 299 removed outlier: 3.532A pdb=" N LEU B 290 " --> pdb=" O THR B 287 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N PHE B 291 " --> pdb=" O HIS B 288 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B 292 " --> pdb=" O ARG B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 318 removed outlier: 3.876A pdb=" N ALA B 317 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE B 318 " --> pdb=" O ALA B 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 313 through 318' Processing helix chain 'B' and resid 413 through 421 Processing helix chain 'B' and resid 434 through 445 Processing helix chain 'B' and resid 460 through 462 No H-bonds generated for 'chain 'B' and resid 460 through 462' Processing helix chain 'B' and resid 465 through 475 Processing helix chain 'B' and resid 490 through 494 Processing helix chain 'B' and resid 497 through 511 Processing helix chain 'B' and resid 516 through 519 Processing helix chain 'B' and resid 522 through 524 No H-bonds generated for 'chain 'B' and resid 522 through 524' Processing helix chain 'B' and resid 539 through 544 Processing helix chain 'B' and resid 560 through 564 Processing helix chain 'B' and resid 571 through 581 Processing helix chain 'B' and resid 587 through 602 Processing helix chain 'B' and resid 607 through 614 Processing helix chain 'B' and resid 621 through 629 Processing helix chain 'B' and resid 635 through 654 Processing helix chain 'B' and resid 656 through 662 Processing helix chain 'B' and resid 666 through 672 Processing helix chain 'B' and resid 675 through 685 removed outlier: 4.056A pdb=" N SER B 680 " --> pdb=" O PRO B 676 " (cutoff:3.500A) Proline residue: B 681 - end of helix removed outlier: 4.810A pdb=" N HIS B 684 " --> pdb=" O SER B 680 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TYR B 685 " --> pdb=" O PRO B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 696 Processing helix chain 'B' and resid 710 through 737 removed outlier: 3.680A pdb=" N LYS B 714 " --> pdb=" O PRO B 710 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG B 715 " --> pdb=" O LEU B 711 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU B 730 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLN B 731 " --> pdb=" O ARG B 727 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLU B 732 " --> pdb=" O MET B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 840 removed outlier: 3.529A pdb=" N GLU B 816 " --> pdb=" O GLU B 812 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N HIS B 817 " --> pdb=" O LYS B 813 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N TYR B 818 " --> pdb=" O PHE B 814 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N HIS B 819 " --> pdb=" O SER B 815 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N SER B 820 " --> pdb=" O GLU B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 870 removed outlier: 3.517A pdb=" N VAL B 869 " --> pdb=" O PRO B 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 900 through 918 Processing helix chain 'B' and resid 952 through 965 Processing helix chain 'B' and resid 983 through 999 Processing helix chain 'B' and resid 1012 through 1019 removed outlier: 3.988A pdb=" N GLU B1016 " --> pdb=" O PRO B1012 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N LEU B1017 " --> pdb=" O PRO B1013 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N GLU B1018 " --> pdb=" O VAL B1014 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LYS B1019 " --> pdb=" O CYS B1015 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1012 through 1019' Processing helix chain 'B' and resid 1069 through 1075 Processing helix chain 'B' and resid 1080 through 1112 Processing sheet with id= A, first strand: chain 'A' and resid 77 through 80 removed outlier: 4.335A pdb=" N HIS A 46 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ARG A 35 " --> pdb=" O HIS A 46 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ARG A 99 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LEU A 36 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N GLU A 101 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ASP A 38 " --> pdb=" O GLU A 101 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N TYR A 103 " --> pdb=" O ASP A 38 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LYS A 104 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N LEU A 119 " --> pdb=" O LYS A 104 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 148 through 152 removed outlier: 4.218A pdb=" N ARG A 159 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLU A 290 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N LEU A 175 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N THR A 292 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N GLU A 177 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 511 through 514 Processing sheet with id= D, first strand: chain 'A' and resid 632 through 635 Processing sheet with id= E, first strand: chain 'A' and resid 817 through 819 removed outlier: 5.786A pdb=" N PHE A 664 " --> pdb=" O ASN A 798 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU A 800 " --> pdb=" O PHE A 664 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ILE A 666 " --> pdb=" O LEU A 800 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N VAL A 802 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR A 668 " --> pdb=" O VAL A 802 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N CYS A 778 " --> pdb=" O HIS A 665 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N ILE A 667 " --> pdb=" O CYS A 778 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N PHE A 780 " --> pdb=" O ILE A 667 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 804 through 806 Processing sheet with id= G, first strand: chain 'B' and resid 282 through 286 removed outlier: 4.431A pdb=" N PHE B 259 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N LEU B 248 " --> pdb=" O PHE B 259 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLN B 309 " --> pdb=" O GLU B 251 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA B 332 " --> pdb=" O VAL B 306 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LYS B 308 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N LEU B 330 " --> pdb=" O LYS B 308 