Starting phenix.real_space_refine (version: 1.21rc1) on Thu Oct 12 11:54:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0x_34417/10_2023/8h0x_34417_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0x_34417/10_2023/8h0x_34417.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0x_34417/10_2023/8h0x_34417.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0x_34417/10_2023/8h0x_34417.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0x_34417/10_2023/8h0x_34417_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0x_34417/10_2023/8h0x_34417_updated.pdb" } resolution = 2.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 141 5.16 5 C 16062 2.51 5 N 4083 2.21 5 O 4836 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 57": "OD1" <-> "OD2" Residue "A ASP 85": "OD1" <-> "OD2" Residue "A PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 267": "OD1" <-> "OD2" Residue "A ARG 306": "NH1" <-> "NH2" Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 376": "OD1" <-> "OD2" Residue "A PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 554": "OD1" <-> "OD2" Residue "A PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 677": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 886": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 961": "OD1" <-> "OD2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1109": "OD1" <-> "OD2" Residue "A TYR 1120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 57": "OD1" <-> "OD2" Residue "B ASP 85": "OD1" <-> "OD2" Residue "B PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 267": "OD1" <-> "OD2" Residue "B ARG 306": "NH1" <-> "NH2" Residue "B PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 376": "OD1" <-> "OD2" Residue "B PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 554": "OD1" <-> "OD2" Residue "B PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 677": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 886": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 961": "OD1" <-> "OD2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1109": "OD1" <-> "OD2" Residue "B TYR 1120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 57": "OD1" <-> "OD2" Residue "C ASP 85": "OD1" <-> "OD2" Residue "C PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 267": "OD1" <-> "OD2" Residue "C ARG 306": "NH1" <-> "NH2" Residue "C PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 376": "OD1" <-> "OD2" Residue "C PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 554": "OD1" <-> "OD2" Residue "C PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 677": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 886": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 961": "OD1" <-> "OD2" Residue "C PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1109": "OD1" <-> "OD2" Residue "C TYR 1120": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 25122 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1039, 8115 Classifications: {'peptide': 1039} Link IDs: {'PTRANS': 49, 'TRANS': 989} Chain breaks: 5 Chain: "B" Number of atoms: 8115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1039, 8115 Classifications: {'peptide': 1039} Link IDs: {'PTRANS': 49, 'TRANS': 989} Chain breaks: 5 Chain: "C" Number of atoms: 8115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1039, 8115 Classifications: {'peptide': 1039} Link IDs: {'PTRANS': 49, 'TRANS': 989} Chain breaks: 5 Chain: "A" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 279 Unusual residues: {'BLA': 1, 'EIC': 2, 'NAG': 14} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen chiralities: 14 Chain: "B" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 259 Unusual residues: {'BLA': 1, 'EIC': 1, 'NAG': 14} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen chiralities: 14 Chain: "C" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 239 Unusual residues: {'BLA': 1, 'NAG': 14} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen chiralities: 14 Time building chain proxies: 13.26, per 1000 atoms: 0.53 Number of scatterers: 25122 At special positions: 0 Unit cell: (124.83, 136.875, 173.01, 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 141 16.00 O 4836 8.00 N 4083 7.00 C 16062 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 288 " distance=2.03 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 348 " distance=2.05 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS A 419 " distance=2.04 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS B 967 " distance=2.05 