Starting phenix.real_space_refine on Thu Aug 8 21:25:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x5b_6705/08_2024/5x5b_6705.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x5b_6705/08_2024/5x5b_6705.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x5b_6705/08_2024/5x5b_6705.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x5b_6705/08_2024/5x5b_6705.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x5b_6705/08_2024/5x5b_6705.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x5b_6705/08_2024/5x5b_6705.cif" } resolution = 3.7 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 ------------------------------------------------------------------------------- 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= 0.007 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 131 5.16 5 C 15678 2.51 5 N 4062 2.21 5 O 4670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 306": "NH1" <-> "NH2" Residue "A ARG 315": "NH1" <-> "NH2" Residue "A ARG 441": "NH1" <-> "NH2" Residue "A PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 544": "NH1" <-> "NH2" Residue "A ARG 563": "NH1" <-> "NH2" Residue "A TYR 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 761": "NH1" <-> "NH2" Residue "A ARG 797": "NH1" <-> "NH2" Residue "A ARG 965": "NH1" <-> "NH2" Residue "A ARG 977": "NH1" <-> "NH2" Residue "A ARG 1073": "NH1" <-> "NH2" Residue "B TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 306": "NH1" <-> "NH2" Residue "B ARG 441": "NH1" <-> "NH2" Residue "B ARG 761": "NH1" <-> "NH2" Residue "B ARG 797": "NH1" <-> "NH2" Residue "B PHE 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 965": "NH1" <-> "NH2" Residue "B ARG 977": "NH1" <-> "NH2" Residue "B ARG 1073": "NH1" <-> "NH2" Residue "C TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 306": "NH1" <-> "NH2" Residue "C ARG 441": "NH1" <-> "NH2" Residue "C ARG 761": "NH1" <-> "NH2" Residue "C ARG 797": "NH1" <-> "NH2" Residue "C PHE 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 965": "NH1" <-> "NH2" Residue "C ARG 977": "NH1" <-> "NH2" Residue "C ARG 1073": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 24541 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8085 Classifications: {'peptide': 1033} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 47, 'TRANS': 983} Chain breaks: 5 Chain: "B" Number of atoms: 8228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1053, 8228 Classifications: {'peptide': 1053} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 50, 'TRANS': 1000} Chain breaks: 3 Chain: "C" Number of atoms: 8228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1053, 8228 Classifications: {'peptide': 1053} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 50, 'TRANS': 1000} Chain breaks: 3 Time building chain proxies: 14.54, per 1000 atoms: 0.59 Number of scatterers: 24541 At special positions: 0 Unit cell: (149.5, 136.5, 179.4, 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 131 16.00 O 4670 8.00 N 4062 7.00 C 15678 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 474 " distance=2.04 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.04 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.04 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.02 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.01 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " distance=2.02 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.03 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.02 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 474 " distance=2.02 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.03 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.03 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.02 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.03 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: 9.92 Conformation dependent library (CDL) restraints added in 4.4 seconds 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5896 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 45 sheets defined 22.5% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.39 Creating SS restraints... Processing helix chain 'A' and resid 281 through 291 removed outlier: 3.861A pdb=" N LEU A 286 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 327 removed outlier: 3.640A pdb=" N GLY A 326 " --> pdb=" O CYS A 323 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU A 327 " --> pdb=" O PRO A 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 323 through 327' Processing helix chain 'A' and resid 390 through 397 removed outlier: 4.191A pdb=" N ARG A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN A 396 " --> pdb=" O ASP A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 492 Processing helix chain 'A' and resid 602 through 612 removed outlier: 3.639A pdb=" N ALA A 609 " --> pdb=" O ASP A 605 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N HIS A 611 " --> pdb=" O SER A 607 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA A 612 " --> pdb=" O THR A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 725 Processing helix chain 'A' and resid 728 through 737 removed outlier: 3.560A pdb=" N ASN A 733 " --> pdb=" O THR A 729 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LEU A 734 " --> pdb=" O GLU A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 749 Processing helix chain 'A' and resid 