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 399 through 407 removed outlier: 3.688A pdb=" N GLU B 399 " --> pdb=" O GLN B 394 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N LEU B 369 " --> pdb=" O VAL B 424 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU B 426 " --> pdb=" O LEU B 369 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ILE B 371 " --> pdb=" O LEU B 426 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N LEU B 428 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 9.600A pdb=" N GLU B 373 " --> pdb=" O LEU B 428 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ARG B 454 " --> pdb=" O LEU B 426 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N LEU B 428 " --> pdb=" O ARG B 454 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLU B 456 " --> pdb=" O LEU B 428 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 754 through 757 removed outlier: 3.507A pdb=" N ILE B 754 " --> pdb=" O PHE B 780 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 882 through 885 removed outlier: 3.796A pdb=" N GLU B 926 " --> pdb=" O LYS B 860 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 1059 through 1061 removed outlier: 6.308A pdb=" N VAL B 891 " --> pdb=" O GLY B1026 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N TYR B1028 " --> pdb=" O VAL B 891 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ILE B 893 " --> pdb=" O TYR B1028 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N MET B1030 " --> pdb=" O ILE B 893 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N THR B 895 " --> pdb=" O MET B1030 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR B1005 " --> pdb=" O MET B 892 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE B 894 " --> pdb=" O THR B1005 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N PHE B1007 " --> pdb=" O ILE B 894 " (cutoff:3.500A) 593 hydrogen bonds defined for protein. 1677 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 92 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 5.52 Time building geometry restraints manager: 6.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3881 1.34 - 1.46: 4136 1.46 - 1.58: 6621 1.58 - 1.70: 87 1.70 - 1.82: 105 Bond restraints: 14830 Sorted by residual: bond pdb=" C4 ADP A1001 " pdb=" C5 ADP A1001 " ideal model delta sigma weight residual 1.490 1.390 0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" C1' DG D 42 " pdb=" N9 DG D 42 " ideal model delta sigma weight residual 1.460 1.376 0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" C1' G C 26 " pdb=" N9 G C 26 " ideal model delta sigma weight residual 1.460 1.376 0.084 2.00e-02 2.50e+03 1.74e+01 bond pdb=" C1' G C 21 " pdb=" N9 G C 21 " ideal model delta sigma weight residual 1.460 1.377 0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" C1' DG D 38 " pdb=" N9 DG D 38 " ideal model delta sigma weight residual 1.460 1.379 0.081 2.00e-02 2.50e+03 1.64e+01 ... (remaining 14825 not shown) Histogram of bond angle deviations from ideal: 84.37 - 94.36: 1 94.36 - 104.36: 324 104.36 - 114.35: 8880 114.35 - 124.35: 10583 124.35 - 134.34: 403 Bond angle restraints: 20191 Sorted by residual: angle pdb=" N PRO A 415 " pdb=" CD PRO A 415 " pdb=" CG PRO A 415 " ideal model delta sigma weight residual 103.20 84.37 18.83 1.50e+00 4.44e-01 1.58e+02 angle pdb=" CA PRO A 415 " pdb=" N PRO A 415 " pdb=" CD PRO A 415 " ideal model delta sigma weight residual 112.00 105.06 6.94 1.40e+00 5.10e-01 2.46e+01 angle pdb=" N PRO A 415 " pdb=" CA PRO A 415 " pdb=" CB PRO A 415 " ideal model delta sigma weight residual 103.25 98.17 5.08 1.05e+00 9.07e-01 2.34e+01 angle pdb=" CA ASP B 320 " pdb=" CB ASP B 320 " pdb=" CG ASP B 320 " ideal model delta sigma weight residual 112.60 116.86 -4.26 1.00e+00 1.00e+00 1.81e+01 angle pdb=" CA ASP B 705 " pdb=" CB ASP B 705 " pdb=" CG ASP B 705 " ideal model delta sigma weight residual 112.60 116.81 -4.21 1.00e+00 1.00e+00 1.77e+01 ... (remaining 20186 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.41: 8159 29.41 - 58.81: 699 58.81 - 88.22: 54 88.22 - 117.62: 4 117.62 - 147.03: 1 Dihedral angle restraints: 8917 sinusoidal: 3947 harmonic: 4970 Sorted by residual: dihedral pdb=" C5' ADP A1001 " pdb=" O5' ADP A1001 " pdb=" PA ADP A1001 " pdb=" O2A ADP A1001 " ideal model delta sinusoidal sigma weight residual -60.00 87.03 -147.03 1 2.00e+01 2.50e-03 4.41e+01 dihedral pdb=" CD ARG B 979 " pdb=" NE ARG B 979 " pdb=" CZ ARG B 979 " pdb=" NH1 ARG B 979 " ideal model delta sinusoidal sigma weight residual 0.00 -50.78 50.78 1 1.00e+01 1.00e-02 3.53e+01 dihedral pdb=" O2A ADP A1001 " pdb=" O3A ADP A1001 " pdb=" PA ADP A1001 " pdb=" PB ADP A1001 " ideal model delta sinusoidal sigma weight residual -60.00 57.59 -117.59 1 2.00e+01 2.50e-03 3.51e+01 ... (remaining 8914 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1555 0.075 - 0.150: 677 0.150 - 0.226: 72 0.226 - 0.301: 4 0.301 - 0.376: 2 Chirality restraints: 2310 Sorted by residual: chirality pdb=" CA PRO A 415 " pdb=" N PRO A 415 " pdb=" C PRO A 415 " pdb=" CB PRO A 415 " both_signs ideal model delta sigma weight residual False 2.72 2.34 0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" CA MET A 492 " pdb=" N MET A 492 " pdb=" C MET A 492 " pdb=" CB MET A 492 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA PRO A 591 " pdb=" N PRO A 591 " pdb=" C PRO A 591 " pdb=" CB PRO A 591 " both_signs ideal model delta sigma weight residual False 2.72 2.43 0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 2307 not shown) Planarity restraints: 2416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 979 " 0.827 9.50e-02 1.11e+02 3.71e-01 8.36e+01 pdb=" NE ARG B 979 " -0.050 2.00e-02 2.50e+03 pdb=" CZ ARG B 979 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG B 979 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B 979 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 414 " 0.018 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C LEU A 414 " -0.059 2.00e-02 2.50e+03 pdb=" O LEU A 414 " 0.021 2.00e-02 2.50e+03 pdb=" N PRO A 415 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 414 " 0.055 5.00e-02 4.00e+02 7.99e-02 1.02e+01 pdb=" N PRO A 415 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO A 415 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 