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 511 " distance=2.03 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 474 " distance=2.03 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " distance=2.03 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.03 Simple disulfide: pdb=" SG CYS A 720 " - pdb=" SG CYS A 742 " distance=2.04 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS A 822 " - pdb=" SG CYS A 833 " distance=2.04 Simple disulfide: pdb=" SG CYS A 967 " - pdb=" SG CYS C 370 " distance=2.06 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.02 Simple disulfide: pdb=" SG CYS A1064 " - pdb=" SG CYS A1108 " distance=2.04 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 288 " distance=2.03 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 348 " distance=2.05 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 419 " distance=2.04 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS C 967 " distance=2.06 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 511 " distance=2.03 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " distance=2.03 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 635 " distance=2.03 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.03 Simple disulfide: pdb=" SG CYS B 720 " - pdb=" SG CYS B 742 " distance=2.04 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B 822 " - pdb=" SG CYS B 833 " distance=2.04 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.02 Simple disulfide: pdb=" SG CYS B1064 " - pdb=" SG CYS B1108 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 288 " distance=2.03 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 348 " distance=2.05 Simple disulfide: pdb=" SG CYS C 366 " - pdb=" SG CYS C 419 " distance=2.04 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 511 " distance=2.03 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 474 " distance=2.03 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.03 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 635 " distance=2.03 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.03 Simple disulfide: pdb=" SG CYS C 720 " - pdb=" SG CYS C 742 " distance=2.04 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.03 Simple disulfide: pdb=" SG CYS C 822 " - pdb=" SG CYS C 833 " distance=2.04 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.01 Simple disulfide: pdb=" SG CYS C1064 " - pdb=" SG CYS C1108 " 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 Links applied NAG-ASN " NAG A1302 " - " ASN A 65 " " NAG A1303 " - " ASN A1080 " " NAG A1304 " - " ASN A 109 " " NAG A1305 " - " ASN A 119 " " NAG A1306 " - " ASN A 158 " " NAG A1307 " - " ASN A 227 " " NAG A1308 " - " ASN A 269 " " NAG A1309 " - " ASN A 318 " " NAG A1310 " - " ASN A 330 " " NAG A1311 " - " ASN A 357 " " NAG A1312 " - " ASN A 602 " " NAG A1313 " - " ASN A 699 " " NAG A1314 " - " ASN A 783 " " NAG A1315 " - " ASN A1116 " " NAG B1301 " - " ASN B 65 " " NAG B1302 " - " ASN B1080 " " NAG B1303 " - " ASN B 109 " " NAG B1304 " - " ASN B 119 " " NAG B1305 " - " ASN B 158 " " NAG B1306 " - " ASN B 227 " " NAG B1307 " - " ASN B 269 " " NAG B1308 " - " ASN B 318 " " NAG B1309 " - " ASN B 330 " " NAG B1310 " - " ASN B 357 " " NAG B1311 " - " ASN B 602 " " NAG B1312 " - " ASN B 699 " " NAG B1313 " - " ASN B 783 " " NAG B1314 " - " ASN B1116 " " NAG C1301 " - " ASN C 65 " " NAG C1302 " - " ASN C1080 " " NAG C1303 " - " ASN C 109 " " NAG C1304 " - " ASN C 119 " " NAG C1305 " - " ASN C 158 " " NAG C1306 " - " ASN C 227 " " NAG C1307 " - " ASN C 269 " " NAG C1308 " - " ASN C 318 " " NAG C1309 " - " ASN C 330 " " NAG C1310 " - " ASN C 357 " " NAG C1311 " - " ASN C 602 " " NAG C1312 " - " ASN C 699 " " NAG C1313 " - " ASN C 783 " " NAG C1314 " - " ASN C1116 " Time building additional restraints: 9.72 Conformation dependent library (CDL) restraints added in 3.7 seconds 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5832 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 63 helices and 36 sheets defined 23.0% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.92 Creating SS restraints... Processing helix chain 'A' and resid 282 through 290 Processing helix chain 'A' and resid 325 through 329 Processing helix chain 'A' and resid 353 through 357 removed outlier: 3.587A pdb=" N TYR A 356 " --> pdb=" O SER A 353 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASN A 357 " --> pdb=" O VAL A 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 353 through 357' Processing helix chain 'A' and resid 371 through 373 