Starting phenix.real_space_refine on Sun Jun 15 00:04:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wkx_37610/06_2025/8wkx_37610.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wkx_37610/06_2025/8wkx_37610.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wkx_37610/06_2025/8wkx_37610.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wkx_37610/06_2025/8wkx_37610.map" model { file = "/net/cci-nas-00/data/ceres_data/8wkx_37610/06_2025/8wkx_37610.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wkx_37610/06_2025/8wkx_37610.cif" } resolution = 4.15 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= 0.033 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: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 10708 2.51 5 N 2676 2.21 5 O 3107 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16555 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 8347 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 19, 'TRANS': 982} Chain: "E" Number of atoms: 8208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 986, 8208 Classifications: {'peptide': 986} Link IDs: {'PTRANS': 19, 'TRANS': 966} Chain breaks: 2 Time building chain proxies: 11.55, per 1000 atoms: 0.70 Number of scatterers: 16555 At special positions: 0 Unit cell: (101.65, 129.47, 156.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 64 16.00 O 3107 8.00 N 2676 7.00 C 10708 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.05 Conformation dependent library (CDL) restraints added in 2.1 seconds 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3784 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 4 sheets defined 61.9% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'A' and resid 12 through 22 Processing helix chain 'A' and resid 23 through 39 Processing helix chain 'A' and resid 48 through 54 removed outlier: 3.643A pdb=" N THR A 52 " --> pdb=" O ALA A 48 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 53 " --> pdb=" O GLY A 49 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 48 through 54' Processing helix chain 'A' and resid 58 through 72 Processing helix chain 'A' and resid 80 through 95 removed outlier: 3.977A pdb=" N LEU A 85 " --> pdb=" O SER A 81 " (cutoff:3.500A) Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 96 through 109 removed outlier: 4.005A pdb=" N PHE A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN A 109 " --> pdb=" O LYS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 123 removed outlier: 4.219A pdb=" N ASP A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 146 Processing helix chain 'A' and resid 154 through 160 Processing helix chain 'A' and resid 186 through 192 Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 197 through 211 removed outlier: 3.780A pdb=" N ALA A 209 " --> pdb=" O LYS A 205 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR A 210 " --> pdb=" O THR A 206 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N HIS A 211 " --> pdb=" O ILE A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 234 removed outlier: 3.658A pdb=" N LYS A 234 " --> pdb=" O ASN A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 265 Processing helix chain 'A' and resid 281 through 296 Processing helix chain 'A' and resid 306 through 317 removed outlier: 3.987A pdb=" N ASP A 310 " --> pdb=" O ASP A 306 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ILE A 312 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 322 Processing helix chain 'A' and resid 329 through 334 removed outlier: 3.513A pdb=" N VAL A 333 " --> pdb=" O ASP A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 366 Processing helix chain 'A' and resid 374 through 392 Processing helix chain 'A' and resid 411 through 416 removed outlier: 4.013A pdb=" N HIS A 415 " --> pdb=" O SER A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 427 removed outlier: 4.133A pdb=" N GLU A 427 " --> pdb=" O LYS A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 443 removed outlier: 3.585A pdb=" N ASP A 435 " --> pdb=" O SER A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 461 removed outlier: 3.684A pdb=" N ASN A 461 " --> pdb=" O ASN A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 496 Processing helix chain 'A' and resid 508 through 520 removed outlier: 3.758A pdb=" N LEU A 512 " --> pdb=" O THR A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 529 Processing helix chain 'A' and resid 532 through 538 removed outlier: 3.640A pdb=" N LYS A 538 " --> pdb=" O GLU A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 547 removed outlier: 4.396A pdb=" N PHE A 544 " --> pdb=" O ILE A 541 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N SER A 546 " --> pdb=" O GLU A 543 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP A 547 " --> pdb=" O PHE A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 570 removed outlier: 3.872A pdb=" N VAL A 556 " --> pdb=" O TYR A 552 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LYS A 557 " --> pdb=" O ASP A 553 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU A 558 " --> pdb=" O ASP A 554 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASN A 563 " --> pdb=" O PHE A 559 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLU A 568 " --> pdb=" O LYS A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 594 Processing helix chain 'A' and resid 610 through 622 removed outlier: 3.644A pdb=" N SER A 617 " --> pdb=" O ARG A 613 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LEU A 618 " --> pdb=" O ASN A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 626 Processing helix chain 'A' and resid 648 through 659 Processing helix chain 'A' and resid 