415 " 0.043 5.00e-02 4.00e+02 ... (remaining 2413 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 140 2.57 - 3.16: 11939 3.16 - 3.74: 24240 3.74 - 4.32: 32720 4.32 - 4.90: 52569 Nonbonded interactions: 121608 Sorted by model distance: nonbonded pdb=" NZ LYS B 757 " pdb=" C7 DT C 20 " model vdw 1.992 3.540 nonbonded pdb=" OG SER A 676 " pdb="MG MG A1000 " model vdw 2.063 2.170 nonbonded pdb="MG MG A1000 " pdb=" O1B ADP A1001 " model vdw 2.088 2.170 nonbonded pdb=" NH2 ARG B 574 " pdb=" OE1 GLU B 622 " model vdw 2.125 2.520 nonbonded pdb=" OG1 THR B 230 " pdb=" OE1 GLU B 233 " model vdw 2.174 2.440 ... (remaining 121603 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=0.39 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: 1.630 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: 7.440 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 47.320 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.070 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 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 : 0.007 0.100 14830 Z= 0.439 Angle : 0.966 18.833 20191 Z= 0.616 Chirality : 0.074 0.376 2310 Planarity : 0.009 0.371 2416 Dihedral : 19.708 147.026 5687 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.00 % Allowed : 25.90 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.32 (0.21), residues: 1674 helix: 0.88 (0.18), residues: 795 sheet: -0.83 (0.36), residues: 211 loop : -1.30 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 807 HIS 0.007 0.002 HIS B 614 PHE 0.025 0.003 PHE B 752 TYR 0.017 0.004 TYR B 236 ARG 0.012 0.001 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 394 time to evaluate : 1.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 VAL cc_start: 0.7838 (OUTLIER) cc_final: 0.7482 (p) REVERT: A 67 MET cc_start: 0.7949 (ttt) cc_final: 0.7643 (ttt) REVERT: A 159 ARG cc_start: 0.7157 (OUTLIER) cc_final: 0.6926 (mtm-85) REVERT: A 254 ASN cc_start: 0.6863 (t0) cc_final: 0.6582 (t0) REVERT: A 313 PHE cc_start: 0.7516 (m-10) cc_final: 0.7283 (m-10) REVERT: A 471 LYS cc_start: 0.8322 (ptpt) cc_final: 0.8097 (ttmt) REVERT: A 574 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.8020 (tt0) REVERT: A 658 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7398 (mt-10) REVERT: B 320 ASP cc_start: 0.8545 (p0) cc_final: 0.8283 (p0) REVERT: B 445 SER cc_start: 0.7952 (t) cc_final: 0.7324 (m) REVERT: B 452 ARG cc_start: 0.8177 (ttt-90) cc_final: 0.7821 (ttt-90) REVERT: B 812 GLU cc_start: 0.8022 (tp30) cc_final: 0.7653 (tp30) REVERT: B 985 ASP cc_start: 0.8280 (m-30) cc_final: 0.7925 (t0) outliers start: 30 outliers final: 16 residues processed: 411 average time/residue: 0.2979 time to fit residues: 171.9389 Evaluate side-chains 403 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 384 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 159 ARG Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 574 GLN Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain B residue 709 PHE Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 1060 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 0.9980 chunk 131 optimal weight: 0.9990 chunk 72 optimal weight: 0.0060 chunk 44 optimal weight: 0.2980 chunk 88 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 135 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 82 optimal weight: 20.0000 chunk 100 optimal weight: 0.7980 chunk 157 optimal weight: 3.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 GLN A 377 GLN ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 ASN A 799 ASN A 824 GLN B 538 ASN ** B 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 HIS B 729 HIS B 743 GLN ** B 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 HIS ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.0748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14830 Z= 0.207 Angle : 0.567 7.453 20191 Z= 0.300 Chirality : 0.041 0.153 2310 Planarity : 0.004 0.043 2416 Dihedral : 17.376 130.648 2344 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.73 % Allowed : 26.43 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.05 (0.21), residues: 1674 helix: 1.07 (0.18), residues: 800 sheet: -0.89 (0.38), residues: 187 loop : -1.05 (0.25), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 764 HIS 0.005 0.001 HIS B 781 PHE 0.020 0.001 PHE A 232 TYR 0.013 0.001 TYR B 236 ARG 0.006 0.000 ARG A 680 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 389 time to evaluate : 2.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.7896 (ttt) cc_final: 0.7625 (ttt) REVERT: A 119 LEU cc_start: 0.8451 (tp) cc_final: 0.8190 (tp) REVERT: A 180 ASP cc_start: 0.7839 (t0) cc_final: 0.7627 (t0) REVERT: A 215 GLN cc_start: 0.7927 (tm-30) cc_final: 0.7559 (tm-30) REVERT: A 254 ASN cc_start: 0.6827 (t0) cc_final: 0.6534 (t0) REVERT: A 351 MET cc_start: 0.7859 (OUTLIER) cc_final: 0.7454 (mpp) REVERT: A 430 LYS cc_start: 0.5867 (mmmt) cc_final: 0.5264 (mmtt) REVERT: A 471 LYS cc_start: 0.8315 (ptpt) cc_final: 0.8093 (ttmt) REVERT: A 530 GLU cc_start: 0.6734 (OUTLIER) cc_final: 0.6370 (mp0) REVERT: A 562 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7802 (mm-30) REVERT: A 569 GLU cc_start: 0.7881 (tp30) cc_final: 0.7563 (tp30) REVERT: A 658 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7432 (mt-10) REVERT: A 672 MET cc_start: 0.7607 (mmt) cc_final: 0.7380 (mpp) REVERT: A 850 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7886 (tm-30) REVERT: A 899 MET cc_start: 0.5051 (tmm) cc_final: 0.4713 (tmm) REVERT: B 264 GLU cc_start: 0.7674 (mp0) cc_final: 0.7425 (mp0) REVERT: B 445 SER cc_start: 0.7874 (t) cc_final: 0.7241 (m) REVERT: B 452 ARG cc_start: 0.8170 (ttt-90) cc_final: 0.7803 (ttt-90) REVERT: B 606 SER cc_start: 0.8360 (m) cc_final: 0.7799 (p) REVERT: B 860 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.8086 (ttpt) REVERT: B 1077 ASP cc_start: 0.8097 (t0) cc_final: 0.7644 (t0) outliers start: 41 outliers final: 17 residues processed: 412 average time/residue: 0.2962 time to fit residues: 171.9051 Evaluate side-chains 391 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 371 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 404 CYS Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 553 ASN Chi-restraints excluded: chain A residue 560 ASN Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 824 GLN Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 860 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 157 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 ASN ** B 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 HIS ** B 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 14830 Z= 0.342 Angle : 0.585 6.917 20191 Z= 0.310 Chirality : 0.043 0.225 2310 Planarity : 0.004 0.051 2416 Dihedral : 17.183 125.862 2308 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.53 % Allowed : 27.10 % Favored : 69.