No H-bonds generated for 'chain 'A' and resid 371 through 373' Processing helix chain 'A' and resid 391 through 396 removed outlier: 3.600A pdb=" N VAL A 394 " --> pdb=" O GLY A 391 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ARG A 395 " --> pdb=" O ASP A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 Processing helix chain 'A' and resid 426 through 429 No H-bonds generated for 'chain 'A' and resid 426 through 429' Processing helix chain 'A' and resid 489 through 491 No H-bonds generated for 'chain 'A' and resid 489 through 491' Processing helix chain 'A' and resid 720 through 724 Processing helix chain 'A' and resid 729 through 764 removed outlier: 4.814A pdb=" N GLN A 737 " --> pdb=" O ASN A 733 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N TYR A 738 " --> pdb=" O LEU A 734 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLY A 739 " --> pdb=" O LEU A 735 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N SER A 740 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N PHE A 741 " --> pdb=" O GLN A 737 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N CYS A 742 " --> pdb=" O TYR A 738 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 807 Processing helix chain 'A' and resid 819 through 824 Processing helix chain 'A' and resid 831 through 838 removed outlier: 3.635A pdb=" N ASN A 838 " --> pdb=" O ALA A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 865 Processing helix chain 'A' and resid 869 through 872 No H-bonds generated for 'chain 'A' and resid 869 through 872' Processing helix chain 'A' and resid 880 through 891 removed outlier: 3.620A pdb=" N ILE A 891 " --> pdb=" O ARG A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 900 Processing helix chain 'A' and resid 902 through 921 removed outlier: 3.593A pdb=" N THR A 921 " --> pdb=" O GLN A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 949 removed outlier: 4.242A pdb=" N VAL A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL A 934 " --> pdb=" O LEU A 930 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU A 948 " --> pdb=" O LEU A 944 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N SER A 949 " --> pdb=" O VAL A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 965 Processing helix chain 'A' and resid 968 through 1014 removed outlier: 3.648A pdb=" N VAL A 973 " --> pdb=" O VAL A 969 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN A 974 " --> pdb=" O GLU A 970 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP A 976 " --> pdb=" O GLU A 972 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ARG A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 978 " --> pdb=" O GLN A 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 290 Processing helix chain 'B' and resid 325 through 329 Processing helix chain 'B' and resid 353 through 357 removed outlier: 3.587A pdb=" N TYR B 356 " --> pdb=" O SER B 353 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASN B 357 " --> pdb=" O VAL B 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 353 through 357' Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 391 through 396 removed outlier: 3.600A pdb=" N VAL B 394 " --> pdb=" O GLY B 391 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ARG B 395 " --> pdb=" O ASP B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 Processing helix chain 'B' and resid 426 through 429 No H-bonds generated for 'chain 'B' and resid 426 through 429' Processing helix chain 'B' and resid 489 through 491 No H-bonds generated for 'chain 'B' and resid 489 through 491' Processing helix chain 'B' and resid 720 through 724 Processing helix chain 'B' and resid 729 through 764 removed outlier: 4.814A pdb=" N GLN B 737 " --> pdb=" O ASN B 733 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N TYR B 738 " --> pdb=" O LEU B 734 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLY B 739 " --> pdb=" O LEU B 735 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N SER B 740 " --> pdb=" O LEU B 736 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N PHE B 741 " --> pdb=" O GLN B 737 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N CYS B 742 " --> pdb=" O TYR B 738 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR B 760 " --> pdb=" O GLN B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 799 through 807 Processing helix chain 'B' and resid 819 through 824 Processing helix chain 'B' and resid 831 through 838 removed outlier: 3.635A pdb=" N ASN B 838 " --> pdb=" O ALA B 834 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 