Starting phenix.real_space_refine on Mon Jul 22 03:07:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wkx_37610/07_2024/8wkx_37610.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wkx_37610/07_2024/8wkx_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wkx_37610/07_2024/8wkx_37610.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wkx_37610/07_2024/8wkx_37610.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wkx_37610/07_2024/8wkx_37610.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wkx_37610/07_2024/8wkx_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 Residue "A PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 624": "OE1" <-> "OE2" Residue "A TYR 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 23": "OD1" <-> "OD2" Residue "E TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 157": "OD1" <-> "OD2" Residue "E ASP 194": "OD1" <-> "OD2" Residue "E TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 811": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 812": "OE1" <-> "OE2" Residue "E ASP 911": "OD1" <-> "OD2" Residue "E TYR 962": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 11.79, per 1000 atoms: 0.71 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 - 3.50 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: 7.30 Conformation dependent library (CDL) restraints added in 3.2 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: 2.06 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: 5.90 Time building geometry restraints manager: 7.92 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: 97.39 - 104.71: 141 104.71 - 112.04: 7826 112.04 - 119.36: 5907 119.36 - 126.68: 8790 126.68 - 134.01: 147 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 2.520 nonbonded pdb=" NH2 ARG A 802 " pdb=" O ARG A 870 " model vdw 2.188 2.520 ... (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 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: 12.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.690 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 50.600 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.080 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.960 ------------------------------------------------------------------------------- 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= 0.176 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 *********************** 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 fitting. rotamer outliers: 1 poor density : 146 time to evaluate : 1.987 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: 0.3144 time to fit residues: 69.1506 Evaluate side-chains 103 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 2.107 ------------------------------------------------------------------------------- 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: 3.9990 chunk 150 optimal weight: 4.9990 chunk 83 optimal weight: 0.2980 chunk 51 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 94 optimal weight: 0.0870 chunk 115 optimal weight: 3.9990 chunk 179 optimal weight: 0.8980 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 895 ASN A 910 ASN A 973 ASN A 975 HIS A 979 HIS E 654 ASN ** E 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 814 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.0932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16937 Z= 0.145 Angle : 0.493 5.921 22811 Z= 0.266 Chirality : 0.039 0.171 2416 Planarity : 0.003 0.049 2914 Dihedral : 4.022 25.240 2189 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % 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: -0.36 (0.19), residues: 1980 helix: 0.71 (0.16), residues: 1067 sheet: -1.36 (0.61), residues: 78 loop : -1.36 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 601 HIS 0.004 0.001 HIS A 979 PHE 0.019 0.001 PHE E 907 TYR 0.017 0.001 TYR A 596 ARG 0.006 0.000 ARG E 566 *********************** 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 145 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 2.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 419 ASP cc_start: 0.8709 (p0) cc_final: 0.8403 (p0) REVERT: A 601 TRP cc_start: 0.7084 (t60) cc_final: 0.6507 (t60) REVERT: A 608 PHE cc_start: 0.7733 (p90) cc_final: 0.7327 (p90) REVERT: E 421 MET cc_start: 0.8401 (tpp) cc_final: 0.8177 (tpp) REVERT: E 525 ASP cc_start: 0.8850 (m-30) cc_final: 0.8548 (p0) REVERT: E 544 PHE cc_start: 0.8856 (m-80) cc_final: 0.8352 (m-10) REVERT: E 827 LEU cc_start: 0.8361 (mt) cc_final: 0.7832 (tp) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.2931 time to fit residues: 65.2945 Evaluate side-chains 99 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 1.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 99 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 chunk 149 optimal weight: 0.8980 chunk 122 optimal weight: 0.0970 chunk 49 optimal weight: 10.0000 chunk 180 optimal weight: 0.9980 chunk 194 optimal weight: 4.9990 chunk 160 optimal weight: 0.9990 chunk 178 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 144 optimal weight: 0.9980 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 881 HIS E 654 ASN ** E 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16937 Z= 0.146 Angle : 0.496 5.934 22811 Z= 0.263 Chirality : 0.039 0.215 2416 Planarity : 0.003 0.058 2914 Dihedral : 4.018 24.730 2189 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % 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: -0.36 (0.19), residues: 1980 helix: 0.67 (0.16), residues: 1081 sheet: -1.29 (0.61), residues: 78 loop : -1.33 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 601 HIS 0.003 0.001 HIS E 339 PHE 0.017 0.001 PHE A 594 TYR 0.019 0.001 TYR A 596 ARG 0.004 0.000 ARG A 760 *********************** 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 143 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 2.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 290 MET cc_start: 0.9448 (mmp) cc_final: 0.9244 (mmm) REVERT: A 523 ASN cc_start: 0.8771 (t0) cc_final: 0.8540 (t0) REVERT: A 601 TRP cc_start: 0.7026 (t60) cc_final: 0.6460 (t60) REVERT: A 608 PHE cc_start: 0.7760 (p90) cc_final: 0.7330 (p90) REVERT: E 421 MET cc_start: 0.8459 (tpp) cc_final: 0.8167 (tpp) REVERT: E 525 ASP cc_start: 0.8811 (m-30) cc_final: 0.8533 (p0) REVERT: E 544 PHE cc_start: 0.8814 (m-80) cc_final: 0.8467 (m-10) REVERT: E 589 TYR cc_start: 0.7396 (m-80) cc_final: 0.7094 (m-80) REVERT: E 827 LEU cc_start: 0.8266 (mt) cc_final: 0.7783 (tp) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.2872 time to fit residues: 63.7367 Evaluate side-chains 100 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 177 optimal weight: 0.0470 chunk 135 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 120 optimal weight: 0.3980 chunk 180 optimal weight: 0.9990 chunk 191 optimal weight: 0.0050 chunk 94 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.4694 ------------------------------------------------------------------------------- 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** ** E 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16937 Z= 0.130 Angle : 0.489 6.431 22811 Z= 0.257 Chirality : 0.039 0.239 2416 Planarity : 0.003 0.062 2914 Dihedral : 3.970 24.606 2189 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % 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: -0.31 (0.19), residues: 1980 helix: 0.73 (0.16), residues: 1078 sheet: -1.17 (0.62), residues: 78 loop : -1.33 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 601 HIS 0.003 0.001 HIS E 979 PHE 0.019 0.001 PHE E 722 TYR 0.018 0.001 TYR A 596 ARG 0.007 0.000 ARG E 593 *********************** 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 144 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 2.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASP cc_start: 0.9034 (t0) cc_final: 0.8702 (t0) REVERT: A 523 ASN cc_start: 0.8729 (t0) cc_final: 0.8499 (t0) REVERT: A 601 TRP cc_start: 0.6335 (t60) cc_final: 0.6106 (t60) REVERT: A 608 PHE cc_start: 0.7727 (p90) cc_final: 0.7277 (p90) REVERT: E 421 MET cc_start: 0.8425 (tpp) cc_final: 0.8177 (tpp) REVERT: E 525 ASP cc_start: 0.8814 (m-30) cc_final: 0.8490 (p0) REVERT: E 544 PHE cc_start: 0.8786 (m-80) cc_final: 0.8525 (m-80) REVERT: E 589 TYR cc_start: 0.7469 (m-80) cc_final: 0.7211 (m-80) REVERT: E 827 LEU cc_start: 0.8254 (mt) cc_final: 0.7787 (tp) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.2784 time to fit residues: 62.9649 Evaluate side-chains 98 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 159 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 163 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 171 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 ASN E 415 HIS ** E 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16937 Z= 0.218 Angle : 0.537 8.055 22811 Z= 0.287 Chirality : 0.040 0.209 2416 Planarity : 0.003 0.067 2914 Dihedral : 4.132 23.278 2189 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.05 % Allowed : 2.96 % Favored : 96.99 % 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: -0.26 (0.19), residues: 1980 helix: 0.77 (0.16), residues: 1073 sheet: -1.36 (0.61), residues: 78 loop : -1.27 (0.21), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 601 HIS 0.006 0.001 HIS A 881 PHE 0.018 0.001 PHE E 608 TYR 0.018 0.001 TYR A 596 ARG 0.007 0.001 ARG E 566 *********************** 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 140 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 139 time to evaluate : 2.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 ASN cc_start: 0.8818 (t0) cc_final: 0.8604 (t0) REVERT: A 578 MET cc_start: 0.1606 (ptt) cc_final: 0.1315 (ptp) REVERT: A 608 PHE cc_start: 0.7915 (p90) cc_final: 0.7438 (p90) REVERT: A 912 TYR cc_start: 0.7553 (m-10) cc_final: 0.6062 (m-80) REVERT: E 421 MET cc_start: 0.8514 (tpp) cc_final: 0.8270 (tpp) REVERT: E 519 MET cc_start: 0.9149 (mmt) cc_final: 0.8924 (mmm) REVERT: E 525 ASP cc_start: 0.8868 (m-30) cc_final: 0.8517 (p0) REVERT: E 589 TYR cc_start: 0.7468 (m-80) cc_final: 0.7214 (m-80) REVERT: E 837 PHE cc_start: 0.8521 (t80) cc_final: 0.8243 (t80) outliers start: 1 outliers final: 1 residues processed: 140 average time/residue: 0.2865 time to fit residues: 62.4929 Evaluate side-chains 97 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 96 time to evaluate : 1.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 64 optimal weight: 0.3980 chunk 172 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 112 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 191 optimal weight: 0.8980 chunk 159 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 63 optimal weight: 0.0070 chunk 100 optimal weight: 0.9980 overall best weight: 0.6198 ------------------------------------------------------------------------------- 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 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16937 Z= 0.139 Angle : 0.509 8.148 22811 Z= 0.267 Chirality : 0.039 0.175 2416 Planarity : 0.003 0.035 2914 Dihedral : 4.074 24.996 2189 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % 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: -0.22 (0.19), residues: 1980 helix: 0.82 (0.16), residues: 1071 sheet: -1.27 (0.61), residues: 78 loop : -1.28 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 231 HIS 0.003 0.001 HIS E 979 PHE 0.018 0.001 PHE E 652 TYR 0.022 0.001 TYR E 611 ARG 0.004 0.000 ARG E 566 *********************** 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 144 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 MET cc_start: 0.8022 (tmm) cc_final: 0.7821 (tmm) REVERT: A 523 ASN cc_start: 0.8794 (t0) cc_final: 0.8583 (t0) REVERT: A 578 MET cc_start: 0.1603 (ptt) cc_final: 0.1374 (ptp) REVERT: A 601 TRP cc_start: 0.6469 (t60) cc_final: 0.6103 (t60) REVERT: A 608 PHE cc_start: 0.7840 (p90) cc_final: 0.7436 (p90) REVERT: E 421 MET cc_start: 0.8520 (tpp) cc_final: 0.8259 (tpp) REVERT: E 525 ASP cc_start: 0.8913 (m-30) cc_final: 0.8577 (p0) REVERT: E 544 PHE cc_start: 0.8795 (m-80) cc_final: 0.8431 (m-80) REVERT: E 589 TYR cc_start: 0.7431 (m-80) cc_final: 0.7166 (m-80) REVERT: E 837 PHE cc_start: 0.8470 (t80) cc_final: 0.8243 (t80) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.2826 time to fit residues: 62.7680 Evaluate side-chains 98 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 184 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 139 optimal weight: 0.0050 chunk 108 optimal weight: 0.7980 chunk 161 optimal weight: 8.9990 chunk 106 optimal weight: 1.9990 chunk 190 optimal weight: 6.9990 chunk 119 optimal weight: 0.8980 chunk 116 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- 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 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 236 GLN ** E 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16937 Z= 0.144 Angle : 0.505 8.074 22811 Z= 0.264 Chirality : 0.039 0.163 2416 Planarity : 0.003 0.041 2914 Dihedral : 4.063 24.719 2189 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % 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 (0.19), residues: 1980 helix: 0.87 (0.16), residues: 1066 sheet: -1.27 (0.62), residues: 78 loop : -1.27 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 231 HIS 0.004 0.001 HIS A 979 PHE 0.019 0.001 PHE E 608 TYR 0.022 0.001 TYR E 611 ARG 0.006 0.000 ARG A 566 *********************** 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 138 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 ASN cc_start: 0.8759 (t0) cc_final: 0.8540 (t0) REVERT: A 578 MET cc_start: 0.1757 (ptt) cc_final: 0.1532 (ptp) REVERT: A 608 PHE cc_start: 0.7855 (p90) cc_final: 0.7448 (p90) REVERT: E 421 MET cc_start: 0.8562 (tpp) cc_final: 0.8295 (tpp) REVERT: E 525 ASP cc_start: 0.8896 (m-30) cc_final: 0.8579 (p0) REVERT: E 544 PHE cc_start: 0.8750 (m-80) cc_final: 0.8411 (m-10) REVERT: E 589 TYR cc_start: 0.7429 (m-80) cc_final: 0.7171 (m-80) REVERT: E 827 LEU cc_start: 0.8439 (mt) cc_final: 0.7831 (tp) REVERT: E 837 PHE cc_start: 0.8460 (t80) cc_final: 0.8249 (t80) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.2838 time to fit residues: 61.0147 Evaluate side-chains 95 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 1.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 118 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 113 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 37 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 121 optimal weight: 0.4980 chunk 130 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16937 Z= 0.157 Angle : 0.528 8.530 22811 Z= 0.276 Chirality : 0.039 0.160 2416 Planarity : 0.003 0.043 2914 Dihedral : 4.085 24.871 2189 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % 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: -0.19 (0.19), residues: 1980 helix: 0.87 (0.16), residues: 1070 sheet: -1.74 (0.57), residues: 90 loop : -1.25 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP A 601 HIS 0.003 0.001 HIS A 658 PHE 0.013 0.001 PHE E 45 TYR 0.026 0.001 TYR E 611 ARG 0.006 0.000 ARG E 566 *********************** 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 135 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 MET cc_start: 0.8074 (tmm) cc_final: 0.7860 (tmm) REVERT: A 523 ASN cc_start: 0.8720 (t0) cc_final: 0.8430 (t0) REVERT: A 608 PHE cc_start: 0.7830 (p90) cc_final: 0.7443 (p90) REVERT: E 421 MET cc_start: 0.8573 (tpp) cc_final: 0.8303 (tpp) REVERT: E 525 ASP cc_start: 0.8896 (m-30) cc_final: 0.8588 (p0) REVERT: E 544 PHE cc_start: 0.8753 (m-80) cc_final: 0.8148 (m-10) REVERT: E 589 TYR cc_start: 0.7452 (m-80) cc_final: 0.7192 (m-80) REVERT: E 837 PHE cc_start: 0.8496 (t80) cc_final: 0.8218 (t80) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.2827 time to fit residues: 59.4495 Evaluate side-chains 96 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 2.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 173 optimal weight: 0.9990 chunk 182 optimal weight: 0.5980 chunk 166 optimal weight: 0.7980 chunk 177 optimal weight: 8.9990 chunk 107 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 chunk 168 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 ASN ** E 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16937 Z= 0.157 Angle : 0.541 10.092 22811 Z= 0.282 Chirality : 0.040 0.156 2416 Planarity : 0.003 0.045 2914 Dihedral : 4.117 25.029 2189 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % 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: -0.19 (0.19), residues: 1980 helix: 0.89 (0.16), residues: 1066 sheet: -1.78 (0.57), residues: 90 loop : -1.25 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 601 HIS 0.004 0.001 HIS A 881 PHE 0.016 0.001 PHE A 594 TYR 0.025 0.001 TYR E 611 ARG 0.007 0.000 ARG E 613 *********************** 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 142 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 ASN cc_start: 0.8736 (t0) cc_final: 0.8446 (t0) REVERT: A 608 PHE cc_start: 0.7850 (p90) cc_final: 0.7486 (p90) REVERT: E 525 ASP cc_start: 0.8890 (m-30) cc_final: 0.8594 (p0) REVERT: E 544 PHE cc_start: 0.8734 (m-80) cc_final: 0.8386 (m-10) REVERT: E 589 TYR cc_start: 0.7451 (m-80) cc_final: 0.7228 (m-80) REVERT: E 827 LEU cc_start: 0.8506 (mt) cc_final: 0.7915 (tp) REVERT: E 837 PHE cc_start: 0.8498 (t80) cc_final: 0.8234 (t80) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.2704 time to fit residues: 60.0213 Evaluate side-chains 94 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 188 optimal weight: 4.9990 chunk 114 optimal weight: 0.0070 chunk 89 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 197 optimal weight: 0.9980 chunk 181 optimal weight: 0.4980 chunk 157 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 121 optimal weight: 0.0070 chunk 96 optimal weight: 4.9990 chunk 124 optimal weight: 0.7980 overall best weight: 0.4016 ------------------------------------------------------------------------------- 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 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16937 Z= 0.140 Angle : 0.545 10.527 22811 Z= 0.280 Chirality : 0.040 0.153 2416 Planarity : 0.003 0.047 2914 Dihedral : 4.065 25.755 2189 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % 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: -0.18 (0.19), residues: 1980 helix: 0.87 (0.16), residues: 1069 sheet: -1.64 (0.58), residues: 90 loop : -1.22 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP A 601 HIS 0.007 0.001 HIS A 978 PHE 0.012 0.001 PHE A 594 TYR 0.025 0.001 TYR E 611 ARG 0.006 0.000 ARG E 613 ********************** 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 142 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 2.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASP cc_start: 0.8999 (t0) cc_final: 0.8579 (t0) REVERT: A 419 ASP cc_start: 0.8726 (p0) cc_final: 0.8434 (p0) REVERT: A 523 ASN cc_start: 0.8724 (t0) cc_final: 0.8423 (t0) REVERT: A 608 PHE cc_start: 0.7766 (p90) cc_final: 0.7452 (p90) REVERT: E 525 ASP cc_start: 0.8846 (m-30) cc_final: 0.8632 (p0) REVERT: E 544 PHE cc_start: 0.8695 (m-80) cc_final: 0.8245 (m-10) REVERT: E 589 TYR cc_start: 0.7457 (m-80) cc_final: 0.7223 (m-80) REVERT: E 827 LEU cc_start: 0.8457 (mt) cc_final: 0.7876 (tp) REVERT: E 837 PHE cc_start: 0.8436 (t80) cc_final: 0.8223 (t80) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.2771 time to fit residues: 61.3453 Evaluate side-chains 99 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 1.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 144 optimal weight: 0.7980 chunk 23 optimal weight: 0.0020 chunk 43 optimal weight: 0.7980 chunk 157 optimal weight: 0.0070 chunk 65 optimal weight: 0.5980 chunk 161 optimal weight: 4.9990 chunk 19 optimal weight: 0.0040 chunk 28 optimal weight: 3.9990 chunk 138 optimal weight: 0.0870 overall best weight: 0.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 867 ASN ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.063456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.051701 restraints weight = 111450.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.052909 restraints weight = 77374.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.053739 restraints weight = 59631.760| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16937 Z= 0.129 Angle : 0.539 10.546 22811 Z= 0.275 Chirality : 0.039 0.160 2416 Planarity : 0.003 0.048 2914 Dihedral : 3.960 25.578 2189 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % 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: -0.10 (0.19), residues: 1980 helix: 0.94 (0.16), residues: 1069 sheet: -1.49 (0.59), residues: 90 loop : -1.23 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP A 601 HIS 0.011 0.001 HIS E 810 PHE 0.013 0.001 PHE E 811 TYR 0.030 0.001 TYR E 611 ARG 0.010 0.000 ARG E 987 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3058.67 seconds wall clock time: 56 minutes 17.09 seconds (3377.09 seconds total)