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.12 (0.21), residues: 1674 helix: 0.95 (0.18), residues: 801 sheet: -0.77 (0.37), residues: 197 loop : -1.06 (0.25), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 807 HIS 0.005 0.001 HIS B 781 PHE 0.020 0.002 PHE A 760 TYR 0.016 0.002 TYR A 678 ARG 0.007 0.001 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 389 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.7941 (ttt) cc_final: 0.7658 (ttt) REVERT: A 180 ASP cc_start: 0.7978 (t0) cc_final: 0.7681 (t0) REVERT: A 215 GLN cc_start: 0.7983 (tm-30) cc_final: 0.7609 (tm-30) REVERT: A 254 ASN cc_start: 0.6952 (t0) cc_final: 0.6650 (t0) REVERT: A 261 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7299 (tmm) REVERT: A 351 MET cc_start: 0.7931 (OUTLIER) cc_final: 0.7501 (mpp) REVERT: A 402 GLN cc_start: 0.7478 (tt0) cc_final: 0.7037 (tp40) REVERT: A 471 LYS cc_start: 0.8339 (ptpt) cc_final: 0.8125 (ttmt) REVERT: A 514 ASP cc_start: 0.8127 (t0) cc_final: 0.7867 (t0) REVERT: A 530 GLU cc_start: 0.6775 (OUTLIER) cc_final: 0.6400 (mp0) REVERT: A 562 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7816 (mm-30) REVERT: A 569 GLU cc_start: 0.7919 (tp30) cc_final: 0.7549 (tp30) REVERT: A 658 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7530 (mt-10) REVERT: A 671 ASN cc_start: 0.8451 (t0) cc_final: 0.8227 (t0) REVERT: A 672 MET cc_start: 0.7686 (mmt) cc_final: 0.7378 (mpp) REVERT: A 850 GLU cc_start: 0.8255 (tm-30) cc_final: 0.7882 (tm-30) REVERT: A 899 MET cc_start: 0.5090 (OUTLIER) cc_final: 0.4539 (tmm) REVERT: B 445 SER cc_start: 0.7915 (t) cc_final: 0.7279 (m) REVERT: B 452 ARG cc_start: 0.8178 (ttt-90) cc_final: 0.7788 (ttt-90) REVERT: B 606 SER cc_start: 0.8394 (m) cc_final: 0.7847 (p) REVERT: B 860 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.8091 (ttpt) REVERT: B 961 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7435 (mm-30) REVERT: B 1077 ASP cc_start: 0.8100 (t0) cc_final: 0.7613 (t0) outliers start: 53 outliers final: 33 residues processed: 414 average time/residue: 0.2945 time to fit residues: 172.5028 Evaluate side-chains 421 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 383 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 404 CYS Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 553 ASN Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 653 ASN Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 824 GLN Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 860 LYS Chi-restraints excluded: chain B residue 951 THR Chi-restraints excluded: chain B residue 1096 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 155 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 81 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 157 optimal weight: 0.8980 chunk 167 optimal weight: 5.9990 chunk 82 optimal weight: 8.9990 chunk 149 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 115 ASN ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 799 ASN ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 ASN ** B 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 HIS ** B 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 14830 Z= 0.324 Angle : 0.592 9.492 20191 Z= 0.310 Chirality : 0.042 0.178 2310 Planarity : 0.004 0.054 2416 Dihedral : 17.154 139.916 2308 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 4.39 % Allowed : 27.10 % Favored : 68.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.14 (0.21), residues: 1674 helix: 0.91 (0.18), residues: 802 sheet: -0.78 (0.36), residues: 195 loop : -1.03 (0.25), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 807 HIS 0.006 0.001 HIS B 781 PHE 0.030 0.002 PHE A 232 TYR 0.015 0.002 TYR A 678 ARG 0.008 0.001 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 385 time to evaluate : 1.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.7932 (ttt) cc_final: 0.7629 (ttt) REVERT: A 97 GLN cc_start: 0.8302 (mm-40) cc_final: 0.7946 (mm-40) REVERT: A 215 GLN cc_start: 0.8011 (tm-30) cc_final: 0.7580 (tm-30) REVERT: A 254 ASN cc_start: 0.6958 (t0) cc_final: 0.6624 (t0) REVERT: A 261 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7305 (tmm) REVERT: A 313 PHE cc_start: 0.7428 (m-10) cc_final: 0.7044 (m-10) REVERT: A 373 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7987 (ttp-110) REVERT: A 402 GLN cc_start: 0.7402 (tt0) cc_final: 0.7016 (tp40) REVERT: A 430 LYS cc_start: 0.6041 (mmmt) cc_final: 0.5082 (mmtt) REVERT: A 471 LYS cc_start: 0.8403 (ptpt) cc_final: 0.8181 (ttmt) REVERT: A 530 GLU cc_start: 0.6820 (OUTLIER) cc_final: 0.6447 (mp0) REVERT: A 562 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7855 (mm-30) REVERT: A 569 GLU cc_start: 0.7890 (tp30) cc_final: 0.7466 (tp30) REVERT: A 638 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7875 (ptt-90) REVERT: A 658 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7547 (mt-10) REVERT: A 691 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.7833 (pt) REVERT: A 728 GLU cc_start: 0.7420 (tm-30) cc_final: 0.7220 (tm-30) REVERT: A 749 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7372 (mt-10) REVERT: A 850 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7892 (tm-30) REVERT: A 899 MET cc_start: 0.5073 (OUTLIER) cc_final: 0.4537 (tmm) REVERT: B 264 GLU cc_start: 0.7686 (mp0) cc_final: 0.7405 (mp0) REVERT: B 342 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7648 (pm20) REVERT: B 445 SER cc_start: 0.7920 (t) cc_final: 0.7286 (m) REVERT: B 458 MET cc_start: 0.8455 (mtp) cc_final: 0.8110 (ttp) REVERT: B 606 SER cc_start: 0.8441 (m) cc_final: 0.7908 (p) REVERT: B 812 GLU cc_start: 0.8078 (tp30) cc_final: 0.7793 (tp30) REVERT: B 860 