660 through 669 Processing helix chain 'A' and resid 682 through 701 removed outlier: 4.076A pdb=" N ALA A 701 " --> pdb=" O LYS A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 723 removed outlier: 3.726A pdb=" N LYS A 717 " --> pdb=" O ILE A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 742 removed outlier: 3.635A pdb=" N GLY A 734 " --> pdb=" O GLU A 730 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LYS A 735 " --> pdb=" O GLU A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 765 Processing helix chain 'A' and resid 769 through 786 removed outlier: 4.302A pdb=" N SER A 773 " --> pdb=" O LYS A 769 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ILE A 774 " --> pdb=" O SER A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 812 removed outlier: 6.721A pdb=" N ILE A 808 " --> pdb=" O TYR A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 826 Processing helix chain 'A' and resid 831 through 841 Processing helix chain 'A' and resid 842 through 845 Processing helix chain 'A' and resid 846 through 855 removed outlier: 3.630A pdb=" N SER A 855 " --> pdb=" O SER A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 872 Processing helix chain 'A' and resid 878 through 903 removed outlier: 3.509A pdb=" N ILE A 897 " --> pdb=" O LYS A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 922 removed outlier: 4.045A pdb=" N THR A 915 " --> pdb=" O ASP A 911 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TRP A 919 " --> pdb=" O THR A 915 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR A 920 " --> pdb=" O PHE A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 934 Processing helix chain 'A' and resid 937 through 945 Processing helix chain 'A' and resid 950 through 954 removed outlier: 4.313A pdb=" N LYS A 953 " --> pdb=" O ASP A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 962 removed outlier: 3.828A pdb=" N TRP A 958 " --> pdb=" O ILE A 955 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR A 962 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 972 removed outlier: 3.831A pdb=" N GLY A 972 " --> pdb=" O GLY A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 990 removed outlier: 3.810A pdb=" N VAL A 983 " --> pdb=" O HIS A 979 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A 984 " --> pdb=" O VAL A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1003 Processing helix chain 'E' and resid 16 through 20 Processing helix chain 'E' and resid 26 through 39 Processing helix chain 'E' and resid 48 through 54 Processing helix chain 'E' and resid 58 through 71 removed outlier: 3.651A pdb=" N LEU E 62 " --> pdb=" O GLN E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 93 removed outlier: 3.693A pdb=" N ILE E 87 " --> pdb=" O GLU E 83 " (cutoff:3.500A) Proline residue: E 88 - end of helix removed outlier: 3.623A pdb=" N PHE E 91 " --> pdb=" O ILE E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 109 removed outlier: 4.023A pdb=" N PHE E 100 " --> pdb=" O GLY E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 124 removed outlier: 3.841A pdb=" N ASP E 119 " --> pdb=" O ASN E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 146 removed outlier: 3.662A pdb=" N CYS E 142 " --> pdb=" O ILE E 138 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N TRP E 143 " --> pdb=" O ASP E 139 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LYS E 144 " --> pdb=" O THR E 140 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG E 145 " --> pdb=" O ALA E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 183 removed outlier: 3.695A pdb=" N ASN E 182 " --> pdb=" O LYS E 179 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL E 183 " --> pdb=" O GLY E 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 179 through 183' Processing helix chain 'E' and resid 186 through 192 removed outlier: 3.501A pdb=" N ASN E 192 " --> pdb=" O ASP E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 197 Processing helix chain 'E' and resid 197 through 211 removed outlier: 3.861A pdb=" N SER E 201 " --> pdb=" O TYR E 197 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN E 202 " --> pdb=" O PRO E 198 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU E 203 " --> pdb=" O LEU E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 236 removed outlier: 4.115A pdb=" N LYS E 234 " --> pdb=" O ASN E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 265 removed outlier: 3.730A pdb=" N LEU E 258 " --> pdb=" O GLU E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 295 removed outlier: 3.772A pdb=" N LEU E 293 " --> pdb=" O VAL E 289 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU E 295 " --> pdb=" O ASP E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 317 Processing helix chain 'E' and resid 326 through 334 removed outlier: 3.731A pdb=" N LEU E 330 " --> pdb=" O ARG E 326 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS E 331 " --> pdb=" O LYS E 327 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N HIS E 332 " --> pdb=" O ILE E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 366 removed outlier: 4.240A pdb=" N GLU E 365 " --> pdb=" O PHE E 361 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER E 366 " --> pdb=" O GLU E 362 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 372 removed outlier: 4.182A pdb=" N LYS E 372 " --> pdb=" O ASP E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 392 Processing helix chain 'E' and resid 396 through 400 removed outlier: 4.071A pdb=" N ALA E 400 " --> pdb=" O ALA E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 411 through 416 removed outlier: 3.885A pdb=" N HIS E 415 " --> pdb=" O SER E 411 " (cutoff:3.500A) Processing helix chain 'E' and resid 418 through 427 Processing helix chain 'E' and resid 431 through 446 Processing helix chain 'E' and resid 452 through 465 removed outlier: 3.854A pdb=" N SER E 456 " --> pdb=" O TYR E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 470 through 492 Processing helix chain 'E' and resid 493 through 500 removed outlier: 3.751A pdb=" N LEU E 498 " --> pdb=" O GLY E 494 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 520 removed outlier: 3.666A pdb=" N LEU E 512 " --> pdb=" O THR E 508 " (cutoff:3.500A) Processing helix chain 'E' and resid 532 through 539 Processing helix chain 'E' and resid 540 through 545 removed outlier: 4.234A pdb=" N PHE E 544 " --> pdb=" O ILE E 541 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU E 545 " --> pdb=" O LEU E 542 " (cutoff:3.500A) Processing helix chain 'E' and resid 561 through 568 removed outlier: 3.699A pdb=" N VAL E 565 " --> pdb=" O LEU E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 585 removed outlier: 4.243A pdb=" N VAL E 584 " --> pdb=" O ASP E 581 " (cutoff:3.500A) Processing helix chain 'E' and resid 588 through 594 Processing helix chain 'E' and resid 608 through 616 removed outlier: 3.682A pdb=" N ASN E 614 " --> pdb=" O GLN E 610 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 623 Processing helix chain 'E' and resid 648 through 659 Processing helix chain 'E' and resid 660 through 670 removed outlier: 3.695A pdb=" N SER E 670 " --> pdb=" O ASN E 666 " (cutoff:3.500A) Processing helix chain 'E' and resid 680 through 702 removed outlier: 3.602A pdb=" N SER E 700 " --> pdb=" O THR E 696 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN E 702 " --> pdb=" O GLN E 698 " (cutoff:3.500A) Processing helix chain 'E' and resid 705 through 721 removed outlier: 5.181A pdb=" N GLN E 711 " --> pdb=" O VAL E 707 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N SER E 714 " --> pdb=" O THR E 710 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU E 715 " --> pdb=" O GLN E 711 " (cutoff:3.500A) Processing helix chain 'E' and resid 729 through 740 removed outlier: 3.630A pdb=" N LEU E 740 " --> pdb=" O ILE E 736 " (cutoff:3.500A) Processing helix chain 'E' and resid 750 through 761 Processing helix chain 'E' and resid 768 through 787 Processing helix chain 'E' and resid 801 through 808 removed outlier: 4.047A pdb=" N GLY E 805 " --> pdb=" O SER E 801 " (cutoff:3.500A) Processing helix chain 'E' and resid 820 through 826 Processing helix chain 'E' and resid 835 through 841 Processing helix chain 'E' and resid 842 through 845 Processing helix chain 'E' and resid 846 through 857 Processing helix chain 'E' and resid 861 through 871 Processing helix chain 'E' and resid 878 through 895 Processing helix chain 'E' and resid 912 through 920 removed outlier: 3.518A pdb=" N TYR E 920 " --> pdb=" O PHE E 916 " (cutoff:3.500A) Processing helix chain 'E' and resid 928 through 933 Processing helix chain 'E' and resid 955 through 960 Processing helix chain 'E' and resid 969 through 974 Processing helix chain 'E' and resid 980 through 991 removed outlier: 4.124A pdb=" N LEU E 984 " --> pdb=" O VAL E 980 " (cutoff:3.500A) Processing helix chain 'E' and resid 993 through 1003 removed outlier: 3.714A pdb=" N LEU E 997 " --> pdb=" O ASP E 993 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 152 removed outlier: 6.247A pdb=" N SER A 150 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N LYS A 169 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE A 152 " --> pdb=" O LYS A 169 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR A 131 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LEU A 42 " --> pdb=" O HIS A 128 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N ILE A 130 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N PHE A 44 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N VAL A 43 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ILE A 216 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N PHE A 45 " --> pdb=" O ILE A 216 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 244 through 247 Processing sheet with id=AA3, first strand: chain 'A' and resid 339 through 340 removed outlier: 3.543A pdb=" N VAL A 347 " --> pdb=" O HIS A 339 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 150 through 152 removed outlier: 6.956A pdb=" N VAL E 129 " --> pdb=" O LEU E 168 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N HIS E 128 " --> pdb=" O LEU E 42 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE E 130 " --> pdb=" O PHE E 44 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL E 43 " --> pdb=" O VAL E 214 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ILE E 216 " --> pdb=" O VAL E 43 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N PHE E 45 " --> pdb=" O ILE E 216 " (cutoff:3.500A) 722 hydrogen bonds defined for protein. 2088 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.38 Time building geometry restraints manager: 4.