749 through 764 removed outlier: 3.672A pdb=" N ASP A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N THR A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 805 Processing helix chain 'A' and resid 848 through 866 Processing helix chain 'A' and resid 868 through 873 Processing helix chain 'A' and resid 879 through 892 Processing helix chain 'A' and resid 895 through 901 removed outlier: 4.082A pdb=" N TYR A 899 " --> pdb=" O GLN A 895 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN A 901 " --> pdb=" O VAL A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 923 removed outlier: 3.555A pdb=" N SER A 914 " --> pdb=" O ASN A 910 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 920 " --> pdb=" O ILE A 916 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N THR A 921 " --> pdb=" O GLN A 917 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 945 removed outlier: 3.546A pdb=" N GLY A 928 " --> pdb=" O SER A 924 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU A 930 " --> pdb=" O ALA A 926 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A 938 " --> pdb=" O VAL A 934 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 941 " --> pdb=" O ASN A 937 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN A 942 " --> pdb=" O ALA A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 965 removed outlier: 3.619A pdb=" N ILE A 962 " --> pdb=" O VAL A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 975 Processing helix chain 'A' and resid 975 through 1014 removed outlier: 3.610A pdb=" N THR A 980 " --> pdb=" O ASP A 976 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY A 981 " --> pdb=" O ARG A 977 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN A 984 " --> pdb=" O THR A 980 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR A 991 " --> pdb=" O GLN A 987 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A1002 " --> pdb=" O ALA A 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 291 removed outlier: 3.573A pdb=" N CYS B 288 " --> pdb=" O ALA B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 330 removed outlier: 3.536A pdb=" N ASN B 330 " --> pdb=" O GLY B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 358 removed outlier: 3.590A pdb=" N LEU B 355 " --> pdb=" O ASP B 351 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER B 358 " --> pdb=" O VAL B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 375 removed outlier: 3.889A pdb=" N ASN B 375 " --> pdb=" O ALA B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 394 No H-bonds generated for 'chain 'B' and resid 392 through 394' Processing helix chain 'B' and resid 488 through 491 Processing helix chain 'B' and resid 602 through 608 removed outlier: 3.793A pdb=" N VAL B 606 " --> pdb=" O ASN B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 726 removed outlier: 3.672A pdb=" N GLY B 726 " --> pdb=" O MET B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 737 removed outlier: 3.896A pdb=" N GLN B 737 " --> pdb=" O ASN B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 757 removed outlier: 3.837A pdb=" N LEU B 749 " --> pdb=" O LEU B 745 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE B 752 " --> pdb=" O ALA B 748 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA B 753 " --> pdb=" O LEU B 749 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASP B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 765 Processing helix chain 'B' and resid 798 through 805 Processing helix chain 'B' and resid 848 through 866 Processing helix chain 'B' and resid 868 through 873 Processing helix chain 'B' and resid 879 through 892 Processing helix chain 'B' and resid 894 through 901 removed outlier: 4.136A pdb=" N LEU B 898 " --> pdb=" O THR B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 919 Processing helix chain 'B' and resid 927 through 947 Processing helix chain 'B' and resid 958 through 967 removed outlier: 3.590A pdb=" N ILE B 962 " --> pdb=" O VAL B 958 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ASP B 967 " --> pdb=" O LEU B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 970 through 1014 removed outlier: 4.062A pdb=" N LEU B 978 " --> pdb=" O GLN B 974 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN B 984 " --> pdb=" O THR B 980 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU B 986 " --> pdb=" O ARG B 982 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 291 removed outlier: 3.573A pdb=" N CYS C 288 " --> pdb=" O ALA C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 330 removed outlier: 3.536A pdb=" N ASN C 330 " --> pdb=" O GLY C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 358 removed outlier: 3.590A pdb=" N LEU C 355 " --> pdb=" O ASP C 351 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER C 358 " --> pdb=" O VAL C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 375 removed outlier: 3.889A pdb=" N ASN C 375 " --> pdb=" O ALA C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 394 No H-bonds generated for 'chain 'C' and resid 392 through 394' Processing helix chain 'C' and resid 488 through 491 Processing helix chain 'C' and resid 602 through 608 removed outlier: 3.793A pdb=" N VAL C 606 " --> pdb=" O ASN C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 719 through 726 removed outlier: 3.672A pdb=" N GLY C 726 " --> pdb=" O MET C 722 " (cutoff:3.500A) Processing