865 Processing helix chain 'B' and resid 869 through 872 No H-bonds generated for 'chain 'B' and resid 869 through 872' Processing helix chain 'B' and resid 880 through 891 removed outlier: 3.620A pdb=" N ILE B 891 " --> pdb=" O ARG B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 900 Processing helix chain 'B' and resid 902 through 921 removed outlier: 3.593A pdb=" N THR B 921 " --> pdb=" O GLN B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 928 through 949 removed outlier: 4.242A pdb=" N VAL B 933 " --> pdb=" O LYS B 929 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL B 934 " --> pdb=" O LEU B 930 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU B 948 " --> pdb=" O LEU B 944 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N SER B 949 " --> pdb=" O VAL B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 965 Processing helix chain 'B' and resid 968 through 1014 removed outlier: 3.648A pdb=" N VAL B 973 " --> pdb=" O VAL B 969 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN B 974 " --> pdb=" O GLU B 970 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP B 976 " --> pdb=" O GLU B 972 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ARG B 977 " --> pdb=" O VAL B 973 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU B 978 " --> pdb=" O GLN B 974 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 290 Processing helix chain 'C' and resid 325 through 329 Processing helix chain 'C' and resid 353 through 357 removed outlier: 3.587A pdb=" N TYR C 356 " --> pdb=" O SER C 353 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASN C 357 " --> pdb=" O VAL C 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 353 through 357' Processing helix chain 'C' and resid 371 through 373 No H-bonds generated for 'chain 'C' and resid 371 through 373' Processing helix chain 'C' and resid 391 through 396 removed outlier: 3.600A pdb=" N VAL C 394 " --> pdb=" O GLY C 391 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ARG C 395 " --> pdb=" O ASP C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 Processing helix chain 'C' and resid 426 through 429 No H-bonds generated for 'chain 'C' and resid 426 through 429' Processing helix chain 'C' and resid 489 through 491 No H-bonds generated for 'chain 'C' and resid 489 through 491' Processing helix chain 'C' and resid 720 through 724 Processing helix chain 'C' and resid 729 through 764 removed outlier: 4.814A pdb=" N GLN C 737 " --> pdb=" O ASN C 733 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N TYR C 738 " --> pdb=" O LEU C 734 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLY C 739 " --> pdb=" O LEU C 735 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N SER C 740 " --> pdb=" O LEU C 736 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N PHE C 741 " --> pdb=" O GLN C 737 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N CYS C 742 " --> pdb=" O TYR C 738 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR C 760 " --> pdb=" O GLN C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 799 through 807 Processing helix chain 'C' and resid 819 through 824 Processing helix chain 'C' and resid 831 through 838 removed outlier: 3.636A pdb=" N ASN C 838 " --> pdb=" O ALA C 834 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 865 Processing helix chain 'C' and resid 869 through 872 No H-bonds generated for 'chain 'C' and resid 869 through 872' Processing helix chain 'C' and resid 880 through 891 removed outlier: 3.621A pdb=" N ILE C 891 " --> pdb=" O ARG C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 900 Processing helix chain 'C' and resid 902 through 921 removed outlier: 3.592A pdb=" N THR C 921 " --> pdb=" O GLN C 917 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 949 removed outlier: 4.242A pdb=" N VAL C 933 " --> pdb=" O LYS C 929 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL C 934 " --> pdb=" O LEU C 930 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU C 948 " --> pdb=" O LEU C 944 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N SER C 949 " --> pdb=" O VAL C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 959 through 965 Processing helix chain 'C' and resid 968 through 1014 removed outlier: 3.647A pdb=" N VAL C 973 " --> pdb=" O VAL C 969 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN C 974 " --> pdb=" O GLU C 970 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASP C 976 " --> pdb=" O GLU C 972 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ARG