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5184 1.34 - 1.46: 2852 1.46 - 1.58: 8793 1.58 - 1.70: 0 1.70 - 1.82: 108 Bond restraints: 16937 Sorted by residual: bond pdb=" N LEU A 551 " pdb=" CA LEU A 551 " ideal model delta sigma weight residual 1.459 1.489 -0.030 9.10e-03 1.21e+04 1.08e+01 bond pdb=" N LYS A 857 " pdb=" CA LYS A 857 " ideal model delta sigma weight residual 1.454 1.492 -0.039 1.23e-02 6.61e+03 9.81e+00 bond pdb=" N GLN E 236 " pdb=" CA GLN E 236 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.21e-02 6.83e+03 7.44e+00 bond pdb=" N SER A 858 " pdb=" CA SER A 858 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.32e-02 5.74e+03 7.09e+00 bond pdb=" N GLN A 549 " pdb=" CA GLN A 549 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.21e-02 6.83e+03 7.01e+00 ... (remaining 16932 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 22341 1.83 - 3.67: 397 3.67 - 5.50: 58 5.50 - 7.33: 13 7.33 - 9.16: 2 Bond angle restraints: 22811 Sorted by residual: angle pdb=" N VAL E 980 " pdb=" CA VAL E 980 " pdb=" C VAL E 980 " ideal model delta sigma weight residual 113.53 107.32 6.21 9.80e-01 1.04e+00 4.01e+01 angle pdb=" N HIS E 810 " pdb=" CA HIS E 810 " pdb=" C HIS E 810 " ideal model delta sigma weight residual 113.38 107.10 6.28 1.23e+00 6.61e-01 2.61e+01 angle pdb=" N PHE E 811 " pdb=" CA PHE E 811 " pdb=" C PHE E 811 " ideal model delta sigma weight residual 113.88 108.16 5.72 1.23e+00 6.61e-01 2.16e+01 angle pdb=" N GLU A 860 " pdb=" CA GLU A 860 " pdb=" C GLU A 860 " ideal model delta sigma weight residual 113.97 109.05 4.92 1.28e+00 6.10e-01 1.48e+01 angle pdb=" N ALA A 623 " pdb=" CA ALA A 623 " pdb=" C ALA A 623 " ideal model delta sigma weight residual 113.21 108.94 4.27 1.15e+00 7.56e-01 1.38e+01 ... (remaining 22806 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 8913 16.52 - 33.04: 946 33.04 - 49.56: 162 49.56 - 66.08: 64 66.08 - 82.60: 14 Dihedral angle restraints: 10099 sinusoidal: 4205 harmonic: 5894 Sorted by residual: dihedral pdb=" CA SER E 317 " pdb=" C SER E 317 " pdb=" N PRO E 318 " pdb=" CA PRO E 318 " ideal model delta harmonic sigma weight residual 180.00 154.63 25.37 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA GLU E 648 " pdb=" C GLU E 648 " pdb=" N TYR E 649 " pdb=" CA TYR E 649 " ideal model delta harmonic sigma weight residual -180.00 -160.03 -19.97 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA TYR A 596 " pdb=" C TYR A 596 " pdb=" N GLU A 597 " pdb=" CA GLU A 597 " ideal model delta harmonic sigma weight residual 180.00 -163.28 -16.72 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 10096 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1793 0.043 - 0.086: 497 0.086 - 0.130: 112 0.130 - 0.173: 9 0.173 - 0.216: 5 Chirality restraints: 2416 Sorted by residual: chirality pdb=" CB ILE A 524 " pdb=" CA ILE A 524 " pdb=" CG1 ILE A 524 " pdb=" CG2 ILE A 524 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA VAL A 859 " pdb=" N VAL A 859 " pdb=" C VAL A 859 " pdb=" CB VAL A 859 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA LEU A 551 " pdb=" N LEU A 551 " pdb=" C LEU A 551 " pdb=" CB LEU A 551 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 2413 not shown) Planarity restraints: 2914 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 247 " -0.453 9.50e-02 1.11e+02 2.03e-01 2.54e+01 pdb=" NE ARG A 247 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ARG A 247 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A 247 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 247 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 601 " 0.018 2.00e-02 2.50e+03 1.62e-02 6.59e+00 pdb=" CG TRP A 601 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP A 601 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP A 601 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 601 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 601 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 601 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 601 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 601 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 601 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 855 " 0.010 2.00e-02 2.50e+03 2.02e-02 4.08e+00 pdb=" C SER A 855 " -0.035 2.00e-02 2.50e+03 pdb=" O SER A 855 " 0.013 2.00e-02 2.50e+03 pdb=" N PHE A 856 " 0.012 2.00e-02 2.50e+03 ... (remaining 2911 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.26: 12 2.26 - 2.92: 7021 2.92 - 3.58: 26056 3.58 - 4.24: 37806 4.24 - 4.90: 61828 Nonbonded interactions: 132723 Sorted by model distance: nonbonded pdb=" O ASN E 230 " pdb=" CD LYS E 234 " model vdw 1.594 3.440 nonbonded pdb=" O ASN E 230 " pdb=" CE LYS E 234 " model vdw 1.937 3.440 nonbonded pdb=" O ASN E 230 " pdb=" CG LYS E 234 " model vdw 1.951 3.440 nonbonded pdb=" OH TYR E 218 " pdb=" ND2 ASN E 224 " model vdw 2.160 3.120 nonbonded pdb=" NH2 ARG A 802 " pdb=" O ARG A 870 " model vdw 2.188 3.120 ... (remaining 132718 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 637 or resid 642 through 895 or resid 897 throu \ gh 1005)) selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 183.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.700 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 39.750 Find NCS groups from input model: 0.710 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: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 228.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 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 : 0.003 0.039 16937 Z= 0.169 Angle : 0.585 9.164 22811 Z= 0.342 Chirality : 0.042 0.216 2416 Planarity : 0.005 0.203 2914 Dihedral : 14.266 82.603 6315 Min Nonbonded Distance : 1.594 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.05 % Allowed : 0.44 % Favored : 99.51 % 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: -0.59 (0.19), residues: 1980 helix: 0.49 (0.16), residues: 1042 sheet: -1.46 (0.62), residues: 75 loop : -1.37 (0.20), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 601 HIS 0.005 0.001 HIS E 339 PHE 0.028 0.001 PHE E 907 TYR 0.020 0.001 TYR A 596 ARG 0.006 0.000 ARG E 566 Details of bonding type rmsd hydrogen bonds : bond 0.18196 ( 722) hydrogen bonds : angle 6.45719 ( 2088) covalent geometry : bond 0.00270 (16937) covalent geometry : angle 0.58479 (22811) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 146 time to evaluate : 1.