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.8075 (ttpt) REVERT: B 899 MET cc_start: 0.6020 (ppp) cc_final: 0.5618 (ppp) REVERT: B 961 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7407 (mm-30) REVERT: B 1077 ASP cc_start: 0.8096 (t0) cc_final: 0.7557 (t0) outliers start: 65 outliers final: 36 residues processed: 420 average time/residue: 0.2986 time to fit residues: 176.9064 Evaluate side-chains 422 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 378 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain A residue 404 CYS Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 553 ASN Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 638 ARG Chi-restraints excluded: chain A residue 653 ASN Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 860 LYS Chi-restraints excluded: chain B residue 880 ASN Chi-restraints excluded: chain B residue 904 SER Chi-restraints excluded: chain B residue 951 THR Chi-restraints excluded: chain B residue 1057 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 139 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 124 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 142 optimal weight: 0.9980 chunk 115 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 150 optimal weight: 0.2980 chunk 42 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 GLN B 309 GLN ** B 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 HIS ** B 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14830 Z= 0.251 Angle : 0.570 9.146 20191 Z= 0.298 Chirality : 0.042 0.243 2310 Planarity : 0.004 0.052 2416 Dihedral : 17.077 147.838 2307 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.99 % Allowed : 27.50 % Favored : 68.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.04 (0.21), residues: 1674 helix: 1.02 (0.18), residues: 801 sheet: -0.75 (0.37), residues: 197 loop : -1.02 (0.25), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 807 HIS 0.006 0.001 HIS B 984 PHE 0.027 0.002 PHE A 232 TYR 0.014 0.001 TYR B 236 ARG 0.009 0.000 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 384 time to evaluate : 1.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.7917 (OUTLIER) cc_final: 0.7641 (ttt) REVERT: A 97 GLN cc_start: 0.8286 (mm-40) cc_final: 0.7888 (mt0) REVERT: A 215 GLN cc_start: 0.7996 (tm-30) cc_final: 0.7549 (tm-30) REVERT: A 253 MET cc_start: 0.6400 (ptp) cc_final: 0.6184 (ptt) REVERT: A 254 ASN cc_start: 0.6950 (t0) cc_final: 0.6555 (t0) REVERT: A 261 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7845 (tmm) REVERT: A 373 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.8000 (ttp-110) REVERT: A 402 GLN cc_start: 0.7298 (tt0) cc_final: 0.6949 (tp40) REVERT: A 430 LYS cc_start: 0.6133 (mmmt) cc_final: 0.5575 (mmmt) REVERT: A 471 LYS cc_start: 0.8394 (ptpt) cc_final: 0.8194 (ttmt) REVERT: A 530 GLU cc_start: 0.6809 (OUTLIER) cc_final: 0.6439 (mp0) REVERT: A 562 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7904 (mm-30) REVERT: A 569 GLU cc_start: 0.7879 (tp30) cc_final: 0.7445 (tp30) REVERT: A 638 ARG cc_start: 0.8251 (mtm-85) cc_final: 0.7850 (ptt-90) REVERT: A 658 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7604 (mt-10) REVERT: A 749 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7379 (mt-10) REVERT: A 784 PHE cc_start: 0.8112 (m-80) cc_final: 0.7838 (m-80) REVERT: A 850 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7866 (tm-30) REVERT: A 899 MET cc_start: 0.5073 (OUTLIER) cc_final: 0.4552 (tmm) REVERT: B 342 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7658 (pm20) REVERT: B 445 SER cc_start: 0.7896 (t) cc_final: 0.7306 (m) REVERT: B 452 ARG cc_start: 0.8185 (ttt-90) cc_final: 0.7874 (ttt-90) REVERT: B 458 MET cc_start: 0.8446 (mtp) cc_final: 0.8113 (ttp) REVERT: B 860 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.8052 (ttpt) REVERT: B 899 MET cc_start: 0.5981 (ppp) cc_final: 0.5597 (ppp) REVERT: B 961 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7402 (mm-30) REVERT: B 1077 ASP cc_start: 0.8111 (t0) cc_final: 0.7561 (t0) outliers start: 60 outliers final: 39 residues processed: 415 average time/residue: 0.3040 time to fit residues: 178.8987 Evaluate side-chains 425 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 379 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 404 CYS Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 465 ASN Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 653 ASN Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 824 GLN Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 860 LYS Chi-restraints excluded: chain B residue 904 SER Chi-restraints excluded: chain B residue 951 THR Chi-restraints excluded: chain B residue 1057 TYR Chi-restraints excluded: chain B residue 1096 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 56 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 chunk 87 optimal weight: 0.0570 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN ** B 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 HIS ** B 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14830 Z= 0.226 Angle : 0.556 8.881 20191 Z= 0.292 Chirality : 0.041 0.175 2310 Planarity : 0.004 0.055 2416 Dihedral : 17.001 156.548 2307 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.99 % Allowed : 27.50 % Favored : 68.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.07 (0.21), residues: 1674 helix: 1.13 (0.18), residues: 801 sheet: -0.77 (0.36), residues: 199 loop : -0.96 (0.25), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 807 HIS 0.008 0.001 HIS B 984 PHE 0.024 0.002 PHE A 760 TYR 0.015 0.001 TYR B 236 ARG 0.008 0.000 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 379 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ASP cc_start: 0.7778 (m-30) cc_final: 0.7538 (m-30) REVERT: A 67 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7619 (ttt) REVERT: A 97 GLN cc_start: 0.8247 (mm-40) cc_final: 0.7802 (mt0) REVERT: A 119 LEU cc_start: 0.8456 (tp) cc_final: 0.8197 (tp) REVERT: A 215 GLN cc_start: 0.7999 (tm-30) cc_final: 0.7532 (tm-30) REVERT: A 253 MET cc_start: 0.6414 (ptp) cc_final: 0.6113 (ptt) REVERT: A 254 ASN cc_start: 0.6944 (t0) cc_final: 0.6565 (t0) REVERT: A 261 MET cc_start: 0.8197 (OUTLIER) cc_final: 0.7897 (tmm) REVERT: A 351 MET cc_start: 0.7720 (tpp) cc_final: 0.7480 (mpp) REVERT: A 373 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.8004 (ttp-110) REVERT: A 402 GLN cc_start: 0.7304 (tt0) cc_final: 0.6951 (tp40) REVERT: A 430 LYS cc_start: 0.6112 (mmmt) cc_final: 0.5476 (mmmt) REVERT: A 515 SER cc_start: 0.8376 (m) cc_final: 0.8111 (t) REVERT: A 569 GLU cc_start: 0.7877 (tp30) cc_final: 0.7405 (tp30) REVERT: A 638 ARG cc_start: 0.8239 (mtm-85) cc_final: 0.7849 (ptt-90) REVERT: A 658 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7610 (mt-10) REVERT: A 691 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.7826 (pt) REVERT: A 850 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7824 (tm-30) REVERT: A 899 MET cc_start: 0.5096 (OUTLIER) cc_final: 0.4575 (tmm) REVERT: B 342 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7662 (pm20) REVERT: B 445 SER cc_start: 0.7892 (t) cc_final: 0.7314 (m) REVERT: B 452 ARG cc_start: 0.8149 (ttt-90) cc_final: 0.7838 (ttt-90) REVERT: B 860 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.8044 (ttpt) REVERT: B 898 ASN cc_start: 0.7949 (t0) cc_final: 0.7546 (t0) REVERT: B 899 MET cc_start: 0.5965 (ppp) cc_final: 0.5650 (ppp) REVERT: B 961 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7374 (mm-30) REVERT: B 1077 ASP cc_start: 0.8088 (t0) cc_final: 0.7494 (t0) outliers start: 60 outliers final: 41 residues processed: 410 average time/residue: 0.2991 time to fit residues: 173.0388 Evaluate side-chains 427 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 379 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 404 CYS Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 465 ASN Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 553 ASN Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 781 HIS Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 860 LYS Chi-restraints excluded: chain B residue 904 SER Chi-restraints excluded: chain B residue 951 THR Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1057 TYR Chi-restraints excluded: chain B residue 1096 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 161 optimal weight: 2.9990 chunk 18 optimal weight: 0.0980 chunk 95 optimal weight: 0.2980 chunk 122 optimal weight: 0.5980 chunk 94 optimal weight: 0.7980 chunk 140 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 166 optimal weight: 0.7980 chunk 104 optimal weight: 0.5980 chunk 101 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 799 ASN ** B 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 HIS ** B 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14830 Z= 0.198 Angle : 0.553 8.466 20191 Z= 0.288 Chirality : 0.040 0.178 2310 Planarity : 0.004 0.056 2416 Dihedral : 16.909 160.291 2307 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 4.13 % Allowed : 27.43 % Favored : 68.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.15 (0.21), residues: 1674 helix: 1.22 (0.18), residues: 800 sheet: -0.63 (0.36), residues: 208 loop : -0.99 (0.25), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 764 HIS 0.007 0.001 HIS B 984 PHE 0.033 0.002 PHE A 232 TYR 0.014 0.001 TYR B 236 ARG 0.008 0.000 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 386 time to evaluate : 1.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ASP cc_start: 0.7770 (m-30) cc_final: 0.7523 (m-30) REVERT: A 48 GLU cc_start: 0.8317 (tp30) cc_final: 0.8066 (tp30) REVERT: A 67 MET cc_start: 0.7889 (OUTLIER) cc_final: 0.7598 (ttt) REVERT: A 97 GLN cc_start: 0.8252 (mm-40) cc_final: 0.7815 (mt0) REVERT: A 119 LEU cc_start: 0.8456 (tp) cc_final: 0.8197 (tp) REVERT: A 215 GLN cc_start: 0.7982 (tm-30) cc_final: 0.7495 (tm-30) REVERT: A 253 MET cc_start: 0.6394 (ptp) cc_final: 0.6084 (ptt) REVERT: A 254 ASN cc_start: 0.6955 (t0) cc_final: 0.6587 (t0) REVERT: A 261 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.7930 (tmm) REVERT: A 402 GLN cc_start: 0.7387 (tt0) cc_final: 0.7030 (tp40) REVERT: A 430 LYS cc_start: 0.6125 (mmmt) cc_final: 0.5451 (mmmt) REVERT: A 515 SER cc_start: 0.8408 (m) cc_final: 0.8170 (t) REVERT: A 562 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7905 (mm-30) REVERT: A 569 GLU cc_start: 0.7873 (tp30) cc_final: 0.7404 (tp30) REVERT: A 638 ARG cc_start: 0.8225 (mtm-85) cc_final: 0.7849 (ptt-90) REVERT: A 691 ILE cc_start: 0.8338 (OUTLIER) cc_final: 0.7786 (pt) REVERT: A 729 MET cc_start: 0.7870 (mmm) cc_final: 0.7593 (mmm) REVERT: A 799 ASN cc_start: 0.8617 (OUTLIER) cc_final: 0.8302 (p0) REVERT: A 850 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7801 (tm-30) REVERT: A 899 MET cc_start: 0.5072 (OUTLIER) cc_final: 0.4544 (tmm) REVERT: B 342 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7640 (pm20) REVERT: B 445 SER cc_start: 0.7889 (t) cc_final: 0.7313 (m) REVERT: B 452 ARG cc_start: 0.8140 (ttt-90) cc_final: 0.7835 (ttt-90) REVERT: B 898 ASN cc_start: 0.7927 (t0) cc_final: 0.7537 (t0) REVERT: B 899 MET cc_start: 0.5864 (ppp) cc_final: 0.5531 (ppp) REVERT: B 1077 ASP cc_start: 0.8074 (t0) cc_final: 0.7457 (t0) outliers start: 62 outliers final: 41 residues processed: 422 average time/residue: 0.2995 time to fit residues: 179.4612 Evaluate side-chains 425 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 378 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 404 CYS Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 465 ASN Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 653 ASN Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 824 GLN Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 781 HIS Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 904 SER Chi-restraints excluded: chain B residue 951 THR Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1057 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 103 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 99 optimal weight: 0.0370 chunk 50 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 113 optimal weight: 0.4980 chunk 82 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 131 optimal weight: 0.6980 chunk 151 optimal weight: 0.5980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN ** B 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 HIS ** B 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14830 Z= 0.197 Angle : 0.558 8.771 20191 Z= 0.290 Chirality : 0.040 0.176 2310 Planarity : 