C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU C 978 " --> pdb=" O GLN C 974 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 32 through 35 removed outlier: 3.897A pdb=" N SER A 64 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ASN A 65 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N TYR A 256 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE A 220 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LYS A 198 " --> pdb=" O PRO A 218 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 52 through 59 removed outlier: 4.095A pdb=" N ASP A 274 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 161 through 164 removed outlier: 6.031A pdb=" N ARG A 99 " --> pdb=" O ASN A 118 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE A 234 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N TRP A 101 " --> pdb=" O ARG A 232 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ARG A 232 " --> pdb=" O TRP A 101 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N PHE A 103 " --> pdb=" O ASN A 230 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ASN A 230 " --> pdb=" O PHE A 103 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 298 through 301 Processing sheet with id= E, first strand: chain 'A' and resid 311 through 315 removed outlier: 4.071A pdb=" N GLY A 311 " --> pdb=" O CYS A 524 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N ASP A 560 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLY A 552 " --> pdb=" O ASP A 560 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 341 through 345 removed outlier: 4.255A pdb=" N VAL A 382 " --> pdb=" O ILE A 345 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 438 through 441 removed outlier: 4.798A pdb=" N TYR A 438 " --> pdb=" O TYR A 481 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 673 through 678 removed outlier: 6.510A pdb=" N ALA A 658 " --> pdb=" O PRO A 651 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 693 through 697 removed outlier: 3.835A pdb=" N ALA A1060 " --> pdb=" O PHE A1077 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N PHE A1077 " --> pdb=" O ALA A1060 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 699 through 710 removed outlier: 6.166A pdb=" N TYR A1049 " --> pdb=" O HIS A1030 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N HIS A1030 " --> pdb=" O TYR A1049 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 715 through 718 removed outlier: 4.493A pdb=" N LYS A 715 " --> pdb=" O LEU A 843 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 1070 through 1072 Processing sheet with id= M, first strand: chain 'B' and resid 32 through 35 removed outlier: 3.897A pdb=" N SER B 64 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE B 220 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LYS B 198 " --> pdb=" O PRO B 218 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 52 through 59 removed outlier: 4.096A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 161 through 164 removed outlier: 6.031A pdb=" N ARG B 99 " --> pdb=" O ASN B 118 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE B 234 " --> pdb=" O ARG B 99 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N TRP B 101 " --> pdb=" O ARG B 232 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ARG B 232 " --> pdb=" O TRP B 101 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N PHE B 103 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ASN B 230 " --> pdb=" O PHE B 103 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 298 through 301 Processing sheet with id= Q, first strand: chain 'B' and resid 311 through 315 removed outlier: 4.071A pdb=" N GLY B 311 " --> pdb=" O CYS B 524 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ASP B 560 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLY B 552 " --> pdb=" O ASP B 560 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 341 through 345 removed outlier: 4.255A pdb=" N VAL B 382 " --> pdb=" O ILE B 345 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 438 through 441 removed outlier: 4.798A pdb=" N TYR B 438 " --> pdb=" O TYR B 481 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 673 through 678 removed outlier: 6.510A pdb=" N ALA B 658 " --> pdb=" O PRO B 651 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 693 through 697 removed outlier: 3.835A pdb=" N ALA B1060 " --> pdb=" O PHE B1077 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N PHE B1077 " --> pdb=" O ALA B1060 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 699 