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 MET cc_start: 0.8068 (tmm) cc_final: 0.7837 (tmm) REVERT: A 419 ASP cc_start: 0.8682 (p0) cc_final: 0.8407 (p0) REVERT: A 523 ASN cc_start: 0.8627 (t0) cc_final: 0.8302 (t0) REVERT: A 608 PHE cc_start: 0.7693 (p90) cc_final: 0.7318 (p90) REVERT: E 544 PHE cc_start: 0.8882 (m-80) cc_final: 0.8166 (m-80) outliers start: 1 outliers final: 0 residues processed: 146 average time/residue: 0.2995 time to fit residues: 65.8620 Evaluate side-chains 103 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 1.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 2.9990 chunk 150 optimal weight: 4.9990 chunk 83 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 101 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 179 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 895 ASN A 910 ASN A 973 ASN A 975 HIS A 979 HIS E 814 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.062453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.050625 restraints weight = 111603.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.051810 restraints weight = 77354.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.052630 restraints weight = 59753.970| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16937 Z= 0.129 Angle : 0.524 5.919 22811 Z= 0.284 Chirality : 0.040 0.171 2416 Planarity : 0.003 0.051 2914 Dihedral : 4.104 24.821 2189 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % 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: -0.41 (0.19), residues: 1980 helix: 0.66 (0.16), residues: 1065 sheet: -1.44 (0.61), residues: 78 loop : -1.35 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 601 HIS 0.005 0.001 HIS E 339 PHE 0.020 0.001 PHE E 907 TYR 0.017 0.001 TYR A 596 ARG 0.006 0.000 ARG E 566 Details of bonding type rmsd hydrogen bonds : bond 0.04283 ( 722) hydrogen bonds : angle 4.78867 ( 2088) covalent geometry : bond 0.00273 (16937) covalent geometry : angle 0.52389 (22811) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 1.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 MET cc_start: 0.8179 (tmm) cc_final: 0.7977 (tmm) REVERT: A 419 ASP cc_start: 0.8575 (p0) cc_final: 0.8246 (p0) REVERT: A 523 ASN cc_start: 0.8776 (t0) cc_final: 0.8562 (t0) REVERT: A 601 TRP cc_start: 0.7005 (t60) cc_final: 0.6363 (t60) REVERT: A 608 PHE cc_start: 0.7781 (p90) cc_final: 0.7339 (p90) REVERT: E 421 MET cc_start: 0.8351 (tpp) cc_final: 0.8145 (tpp) REVERT: E 525 ASP cc_start: 0.8842 (m-30) cc_final: 0.8532 (p0) REVERT: E 544 PHE cc_start: 0.8916 (m-80) cc_final: 0.8415 (m-10) REVERT: E 827 LEU cc_start: 0.8296 (mt) cc_final: 0.7748 (tp) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.3043 time to fit residues: 66.8635 Evaluate side-chains 96 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 1.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 32 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 110 optimal weight: 0.3980 chunk 67 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 185 optimal weight: 6.9990 chunk 184 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 158 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 881 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.061770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.049989 restraints weight = 111512.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.051149 restraints weight = 77530.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.051961 restraints weight = 60117.626| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16937 Z= 0.145 Angle : 0.541 6.343 22811 Z= 0.291 Chirality : 0.040 0.257 2416 Planarity : 0.004 0.072 2914 Dihedral : 4.203 23.596 2189 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % 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: -0.51 (0.19), residues: 1980 helix: 0.57 (0.16), residues: 1076 sheet: -1.49 (0.60), residues: 77 loop : -1.41 (0.21), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 601 HIS 0.004 0.001 HIS E 339 PHE 0.020 0.001 PHE A 594 TYR 0.020 0.001 TYR A 596 ARG 0.006 0.000 ARG A 760 Details of bonding type rmsd hydrogen bonds : bond 0.04059 ( 722) hydrogen bonds : angle 4.74208 ( 2088) covalent geometry : bond 0.00312 (16937) covalent geometry : angle 0.54087 (22811) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 1.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 419 ASP cc_start: 0.8573 (p0) cc_final: 0.8188 (p0) REVERT: A 523 ASN cc_start: 0.8844 (t0) cc_final: 0.8609 (t0) REVERT: A 601 TRP cc_start: 0.7016 (t60) cc_final: 0.6384 (t60) REVERT: A 608 PHE cc_start: 0.7893 (p90) cc_final: 0.7425 (p90) REVERT: E 525 ASP cc_start: 0.8771 (m-30) cc_final: 0.8448 (p0) REVERT: E 544 PHE cc_start: 0.9023 (m-80) cc_final: 0.8570 (m-10) REVERT: E 837 PHE cc_start: 0.8554 (t80) cc_final: 0.8349 (t80) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.2857 time to fit residues: 62.1265 Evaluate side-chains 96 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 1.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 169 optimal weight: 0.5980 chunk 79 optimal weight: 4.9990 chunk 136 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 173 optimal weight: 4.9990 chunk 125 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 128 optimal weight: 6.9990 chunk 189 optimal weight: 4.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.059492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.046731 restraints weight = 114263.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.047914 restraints weight = 79768.