0.004 0.060 2416 Dihedral : 16.869 163.297 2307 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.79 % Allowed : 28.30 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.17 (0.21), residues: 1674 helix: 1.27 (0.18), residues: 800 sheet: -0.65 (0.35), residues: 211 loop : -1.03 (0.25), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 764 HIS 0.008 0.001 HIS B 984 PHE 0.039 0.002 PHE A 232 TYR 0.015 0.001 TYR B 236 ARG 0.009 0.000 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 384 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ASP cc_start: 0.7761 (m-30) cc_final: 0.7525 (m-30) REVERT: A 48 GLU cc_start: 0.8322 (tp30) cc_final: 0.8062 (tp30) REVERT: A 57 VAL cc_start: 0.7818 (OUTLIER) cc_final: 0.7455 (p) REVERT: A 67 MET cc_start: 0.7841 (ttt) cc_final: 0.7537 (ttt) REVERT: A 97 GLN cc_start: 0.8232 (mm-40) cc_final: 0.7791 (mt0) REVERT: A 119 LEU cc_start: 0.8460 (tp) cc_final: 0.8200 (tp) REVERT: A 215 GLN cc_start: 0.7981 (tm-30) cc_final: 0.7488 (tm-30) REVERT: A 254 ASN cc_start: 0.7057 (t0) cc_final: 0.6731 (t0) REVERT: A 261 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7925 (tmm) REVERT: A 402 GLN cc_start: 0.7377 (tt0) cc_final: 0.7020 (tp40) REVERT: A 430 LYS cc_start: 0.6121 (mmmt) cc_final: 0.5493 (mmmt) REVERT: A 515 SER cc_start: 0.8430 (m) cc_final: 0.8198 (t) REVERT: A 562 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7925 (mm-30) REVERT: A 569 GLU cc_start: 0.7862 (tp30) cc_final: 0.7394 (tp30) REVERT: A 691 ILE cc_start: 0.8313 (OUTLIER) cc_final: 0.7776 (pt) REVERT: A 850 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7760 (tm-30) REVERT: A 899 MET cc_start: 0.5083 (OUTLIER) cc_final: 0.4569 (tmm) REVERT: B 342 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7641 (pm20) REVERT: B 445 SER cc_start: 0.7866 (t) cc_final: 0.7294 (m) REVERT: B 452 ARG cc_start: 0.8144 (ttt-90) cc_final: 0.7836 (ttt-90) REVERT: B 860 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.8069 (ptmt) REVERT: B 898 ASN cc_start: 0.7937 (t0) cc_final: 0.7527 (t0) REVERT: B 899 MET cc_start: 0.5856 (ppp) cc_final: 0.5532 (ppp) REVERT: B 1077 ASP cc_start: 0.8124 (t0) cc_final: 0.7460 (t0) outliers start: 57 outliers final: 42 residues processed: 416 average time/residue: 0.2946 time to fit residues: 173.0071 Evaluate side-chains 426 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 378 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 404 CYS Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 465 ASN Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 553 ASN Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 653 ASN Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 824 GLN Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 781 HIS Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 860 LYS Chi-restraints excluded: chain B residue 904 SER Chi-restraints excluded: chain B residue 951 THR Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1057 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 159 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 140 optimal weight: 0.5980 chunk 146 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 chunk 102 optimal weight: 0.5980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 799 ASN B 613 ASN ** B 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 HIS ** B 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 14830 Z= 0.314 Angle : 0.603 8.718 20191 Z= 0.315 Chirality : 0.043 0.179 2310 Planarity : 0.004 0.063 2416 Dihedral : 16.955 170.820 2307 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 4.06 % Allowed : 28.63 % Favored : 67.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.00 (0.21), residues: 1674 helix: 1.14 (0.18), residues: 800 sheet: -0.75 (0.36), residues: 206 loop : -1.10 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 807 HIS 0.009 0.001 HIS B 984 PHE 0.043 0.002 PHE A 232 TYR 0.018 0.002 TYR A 43 ARG 0.010 0.001 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 384 time to evaluate : 1.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ASP cc_start: 0.7793 (m-30) cc_final: 0.7553 (m-30) REVERT: A 57 VAL cc_start: 0.7869 (OUTLIER) cc_final: 0.7507 (p) REVERT: A 67 MET cc_start: 0.7853 (OUTLIER) cc_final: 0.7626 (ttt) REVERT: A 97 GLN cc_start: 0.8252 (mm-40) cc_final: 0.7822 (mt0) REVERT: A 119 LEU cc_start: 0.8452 (tp) cc_final: 0.8158 (tp) REVERT: A 215 GLN cc_start: 0.8016 (tm-30) cc_final: 0.7527 (tm-30) REVERT: A 253 MET cc_start: 0.6476 (ptp) cc_final: 0.6180 (ptt) REVERT: A 254 ASN cc_start: 0.7122 (t0) cc_final: 0.6762 (t0) REVERT: A 261 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.7943 (tmm) REVERT: A 298 GLN cc_start: 0.8369 (mt0) cc_final: 0.8070 (mt0) REVERT: A 430 LYS cc_start: 0.6167 (mmmt) cc_final: 0.5534 (mmmt) REVERT: A 515 SER cc_start: 0.8536 (m) cc_final: 0.8336 (t) REVERT: A 562 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7940 (mm-30) REVERT: A 569 GLU cc_start: 0.7878 (tp30) cc_final: 0.7407 (tp30) REVERT: A 638 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7876 (ptt-90) REVERT: A 691 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.7875 (pt) REVERT: A 729 MET cc_start: 0.8013 (mmm) cc_final: 0.7681 (mmm) REVERT: A 749 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7375 (mt-10) REVERT: A 799 ASN cc_start: 0.8580 (OUTLIER) cc_final: 0.8221 (p0) REVERT: A 809 GLU cc_start: 0.7876 (tp30) cc_final: 0.7280 (tp30) REVERT: A 899 MET cc_start: 0.5140 (OUTLIER) cc_final: 0.4619 (tmm) REVERT: B 342 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7635 (pm20) REVERT: B 445 SER cc_start: 0.7913 (t) cc_final: 0.7343 (m) REVERT: B 452 ARG cc_start: 0.8172 (ttt-90) cc_final: 0.7845 (ttt-90) REVERT: B 860 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8110 (ptmt) REVERT: B 898 ASN cc_start: 0.8008 (t0) cc_final: 0.7575 (t0) REVERT: B 899 MET cc_start: 0.5920 (ppp) cc_final: 0.5597 (ppp) REVERT: B 1077 ASP cc_start: 0.8116 (t0) cc_final: 0.7485 (t0) outliers start: 61 outliers final: 45 residues processed: 416 average time/residue: 0.2993 time to fit residues: 175.2764 Evaluate side-chains 433 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 379 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain A residue 404 