through 710 removed outlier: 6.165A pdb=" N TYR B1049 " --> pdb=" O HIS B1030 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N HIS B1030 " --> pdb=" O TYR B1049 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 715 through 718 removed outlier: 4.493A pdb=" N LYS B 715 " --> pdb=" O LEU B 843 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 1070 through 1072 Processing sheet with id= Y, first strand: chain 'C' and resid 32 through 35 removed outlier: 3.897A pdb=" N SER C 64 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE C 220 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LYS C 198 " --> pdb=" O PRO C 218 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 52 through 59 removed outlier: 4.096A pdb=" N ASP C 274 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'C' and resid 161 through 164 removed outlier: 6.030A pdb=" N ARG C 99 " --> pdb=" O ASN C 118 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE C 234 " --> pdb=" O ARG C 99 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N TRP C 101 " --> pdb=" O ARG C 232 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ARG C 232 " --> pdb=" O TRP C 101 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N PHE C 103 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ASN C 230 " --> pdb=" O PHE C 103 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 298 through 301 Processing sheet with id= AC, first strand: chain 'C' and resid 311 through 315 removed outlier: 4.071A pdb=" N GLY C 311 " --> pdb=" O CYS C 524 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N ASP C 560 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLY C 552 " --> pdb=" O ASP C 560 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'C' and resid 341 through 345 removed outlier: 4.255A pdb=" N VAL C 382 " --> pdb=" O ILE C 345 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'C' and resid 438 through 441 removed outlier: 4.798A pdb=" N TYR C 438 " --> pdb=" O TYR C 481 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'C' and resid 673 through 678 removed outlier: 6.510A pdb=" N ALA C 658 " --> pdb=" O PRO C 651 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'C' and resid 693 through 697 removed outlier: 3.836A pdb=" N ALA C1060 " --> pdb=" O PHE C1077 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N PHE C1077 " --> pdb=" O ALA C1060 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'C' and resid 699 through 710 removed outlier: 6.165A pdb=" N TYR C1049 " --> pdb=" O HIS C1030 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N HIS C1030 " --> pdb=" O TYR C1049 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'C' and resid 715 through 718 removed outlier: 4.494A pdb=" N LYS C 715 " --> pdb=" O LEU C 843 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'C' and resid 1070 through 1072 900 hydrogen bonds defined for protein. 2529 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: 10.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4071 1.31 - 1.45: 7474 1.45 - 1.59: 13964 1.59 - 1.73: 0 1.73 - 1.86: 189 Bond restraints: 25698 Sorted by residual: bond pdb=" ND BLA A1316 " pdb=" C1D BLA A1316 " ideal model delta sigma weight residual 1.319 1.481 -0.162 2.00e-02 2.50e+03 6.53e+01 bond pdb=" ND BLA B1315 " pdb=" C1D BLA B1315 " ideal model delta sigma weight residual 1.319 1.481 -0.162 2.00e-02 2.50e+03 6.52e+01 bond pdb=" ND BLA C1315 " pdb=" C1D BLA C1315 " ideal model delta sigma weight residual 1.319 1.480 -0.161 2.00e-02 2.50e+03 6.49e+01 bond pdb=" C1C BLA C1315 " pdb=" NC BLA C1315 " ideal model delta sigma weight residual 1.368 1.529 -0.161 2.00e-02 2.50e+03 6.47e+01 bond pdb=" C1C BLA A1316 " pdb=" NC BLA A1316 " ideal model delta sigma weight residual 1.368 1.529 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 25693 not shown) Histogram of bond angle deviations from ideal: 97.73 - 105.00: 472 105.00 - 112.28: 12695 112.28 - 119.56: 8233 119.56 - 126.84: 13257 126.84 - 134.12: 278 Bond angle restraints: 34935 Sorted by residual: angle pdb=" CB MET C 884 " pdb=" CG MET C 884 " pdb=" SD MET C 884 " ideal model delta sigma weight residual 112.70 133.75 -21.05 3.00e+00 1.11e-01 4.92e+01 angle pdb=" CB MET A 884 " pdb=" CG MET A 884 " pdb=" SD MET A 884 " ideal model delta sigma weight residual 112.70 133.74 -21.04 3.00e+00 1.11e-01 4.92e+01 angle pdb=" CB MET B 884 " pdb=" CG MET B 884 " pdb=" SD MET B 884 " ideal model delta sigma weight residual 112.70 133.68 -20.98 3.00e+00 1.11e-01 4.89e+01 angle pdb=" C CYS A 967 " pdb=" CA CYS A 967 " pdb=" CB CYS A 967 " ideal model delta sigma weight residual 109.66 118.70 -9.04 1.94e+00 2.66e-01 2.17e+01 angle pdb=" C THR A 150 " pdb=" N MET A 151 " pdb=" CA MET A 151 " ideal model delta sigma weight residual 123.11 116.50 6.61 1.42e+00 4.96e-01 2.17e+01 ... (remaining 34930 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 13820 17.44 - 34.89: 837 34.89 - 52.33: 182 52.33 - 69.78: 35 69.78 - 87.22: 39 Dihedral angle restraints: 14913 sinusoidal: 5838 harmonic: 9075 Sorted by residual: dihedral pdb=" CB CYS B 648 " pdb=" SG CYS B 648 " pdb=" SG CYS B 657 " pdb=" CB CYS B 657 " ideal model delta sinusoidal sigma weight residual 93.00 6.09 86.91 1 1.00e+01 1.00e-02 9.08e+01 dihedral pdb=" CB CYS C 648 " pdb=" SG CYS C 648 " pdb=" SG CYS C 657 " pdb=" CB CYS C 657 " ideal model delta sinusoidal sigma weight residual 93.00 6.10 86.90 1 1.00e+01 1.00e-02 9.08e+01 dihedral pdb=" CB CYS A 648 " pdb=" SG CYS A 648 " pdb=" SG CYS A 657 " pdb=" CB CYS A 657 " ideal model delta sinusoidal sigma weight residual 93.00 6.12 86.88 1 1.00e+01 1.00e-02 9.08e+01 ... (remaining 14910 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 3784 0.107 - 0.215: 220 0.215 - 0.322: 13 0.322 - 0.429: 6 0.429 - 0.536: 6 Chirality restraints: 4029 Sorted by residual: chirality pdb=" C1 NAG C1312 " pdb=" ND2 ASN C 699 " pdb=" C2 NAG C1312 " pdb=" O5 NAG C1312 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.19e+00 chirality pdb=" C1 NAG A1313 " pdb=" ND2 ASN A 699 " pdb=" C2 NAG A1313 " pdb=" O5 NAG A1313 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.17e+00 chirality pdb=" C1 NAG B1312 " pdb=" ND2 ASN B 699 " pdb=" C2 NAG B1312 " pdb=" O5 NAG B1312 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 7.08e+00 ... (remaining 4026 not shown) Planarity restraints: 4500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C BLA A1316 " -0.014 2.00e-02 2.50e+03 8.75e-02 1.92e+02 pdb=" C1D BLA A1316 " 0.198 2.00e-02 2.50e+03 pdb=" C2C BLA A1316 " 0.020 2.00e-02 2.50e+03 pdb=" C3C BLA A1316 " -0.014 2.00e-02 2.50e+03 pdb=" C4C BLA A1316 " -0.079 2.00e-02 2.50e+03 pdb=" CAC BLA A1316 " 0.001 2.00e-02 2.50e+03 pdb=" CHD BLA A1316 " -0.127 2.00e-02 2.50e+03 pdb=" CMC BLA A1316 " 0.088 2.00e-02 2.50e+03 pdb=" NC BLA A1316 " -0.078 2.00e-02 2.50e+03 pdb=" OC BLA A1316 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C BLA B1315 " -0.014 2.00e-02 2.50e+03 8.74e-02 1.91e+02 pdb=" C1D BLA B1315 " 0.198 2.00e-02 2.50e+03 pdb=" C2C BLA B1315 " 0.021 2.00e-02 2.50e+03 pdb=" C3C BLA B1315 " -0.014 2.00e-02 2.50e+03 pdb=" C4C BLA B1315 " -0.078 2.00e-02 2.50e+03 pdb=" CAC BLA B1315 " 0.001 2.00e-02 2.50e+03 pdb=" CHD BLA B1315 " -0.128 2.00e-02 2.50e+03 pdb=" CMC BLA B1315 " 0.088 2.00e-02 2.50e+03 pdb=" NC BLA B1315 " -0.079 2.00e-02 2.50e+03 pdb=" OC BLA B1315 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C BLA C1315 " -0.013 2.00e-02 2.50e+03 8.74e-02 1.91e+02 pdb=" C1D BLA C1315 " 0.198 2.00e-02 2.50e+03 pdb=" C2C BLA C1315 " 0.020 2.00e-02 2.50e+03 pdb=" C3C BLA C1315 " -0.014 2.00e-02 2.50e+03 pdb=" C4C BLA C1315 " -0.079 2.00e-02 2.50e+03 pdb=" CAC BLA C1315 " 0.001 2.00e-02 2.50e+03 pdb=" CHD BLA C1315 " -0.127 2.00e-02 2.50e+03 pdb=" CMC BLA C1315 " 0.088 2.00e-02 2.50e+03 pdb=" NC BLA C1315 " -0.079 2.00e-02 2.50e+03 pdb=" OC BLA C1315 " 0.005 2.00e-02 2.50e+03 ... (remaining 4497 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5434 2.79 - 3.31: 20599 3.31 - 3.84: 39182 3.84 - 4.37: 47777 4.37 - 4.90: 83015 Nonbonded interactions: 196007 Sorted by model distance: nonbonded pdb=" N ASN A 589 " pdb=" OD1 ASN A 589 " model vdw 2.257 2.520 nonbonded pdb=" N ASN B 589 " pdb=" OD1 ASN B 589 " model vdw 2.257 2.520 nonbonded pdb=" N ASN C 589 " pdb=" OD1 ASN C 589 " model vdw 2.257 2.520 nonbonded pdb=" OG SER A 461 " pdb=" OD1 ASP A 463 " model vdw 2.282 2.440 nonbonded pdb=" OG SER C 461 " pdb=" OD1 ASP C 463 " model vdw 2.282 2.440 ... (remaining 196002 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 31 through 1123 or resid 1302 through 1314)) selection = (chain 'B' and (resid 31 through 1123 or resid 1302 through 1314)) selection = (chain 'C' and (resid 31 through 1123 or resid 1302 through 1314)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.600 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: 0.020 Extract box with map and model: 9.030 Check model and map are aligned: 0.400 Set scattering table: 0.240 Process input model: 68.700 Find NCS groups from input model: 1.910 Set up NCS constraints: 0.180 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:12.