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.048706 restraints weight = 62258.456| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 16937 Z= 0.239 Angle : 0.650 9.683 22811 Z= 0.351 Chirality : 0.043 0.233 2416 Planarity : 0.005 0.082 2914 Dihedral : 4.678 22.650 2189 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.05 % Allowed : 4.60 % Favored : 95.35 % 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: -0.67 (0.19), residues: 1980 helix: 0.38 (0.16), residues: 1070 sheet: -1.94 (0.62), residues: 68 loop : -1.35 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 601 HIS 0.007 0.001 HIS E 658 PHE 0.019 0.002 PHE A 954 TYR 0.021 0.002 TYR A 596 ARG 0.011 0.001 ARG E 593 Details of bonding type rmsd hydrogen bonds : bond 0.04593 ( 722) hydrogen bonds : angle 4.98384 ( 2088) covalent geometry : bond 0.00512 (16937) covalent geometry : angle 0.64981 (22811) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 1.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 ASN cc_start: 0.8769 (t0) cc_final: 0.8508 (t0) REVERT: A 531 MET cc_start: 0.8375 (ttt) cc_final: 0.7895 (ttt) REVERT: A 608 PHE cc_start: 0.7823 (p90) cc_final: 0.7356 (p90) REVERT: A 912 TYR cc_start: 0.7536 (m-10) cc_final: 0.5812 (m-80) REVERT: E 421 MET cc_start: 0.8587 (tpp) cc_final: 0.8364 (tpp) REVERT: E 525 ASP cc_start: 0.8796 (m-30) cc_final: 0.8515 (p0) REVERT: E 589 TYR cc_start: 0.7285 (m-80) cc_final: 0.7021 (m-80) REVERT: E 827 LEU cc_start: 0.8601 (mt) cc_final: 0.7992 (tp) outliers start: 1 outliers final: 0 residues processed: 131 average time/residue: 0.3006 time to fit residues: 60.8236 Evaluate side-chains 91 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 2.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 93 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 138 optimal weight: 8.9990 chunk 121 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 20 optimal weight: 0.3980 chunk 193 optimal weight: 0.0970 chunk 11 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.060908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.049278 restraints weight = 113294.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.050431 restraints weight = 78836.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.051238 restraints weight = 60973.615| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16937 Z= 0.118 Angle : 0.559 13.172 22811 Z= 0.294 Chirality : 0.040 0.171 2416 Planarity : 0.003 0.042 2914 Dihedral : 4.481 26.262 2189 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % 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: -0.56 (0.19), residues: 1980 helix: 0.54 (0.16), residues: 1070 sheet: -1.79 (0.58), residues: 78 loop : -1.40 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 601 HIS 0.003 0.001 HIS E 979 PHE 0.015 0.001 PHE A 605 TYR 0.022 0.001 TYR E 611 ARG 0.006 0.000 ARG E 165 Details of bonding type rmsd hydrogen bonds : bond 0.03820 ( 722) hydrogen bonds : angle 4.59173 ( 2088) covalent geometry : bond 0.00250 (16937) covalent geometry : angle 0.55884 (22811) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 2.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 ASN cc_start: 0.8810 (t0) cc_final: 0.8602 (t0) REVERT: A 608 PHE cc_start: 0.7900 (p90) cc_final: 0.7371 (p90) REVERT: E 525 ASP cc_start: 0.8911 (m-30) cc_final: 0.8615 (p0) REVERT: E 589 TYR cc_start: 0.7471 (m-80) cc_final: 0.7182 (m-80) REVERT: E 671 CYS cc_start: 0.8833 (t) cc_final: 0.8319 (t) REVERT: E 837 PHE cc_start: 0.8378 (t80) cc_final: 0.8143 (t80) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.3632 time to fit residues: 74.5996 Evaluate side-chains 95 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 2.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 4 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 161 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 179 optimal weight: 7.9990 chunk 197 optimal weight: 5.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 979 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.059688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.048153 restraints weight = 114199.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.049266 restraints weight = 79413.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.050043 restraints weight = 61522.454| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16937 Z= 0.170 Angle : 0.579 8.348 22811 Z= 0.310 Chirality : 0.041 0.159 2416 Planarity : 0.004 0.063 2914 Dihedral : 4.560 24.933 2189 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % 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: -0.56 (0.19), residues: 1980 helix: 0.53 (0.16), residues: 1080 sheet: -1.85 (0.58), residues: 78 loop : -1.42 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 448 HIS 0.004 0.001 HIS A 658 PHE 0.022 0.001 PHE A 594 TYR 0.025 0.001 TYR E 611 ARG 0.007 0.001 ARG A 760 Details of bonding type rmsd hydrogen bonds : bond 0.04015 ( 722) hydrogen bonds : angle 4.67764 ( 2088) covalent geometry : bond 0.00367 (16937) covalent geometry : angle 0.57943 (22811) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 2.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 ASN cc_start: 0.8838 (t0) cc_final: 0.8569 (t0) REVERT: A 608 PHE cc_start: 0.7966 (p90) cc_final: 0.7436 (p90) REVERT: E 421 MET cc_start: 0.8510 (tpp) cc_final: 0.8236 (tpp) REVERT: E 525 ASP cc_start: 0.8940 (m-30) cc_final: 0.8616 (p0) REVERT: E 544 PHE cc_start: 0.8897 (m-10) cc_final: 0.8627 (m-10) REVERT: E 586 LEU cc_start: 0.8291 (mp) cc_final: 0.7890 (tp) REVERT: E 589 TYR cc_start: 0.7509 (m-80) cc_final: 0.7211 (m-80) REVERT: E 837 PHE cc_start: 0.8411 (t80) cc_final: 0.8062 (t80) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.4081 time to fit residues: 83.8632 Evaluate side-chains 92 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 2.