helix chain 'C' and resid 728 through 737 removed outlier: 3.896A pdb=" N GLN C 737 " --> pdb=" O ASN C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 743 through 757 removed outlier: 3.836A pdb=" N LEU C 749 " --> pdb=" O LEU C 745 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE C 752 " --> pdb=" O ALA C 748 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA C 753 " --> pdb=" O LEU C 749 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASP C 757 " --> pdb=" O ALA C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 765 Processing helix chain 'C' and resid 798 through 805 Processing helix chain 'C' and resid 848 through 866 Processing helix chain 'C' and resid 868 through 873 Processing helix chain 'C' and resid 879 through 892 Processing helix chain 'C' and resid 894 through 901 removed outlier: 4.137A pdb=" N LEU C 898 " --> pdb=" O THR C 894 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 919 Processing helix chain 'C' and resid 927 through 947 Processing helix chain 'C' and resid 958 through 967 removed outlier: 3.590A pdb=" N ILE C 962 " --> pdb=" O VAL C 958 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ASP C 967 " --> pdb=" O LEU C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 970 through 1014 removed outlier: 4.062A pdb=" N LEU C 978 " --> pdb=" O GLN C 974 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN C 984 " --> pdb=" O THR C 980 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU C 986 " --> pdb=" O ARG C 982 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 33 removed outlier: 4.115A pdb=" N THR A 31 " --> pdb=" O GLY A 68 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A 186 " --> pdb=" O TYR A 197 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS A 190 " --> pdb=" O PHE A 193 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LEU A 194 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS A 221 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL A 196 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N TYR A 200 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N THR A 215 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N VAL A 40 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 59 removed outlier: 3.659A pdb=" N THR A 51 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP A 57 " --> pdb=" O THR A 260 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASP A 274 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 81 through 82 removed outlier: 3.728A pdb=" N GLY A 100 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ARG A 99 " --> pdb=" O ASN A 118 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ASN A 118 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS A 128 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N VAL A 123 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ASN A 129 " --> pdb=" O CYS A 159 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N CYS A 159 " --> pdb=" O ASN A 129 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 140 through 141 removed outlier: 5.437A pdb=" N VAL A 140 " --> pdb=" O SER A 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 298 through 299 removed outlier: 3.681A pdb=" N GLY A 298 " --> pdb=" O THR A 585 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 341 through 345 removed outlier: 3.961A pdb=" N GLU A 341 " --> pdb=" O SER A 386 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL A 382 " --> pdb=" O ILE A 345 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 525 through 526 removed outlier: 3.671A pdb=" N LEU A 571 " --> pdb=" O VAL A 562 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ASP A 560 " --> pdb=" O ILE A 573 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 640 through 641 removed outlier: 5.401A pdb=" N GLU A 640 " --> pdb=" O ALA A 676 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N THR A 678 " --> pdb=" O GLU A 640 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ILE A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE A 652 " --> pdb=" O ILE A 656 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 684 through 685 Processing sheet with id=AB1, first strand: chain 'A' and resid 693 through 700 removed outlier: 3.590A pdb=" N ILE A 696 " --> pdb=" O ARG A1055 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N GLN A1053 " --> pdb=" O THR A 698 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N PHE A 700 " --> pdb=" O PRO A1051 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR A1058 " --> pdb=" O PHE A1079 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER A1083 " --> pdb=" O ASN A1080 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 706 through 710 Processing sheet with id=AB3, first strand: chain 'A' and resid 715 through 716 removed outlier: 4.202A pdb=" N LYS A 715 " --> pdb=" O LEU A 843 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 770 through 771 removed outlier: 6.436A pdb=" N MET A 770 " --> pdb=" O SER C 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 1071 through 1072 Processing sheet with id=AB6, first strand: chain 'B' and resid 31 through 34 removed outlier: 4.278A pdb=" N THR B 31 " --> pdb=" O GLY B 68 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS B 180 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL B 196 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N TYR B 200 