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 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 : 0.008 0.162 25698 Z= 0.532 Angle : 0.928 21.053 34935 Z= 0.500 Chirality : 0.059 0.536 4029 Planarity : 0.006 0.088 4458 Dihedral : 12.741 87.220 8946 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.11 % Allowed : 1.48 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.82 (0.14), residues: 3081 helix: 0.22 (0.19), residues: 696 sheet: 1.07 (0.20), residues: 669 loop : -1.61 (0.12), residues: 1716 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 255 time to evaluate : 2.692 Fit side-chains outliers start: 30 outliers final: 7 residues processed: 273 average time/residue: 1.4820 time to fit residues: 463.7752 Evaluate side-chains 167 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 160 time to evaluate : 2.566 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 3 average time/residue: 0.3498 time to fit residues: 5.3206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 260 optimal weight: 0.9990 chunk 234 optimal weight: 0.6980 chunk 129 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 157 optimal weight: 0.9990 chunk 125 optimal weight: 0.9980 chunk 242 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 147 optimal weight: 0.9980 chunk 180 optimal weight: 0.8980 chunk 280 optimal weight: 8.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 HIS B 626 ASN C 721 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 25698 Z= 0.188 Angle : 0.558 19.298 34935 Z= 0.290 Chirality : 0.047 0.348 4029 Planarity : 0.004 0.059 4458 Dihedral : 5.974 67.450 3426 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.63 % Allowed : 6.12 % Favored : 92.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: -0.47 (0.14), residues: 3081 helix: 0.90 (0.20), residues: 711 sheet: 1.08 (0.19), residues: 690 loop : -1.54 (0.13), residues: 1680 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 181 time to evaluate : 2.992 Fit side-chains outliers start: 44 outliers final: 19 residues processed: 205 average time/residue: 1.3281 time to fit residues: 322.1067 Evaluate side-chains 173 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 154 time to evaluate : 2.738 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 15 residues processed: 5 average time/residue: 0.7817 time to fit residues: 8.7215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.0385 > 50: distance: 11 - 99: 29.165 distance: 47 - 69: 3.438 distance: 52 - 75: 8.030 distance: 69 - 70: 5.212 distance: 70 - 71: 8.000 distance: 70 - 73: 3.195 distance: 71 - 72: 18.541 distance: 71 - 75: 7.775 distance: 73 - 74: 12.576 distance: 75 - 76: 4.063 distance: 76 - 77: 4.300 distance: 76 - 79: 3.444 distance: 77 - 78: 7.442 distance: 77 - 86: 8.004 distance: 79 - 80: 9.096 distance: 80 - 81: 3.585 distance: 83 - 84: 5.743 distance: 83 - 85: 4.424 distance: 86 - 87: 7.696 distance: 87 - 88: 5.130 distance: 87 - 90: 9.875 distance: 88 - 89: 3.079 distance: 90 - 91: 14.770 distance: 91 - 92: 5.084 distance: 91 - 93: 17.794 distance: 94 - 95: 23.683 distance: 95 - 96: 23.927 distance: 95 - 98: 27.298 distance: 96 - 97: 22.612 distance: 96 - 100: 31.722 distance: 100 - 101: 16.066 distance: 101 - 102: 14.855 distance: 101 - 104: 25.902 distance: 102 - 103: 13.931 distance: 102 - 109: 20.897 distance: 103 - 130: 12.632 distance: 104 - 105: 6.167 distance: 105 - 106: 13.312 distance: 106 - 107: 13.409 distance: 107 - 108: 31.118 distance: 109 - 110: 12.623 distance: 110 - 111: 12.875 distance: 110 - 113: 9.430 distance: 111 - 112: 6.107 distance: 111 - 116: 11.925 distance: 113 - 114: 19.491 distance: 113 - 115: 21.676 distance: 116 - 117: 4.508 distance: 117 - 118: 11.836 distance: 117 - 120: 14.909 distance: 118 - 119: 14.728 distance: 118 - 125: 7.015 distance: 120 - 121: 15.378 distance: 122 - 123: 9.068 distance: 122 - 124: 8.874 distance: 125 - 126: 6.289 distance: 126 - 127: 10.308 distance: 126 - 129: 12.229 distance: 127 - 128: 24.690 distance: 127 - 130: 16.111 distance: 128 - 155: 29.922 distance: 130 - 131: 18.558 distance: 131 - 132: 15.576 distance: 131 - 134: 9.115 distance: 132 - 133: 18.904 distance: 132 - 139: 21.191 distance: 134 - 135: 19.811 distance: 135 - 136: 10.635 distance: 136 - 137: 6.478 distance: 139 - 140: 13.144 distance: 140 - 141: 9.376 distance: 140 - 143: 8.786 distance: 141 - 142: 8.321 distance: 141 - 146: 8.390 distance: 143 - 144: 33.200 distance: 143 - 145: 32.269