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 96 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 119 optimal weight: 0.9990 chunk 175 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 138 optimal weight: 7.9990 chunk 103 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.060367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.048912 restraints weight = 111942.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.050041 restraints weight = 77870.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.050832 restraints weight = 60207.679| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 16937 Z= 0.127 Angle : 0.567 10.174 22811 Z= 0.299 Chirality : 0.041 0.147 2416 Planarity : 0.003 0.047 2914 Dihedral : 4.507 27.482 2189 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % 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: -0.56 (0.19), residues: 1980 helix: 0.59 (0.16), residues: 1080 sheet: -2.07 (0.54), residues: 90 loop : -1.46 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 143 HIS 0.006 0.001 HIS A 881 PHE 0.013 0.001 PHE E 916 TYR 0.023 0.001 TYR E 611 ARG 0.005 0.000 ARG A 233 Details of bonding type rmsd hydrogen bonds : bond 0.03796 ( 722) hydrogen bonds : angle 4.58429 ( 2088) covalent geometry : bond 0.00277 (16937) covalent geometry : angle 0.56681 (22811) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 2.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 MET cc_start: 0.8539 (tmm) cc_final: 0.8074 (tmm) REVERT: A 419 ASP cc_start: 0.8566 (p0) cc_final: 0.8247 (p0) REVERT: A 523 ASN cc_start: 0.8805 (t0) cc_final: 0.8525 (t0) REVERT: A 608 PHE cc_start: 0.7949 (p90) cc_final: 0.7390 (p90) REVERT: E 525 ASP cc_start: 0.8889 (m-30) cc_final: 0.8579 (p0) REVERT: E 544 PHE cc_start: 0.8786 (m-10) cc_final: 0.8522 (m-10) REVERT: E 586 LEU cc_start: 0.8217 (mp) cc_final: 0.7905 (tp) REVERT: E 589 TYR cc_start: 0.7458 (m-80) cc_final: 0.7180 (m-80) REVERT: E 827 LEU cc_start: 0.8441 (mt) cc_final: 0.7901 (tp) REVERT: E 837 PHE cc_start: 0.8359 (t80) cc_final: 0.7895 (t80) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.3401 time to fit residues: 68.7359 Evaluate side-chains 90 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 2.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 22 optimal weight: 1.9990 chunk 73 optimal weight: 0.0980 chunk 192 optimal weight: 0.9990 chunk 45 optimal weight: 0.0970 chunk 196 optimal weight: 0.1980 chunk 130 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 186 optimal weight: 0.9990 chunk 155 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.061262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.049536 restraints weight = 111376.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.050764 restraints weight = 75588.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.051621 restraints weight = 57590.020| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 16937 Z= 0.107 Angle : 0.567 13.259 22811 Z= 0.292 Chirality : 0.041 0.281 2416 Planarity : 0.003 0.036 2914 Dihedral : 4.347 27.813 2189 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % 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: -0.48 (0.19), residues: 1980 helix: 0.66 (0.16), residues: 1080 sheet: -1.86 (0.55), residues: 90 loop : -1.44 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP A 601 HIS 0.004 0.001 HIS A 881 PHE 0.014 0.001 PHE A 594 TYR 0.024 0.001 TYR E 611 ARG 0.004 0.000 ARG E 566 Details of bonding type rmsd hydrogen bonds : bond 0.03497 ( 722) hydrogen bonds : angle 4.43720 ( 2088) covalent geometry : bond 0.00227 (16937) covalent geometry : angle 0.56750 (22811) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 2.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 MET cc_start: 0.8568 (tmm) cc_final: 0.8074 (tmm) REVERT: A 419 ASP cc_start: 0.8598 (p0) cc_final: 0.8279 (p0) REVERT: A 523 ASN cc_start: 0.8822 (t0) cc_final: 0.8490 (t0) REVERT: A 608 PHE cc_start: 0.7940 (p90) cc_final: 0.7458 (p90) REVERT: E 22 LEU cc_start: 0.8126 (tt) cc_final: 0.7669 (mt) REVERT: E 421 MET cc_start: 0.8479 (tpp) cc_final: 0.8188 (tpp) REVERT: E 525 ASP cc_start: 0.8899 (m-30) cc_final: 0.8606 (p0) REVERT: E 544 PHE cc_start: 0.8796 (m-10) cc_final: 0.8513 (m-10) REVERT: E 586 LEU cc_start: 0.8181 (mp) cc_final: 0.7877 (tp) REVERT: E 589 TYR cc_start: 0.7492 (m-80) cc_final: 0.7157 (m-80) REVERT: E 827 LEU cc_start: 0.8452 (mt) cc_final: 0.7914 (tp) REVERT: E 837 PHE cc_start: 0.8232 (t80) cc_final: 0.7841 (t80) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.2879 time to fit residues: 59.3273 Evaluate side-chains 98 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 2.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 86 optimal weight: 0.9980 chunk 155 optimal weight: 0.0370 chunk 38 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 138 optimal weight: 5.9990 chunk 108 optimal weight: 0.2980 chunk 187 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 177 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.061127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.049394 restraints weight = 111453.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.050617 restraints weight = 75577.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.051467 restraints weight = 57548.950| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16937 Z= 0.111 Angle : 0.554 12.005 22811 Z= 0.289 Chirality : 0.041 0.259 2416 Planarity : 0.003 0.048 2914 Dihedral : 4.280 27.758 2189 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % 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: -0.44 (0.19), residues: 1980 helix: 0.68 (0.16), residues: 1083 sheet: -1.80 (0.55), residues: 90 loop : -1.44 (0.21), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 143 HIS 0.003 0.001 HIS A 881 PHE 0.026 0.001 PHE A 605 TYR 0.031 0.001 TYR E 721 ARG 0.007 0.000 ARG E 566 Details of bonding type rmsd hydrogen bonds : bond 0.03515 ( 722) hydrogen bonds : angle 4.43865 ( 2088) covalent geometry : bond 0.00240 (16937) covalent geometry : angle 0.55446 (22811) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 3.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 MET cc_start: 0.8563 (tmm) cc_final: 0.8089 (tmm) REVERT: A 419 ASP cc_start: 0.8619 (p0) cc_final: 0.8298 (p0) REVERT: A 523 ASN cc_start: 0.8832 (t0) cc_final: 0.8586 (t0) REVERT: A 608 PHE cc_start: 0.7957 (p90) cc_final: 0.7466 (p90) REVERT: E 22 LEU cc_start: 0.8152 (tt) cc_final: 0.7751 (mt) REVERT: E 421 MET cc_start: 0.8433 (tpp) cc_final: 0.8132 (tpp) REVERT: E 525 ASP cc_start: 0.8950 (m-30) cc_final: 0.8619 (p0) REVERT: E 544 PHE cc_start: 0.8786 (m-10) cc_final: 0.8473 (m-10) REVERT: E 586 LEU cc_start: 0.8119 (mp) cc_final: 0.7852 (tp) REVERT: E 589 TYR cc_start: 0.7501 (m-80) cc_final: 0.7183 (m-80) REVERT: E 827 LEU cc_start: 0.8466 (mt) cc_final: 0.7926 (tp) REVERT: E 837 PHE cc_start: 0.8233 (t80) cc_final: 0.7821 (t80) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.3619 time to fit residues: 74.0792 Evaluate side-chains 94 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 1.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 128 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 167 optimal weight: 0.5980 chunk 114 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 961 ASN E 475 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.062342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.050815 restraints weight = 118548.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.051958 restraints weight = 82576.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.052739 restraints weight = 64436.088| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16937 Z= 0.121 Angle : 0.579 13.883 22811 Z= 0.298 Chirality : 0.041 0.254 2416 Planarity : 0.004 0.067 2914 Dihedral : 4.307 27.641 2189 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % 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: -0.44 (0.19), residues: 1980 helix: 0.69 (0.16), residues: 1083 sheet: -1.86 (0.54), residues: 90 loop : -1.42 (0.21), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 601 HIS 0.003 0.001 HIS A 658 PHE 0.026 0.001 PHE A 605 TYR 0.035 0.001 TYR E 721 ARG 0.017 0.001 ARG E 987 Details of bonding type rmsd hydrogen bonds : bond 0.03578 ( 722) hydrogen bonds : angle 4.45327 ( 2088) covalent geometry : bond 0.00265 (16937) covalent geometry : angle 0.57923 (22811) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 2.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 MET cc_start: 0.8420 (tmm) cc_final: 0.7967 (tmm) REVERT: A 419 ASP cc_start: 0.8419 (p0) cc_final: 0.8093 (p0) REVERT: A 523 ASN cc_start: 0.8811 (t0) cc_final: 0.8591 (t0) REVERT: A 608 PHE cc_start: 0.7881 (p90) cc_final: 0.7430 (p90) REVERT: A 616 MET cc_start: 0.8254 (mmp) cc_final: 0.8048 (mmp) REVERT: E 22 LEU cc_start: 0.8096 (tt) cc_final: 0.7680 (mt) REVERT: E 421 MET cc_start: 0.8415 (tpp) cc_final: 0.8146 (tpp) REVERT: E 448 TRP cc_start: 0.7080 (t60) cc_final: 0.6367 (t60) REVERT: E 525 ASP cc_start: 0.8903 (m-30) cc_final: 0.8593 (p0) REVERT: E 544 PHE cc_start: 0.8700 (m-10) cc_final: 0.8428 (m-10) REVERT: E 586 LEU cc_start: 0.8141 (mp) cc_final: 0.7936 (tp) REVERT: E 589 TYR cc_start: 0.7514 (m-80) cc_final: 0.7229 (m-80) REVERT: E 827 LEU cc_start: 0.8488 (mt) cc_final: 0.7966 (tp) REVERT: E 837 PHE cc_start: 0.8181 (t80) cc_final: 0.7717 (t80) REVERT: E 969 LYS cc_start: 0.6476 (mttt) cc_final: 0.6073 (mmtt) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.2812 time to fit residues: 54.7506 Evaluate side-chains 93 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 2.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 29 optimal weight: 0.9990 chunk 194 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 121 optimal weight: 0.0770 chunk 81 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 186 optimal weight: 0.4980 overall best weight: 0.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.062591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.051052 restraints weight = 119010.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.052199 restraints weight = 82679.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.052993 restraints weight = 64547.272| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16937 Z= 0.112 Angle : 0.565 12.821 22811 Z= 0.292 Chirality : 0.041 0.254 2416 Planarity : 0.003 0.048 2914 Dihedral : 4.268 28.299 2189 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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: -0.41 (0.19), residues: 1980 helix: 0.70 (0.16), residues: 1083 sheet: -1.80 (0.55), residues: 90 loop : -1.40 (0.21), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 601 HIS 0.003 0.001 HIS E 979 PHE 0.012 0.001 PHE A 837 TYR 0.042 0.001 TYR E 721 ARG 0.015 0.001 ARG E 987 Details of bonding type rmsd hydrogen bonds : bond 0.03496 ( 722) hydrogen bonds : angle 4.37593 ( 2088) covalent geometry : bond 0.00244 (16937) covalent geometry : angle 0.56458 (22811) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5710.39 seconds wall clock time: 103 minutes 55.72 seconds (6235.72 seconds total)