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N THR B 215 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL B 40 " --> pdb=" O LEU B 216 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 52 through 59 removed outlier: 3.681A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 81 through 82 removed outlier: 3.567A pdb=" N GLY B 104 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY B 100 " --> pdb=" O ILE B 234 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 112 through 116 removed outlier: 4.722A pdb=" N VAL B 123 " --> pdb=" O SER B 165 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ASN B 129 " --> pdb=" O CYS B 159 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N CYS B 159 " --> pdb=" O ASN B 129 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 140 through 141 removed outlier: 6.485A pdb=" N VAL B 140 " --> pdb=" O SER B 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 298 through 299 Processing sheet with id=AC3, first strand: chain 'B' and resid 321 through 322 removed outlier: 6.440A pdb=" N ASN B 321 " --> pdb=" O VAL B 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 341 through 344 removed outlier: 3.555A pdb=" N GLU B 341 " --> pdb=" O SER B 386 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B 384 " --> pdb=" O LYS B 343 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 570 through 572 removed outlier: 7.102A pdb=" N PHE B 551 " --> pdb=" O PHE C 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 650 through 651 Processing sheet with id=AC7, first strand: chain 'B' and resid 684 through 685 Processing sheet with id=AC8, first strand: chain 'B' and resid 695 through 697 removed outlier: 3.572A pdb=" N ILE B 696 " --> pdb=" O ARG B1055 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 704 through 710 Processing sheet with id=AD1, first strand: chain 'B' and resid 715 through 718 removed outlier: 4.283A pdb=" N LYS B 715 " --> pdb=" O LEU B 843 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1058 through 1059 removed outlier: 4.200A pdb=" N THR B1058 " --> pdb=" O PHE B1079 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER B1083 " --> pdb=" O ASN B1080 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N GLN B1088 " --> pdb=" O SER B1093 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N SER B1093 " --> pdb=" O GLN B1088 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1071 through 1072 Processing sheet with id=AD4, first strand: chain 'C' and resid 31 through 34 removed outlier: 4.278A pdb=" N THR C 31 " --> pdb=" O GLY C 68 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS C 180 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL C 196 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N TYR C 200 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR C 215 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL C 40 " --> pdb=" O LEU C 216 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 52 through 59 removed outlier: 3.681A pdb=" N ASP C 274 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 81 through 82 removed outlier: 3.567A pdb=" N GLY C 104 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY C 100 " --> pdb=" O ILE C 234 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 112 through 116 removed outlier: 4.722A pdb=" N VAL C 123 " --> pdb=" O SER C 165 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ASN C 129 " --> pdb=" O CYS C 159 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N CYS C 159 " --> pdb=" O ASN C 129 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 140 through 141 removed outlier: 6.485A pdb=" N VAL C 140 " --> pdb=" O SER C 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 298 through 299 Processing sheet with id=AE1, first strand: chain 'C' and resid 321 through 322 removed outlier: 6.439A pdb=" N ASN C 321 " --> pdb=" O VAL C 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'C' and resid 341 through 344 removed outlier: 3.556A pdb=" N GLU C 341 " --> pdb=" O SER C 386 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA C 384 " --> pdb=" O LYS C 343 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 551 through 552 Processing sheet with id=AE4, first strand: chain 'C' and resid 650 through 651 Processing sheet with id=AE5, first strand: chain 'C' and resid 695 through 697 removed outlier: 3.573A pdb=" N ILE C 696 " --> pdb=" O ARG C1055 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 704 through 710 Processing sheet with id=AE7, first strand: chain 'C' and resid 715 through 718 removed outlier: 4.282A pdb=" N LYS C 715 " --> pdb=" O LEU C 843 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1058 through 1059 removed outlier: 4.199A pdb=" N THR C1058 " --> pdb=" O PHE C1079 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER C1083 " --> pdb=" O ASN C1080 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N GLN C1088 " --> pdb=" O SER C1093 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N SER C1093 " --> pdb=" O GLN C1088 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1071 through 1072 746 hydrogen bonds defined for protein. 