CYS Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 465 ASN Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 553 ASN Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 638 ARG Chi-restraints excluded: chain A residue 653 ASN Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 824 GLN Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 781 HIS Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 860 LYS Chi-restraints excluded: chain B residue 904 SER Chi-restraints excluded: chain B residue 951 THR Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1057 TYR Chi-restraints excluded: chain B residue 1060 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 164 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 172 optimal weight: 3.9990 chunk 158 optimal weight: 0.5980 chunk 137 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 109 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN A 799 ASN ** B 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 HIS ** B 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14830 Z= 0.270 Angle : 0.606 9.819 20191 Z= 0.314 Chirality : 0.042 0.187 2310 Planarity : 0.004 0.065 2416 Dihedral : 16.927 170.629 2307 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.60 % Allowed : 29.03 % Favored : 67.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.01 (0.21), residues: 1674 helix: 1.15 (0.18), residues: 801 sheet: -0.86 (0.35), residues: 208 loop : -1.06 (0.25), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 807 HIS 0.006 0.001 HIS B 984 PHE 0.049 0.002 PHE A 232 TYR 0.015 0.002 TYR B 236 ARG 0.010 0.000 ARG A 382 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 387 time to evaluate : 1.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ASP cc_start: 0.7813 (m-30) cc_final: 0.7568 (m-30) REVERT: A 57 VAL cc_start: 0.7854 (OUTLIER) cc_final: 0.7493 (p) REVERT: A 67 MET cc_start: 0.7836 (OUTLIER) cc_final: 0.7612 (ttt) REVERT: A 97 GLN cc_start: 0.8240 (mm-40) cc_final: 0.7799 (mt0) REVERT: A 119 LEU cc_start: 0.8440 (tp) cc_final: 0.8179 (tp) REVERT: A 215 GLN cc_start: 0.8008 (tm-30) cc_final: 0.7527 (tm-30) REVERT: A 253 MET cc_start: 0.6499 (ptp) cc_final: 0.6236 (ptt) REVERT: A 254 ASN cc_start: 0.7131 (t0) cc_final: 0.6771 (t0) REVERT: A 261 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.7941 (tmm) REVERT: A 298 GLN cc_start: 0.8342 (mt0) cc_final: 0.8060 (mt0) REVERT: A 430 LYS cc_start: 0.6143 (mmmt) cc_final: 0.5468 (mmmt) REVERT: A 562 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7931 (mm-30) REVERT: A 565 LYS cc_start: 0.9141 (tmtt) cc_final: 0.8804 (tmtt) REVERT: A 567 LYS cc_start: 0.8404 (tppp) cc_final: 0.8159 (tppp) REVERT: A 569 GLU cc_start: 0.7857 (tp30) cc_final: 0.7386 (tp30) REVERT: A 638 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7862 (ptt-90) REVERT: A 691 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.7875 (pt) REVERT: A 729 MET cc_start: 0.7949 (mmm) cc_final: 0.7583 (mmm) REVERT: A 749 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7371 (mt-10) REVERT: A 799 ASN cc_start: 0.8603 (OUTLIER) cc_final: 0.8309 (p0) REVERT: A 809 GLU cc_start: 0.7869 (tp30) cc_final: 0.7274 (tp30) REVERT: A 899 MET cc_start: 0.5146 (OUTLIER) cc_final: 0.4627 (tmm) REVERT: B 342 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7634 (pm20) REVERT: B 445 SER cc_start: 0.7887 (t) cc_final: 0.7300 (m) REVERT: B 452 ARG cc_start: 0.8185 (ttt-90) cc_final: 0.7855 (ttt-90) REVERT: B 860 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.8107 (ptmt) REVERT: B 886 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7835 (mm-30) REVERT: B 898 ASN cc_start: 0.7988 (t0) cc_final: 0.7558 (t0) REVERT: B 899 MET cc_start: 0.5901 (ppp) cc_final: 0.5587 (ppp) REVERT: B 1077 ASP cc_start: 0.8110 (t0) cc_final: 0.7464 (t0) outliers start: 54 outliers final: 41 residues processed: 418 average time/residue: 0.3044 time to fit residues: 178.7529 Evaluate side-chains 435 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 385 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 404 CYS Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 465 ASN Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 553 ASN Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 638 ARG Chi-restraints excluded: chain A residue 653 ASN Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 781 HIS Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 860 LYS Chi-restraints excluded: chain B residue 904 SER Chi-restraints excluded: chain B residue 951 THR Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1057 TYR Chi-restraints excluded: chain B residue 1060 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 3.9990 chunk 42 optimal weight: 0.0970 chunk 126 optimal weight: 0.0170 chunk 20 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 141 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 120 optimal weight: 0.9990 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 799 ASN A 824 GLN ** B 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 HIS ** B 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.161112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.129495 restraints weight = 28674.985| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.76 r_work: 0.3514 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3509 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3509 r_free = 0.3509 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3509 r_free = 0.3509 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3509 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 14830 Z= 0.257 Angle : 0.813 59.173 20191 Z= 0.448 Chirality : 0.042 0.321 2310 Planarity : 0.004 0.067 2416 Dihedral : 16.936 170.521 2307 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.60 % Allowed : 28.83 % Favored : 67.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.03 (0.21), residues: 1674 helix: 1.17 (0.18), residues: 801 sheet: -0.92 (0.35), residues: 208 loop : -1.05 (0.25), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 807 HIS 0.008 0.001 HIS B 984 PHE 0.038 0.002 PHE A 232 TYR 0.016 0.002 TYR B 996 ARG 0.009 0.000 ARG A 382 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4094.46 seconds wall clock time: 74 minutes 29.52 seconds (4469.52 seconds total)