2082 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: 11.12 Time building geometry restraints manager: 10.70 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: 7807 1.34 - 1.46: 5407 1.46 - 1.58: 11736 1.58 - 1.69: 0 1.69 - 1.81: 179 Bond restraints: 25129 Sorted by residual: bond pdb=" C LEU A 222 " pdb=" N PRO A 223 " ideal model delta sigma weight residual 1.334 1.242 0.092 2.34e-02 1.83e+03 1.55e+01 bond pdb=" C ASP A 790 " pdb=" N PRO A 791 " ideal model delta sigma weight residual 1.336 1.384 -0.048 1.23e-02 6.61e+03 1.54e+01 bond pdb=" C ASP C 790 " pdb=" N PRO C 791 " ideal model delta sigma weight residual 1.336 1.382 -0.046 1.23e-02 6.61e+03 1.40e+01 bond pdb=" C ASP B 790 " pdb=" N PRO B 791 " ideal model delta sigma weight residual 1.336 1.381 -0.046 1.23e-02 6.61e+03 1.38e+01 bond pdb=" C LYS B 142 " pdb=" N PRO B 143 " ideal model delta sigma weight residual 1.337 1.379 -0.041 1.24e-02 6.50e+03 1.12e+01 ... (remaining 25124 not shown) Histogram of bond angle deviations from ideal: 95.57 - 103.39: 313 103.39 - 111.21: 9654 111.21 - 119.03: 10082 119.03 - 126.84: 13854 126.84 - 134.66: 288 Bond angle restraints: 34191 Sorted by residual: angle pdb=" N SER A 303 " pdb=" CA SER A 303 " pdb=" C SER A 303 " ideal model delta sigma weight residual 111.04 126.16 -15.12 1.55e+00 4.16e-01 9.51e+01 angle pdb=" N ARG A 306 " pdb=" CA ARG A 306 " pdb=" C ARG A 306 " ideal model delta sigma weight residual 110.91 120.02 -9.11 1.17e+00 7.31e-01 6.06e+01 angle pdb=" N VAL A 969 " pdb=" CA VAL A 969 " pdb=" C VAL A 969 " ideal model delta sigma weight residual 113.71 107.06 6.65 9.50e-01 1.11e+00 4.90e+01 angle pdb=" N PHE B 305 " pdb=" CA PHE B 305 " pdb=" C PHE B 305 " ideal model delta sigma weight residual 108.76 119.74 -10.98 1.58e+00 4.01e-01 4.83e+01 angle pdb=" N PHE C 305 " pdb=" CA PHE C 305 " pdb=" C PHE C 305 " ideal model delta sigma weight residual 108.76 119.67 -10.91 1.58e+00 4.01e-01 4.77e+01 ... (remaining 34186 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.46: 14158 16.46 - 32.91: 566 32.91 - 49.37: 119 49.37 - 65.82: 15 65.82 - 82.28: 25 Dihedral angle restraints: 14883 sinusoidal: 5721 harmonic: 9162 Sorted by residual: dihedral pdb=" CB CYS A 524 " pdb=" SG CYS A 524 " pdb=" SG CYS A 576 " pdb=" CB CYS A 576 " ideal model delta sinusoidal sigma weight residual -86.00 -165.24 79.24 1 1.00e+01 1.00e-02 7.81e+01 dihedral pdb=" CB CYS B 524 " pdb=" SG CYS B 524 " pdb=" SG CYS B 576 " pdb=" CB CYS B 576 " ideal model delta sinusoidal sigma weight residual -86.00 -159.32 73.32 1 1.00e+01 1.00e-02 6.84e+01 dihedral pdb=" CB CYS C 524 " pdb=" SG CYS C 524 " pdb=" SG CYS C 576 " pdb=" CB CYS C 576 " ideal model delta sinusoidal sigma weight residual -86.00 -159.29 73.29 1 1.00e+01 1.00e-02 6.84e+01 ... (remaining 14880 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 3454 0.095 - 0.190: 366 0.190 - 0.285: 26 0.285 - 0.380: 10 0.380 - 0.475: 2 Chirality restraints: 3858 Sorted by residual: chirality pdb=" CB ILE A1097 " pdb=" CA ILE A1097 " pdb=" CG1 ILE A1097 " pdb=" CG2 ILE A1097 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.47 2.00e-01 2.50e+01 5.64e+00 chirality pdb=" CB ILE A 621 " pdb=" CA ILE A 621 " pdb=" CG1 ILE A 621 " pdb=" CG2 ILE A 621 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.45 2.00e-01 2.50e+01 5.11e+00 chirality pdb=" CB ILE A 787 " pdb=" CA ILE A 787 " pdb=" CG1 ILE A 787 " pdb=" CG2 ILE A 787 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.42e+00 ... (remaining 3855 not shown) Planarity restraints: 4427 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 616 " -0.058 5.00e-02 4.00e+02 8.65e-02 1.20e+01 pdb=" N PRO B 617 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO B 617 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 617 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 616 " 0.057 5.00e-02 4.00e+02 8.62e-02 1.19e+01 pdb=" N PRO C 617 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO C 617 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 617 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 469 " -0.047 5.00e-02 4.00e+02 7.17e-02 8.23e+00 pdb=" N PRO C 470 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO C 470 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO C 470 " -0.034 5.00e-02 4.00e+02 ... (remaining 4424 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 5162 2.77 - 3.30: 22639 3.30 - 3.84: 41136 3.84 - 4.37: 48496 4.37 - 4.90: 81134 Nonbonded interactions: 198567 Sorted by model distance: nonbonded pdb=" OH TYR C 41 " pdb=" O LEU C 58 " model vdw 2.241 3.040 nonbonded pdb=" OH TYR B 41 " pdb=" O LEU B 58 " model vdw 2.242 3.040 nonbonded pdb=" O GLU A 647 " pdb=" OH TYR A 677 " model vdw 2.247 3.040 nonbonded pdb=" O ASP A 564 " pdb=" N SER A 568 " model vdw 2.255 3.120 nonbonded pdb=" O GLU B 647 " pdb=" OH TYR B 677 " model vdw 2.261 3.040 ... (remaining 198562 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 18 through 809 or resid 831 through 1104)) selection = (chain 'B' and (resid 18 through 315 or resid 322 through 502 or resid 518 throu \ gh 1104)) selection = (chain 'C' and (resid 18 through 315 or resid 322 through 502 or resid 518 throu \ gh 1104)) } 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: 0.730 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: 0.040 Extract box with map and model: 0.970 Check model and map are aligned: 0.190 Set scattering table: 0.190 Process input model: 68.490 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.100 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.0000 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: