Starting phenix.real_space_refine on Mon Feb 19 15:50:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0x_34417/02_2024/8h0x_34417_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0x_34417/02_2024/8h0x_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_34417/02_2024/8h0x_34417.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0x_34417/02_2024/8h0x_34417.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0x_34417/02_2024/8h0x_34417_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0x_34417/02_2024/8h0x_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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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 dihedrals: 42 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 dihedrals: 42 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 dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Time building chain proxies: 13.83, per 1000 atoms: 0.55 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: 8.57 Conformation dependent library (CDL) restraints added in 4.3 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: 6.78 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: 10.07 Time building geometry restraints manager: 9.44 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: 14654 17.44 - 34.89: 864 34.89 - 52.33: 245 52.33 - 69.78: 41 69.78 - 87.22: 39 Dihedral angle restraints: 15843 sinusoidal: 6768 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 15840 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: 1.710 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: 8.700 Check model and map are aligned: 0.320 Set scattering table: 0.200 Process input model: 65.890 Find NCS groups from input model: 1.700 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.640 ------------------------------------------------------------------------------- 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 : 12.824 87.220 9876 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP C 868 HIS 0.005 0.001 HIS A1046 PHE 0.057 0.002 PHE B 334 TYR 0.037 0.002 TYR C 886 ARG 0.042 0.001 ARG A 306 *********************** 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 : 2.686 Fit side-chains REVERT: A 685 SER cc_start: 0.7873 (OUTLIER) cc_final: 0.7483 (m) REVERT: B 151 MET cc_start: 0.6690 (mmt) cc_final: 0.6395 (mmt) REVERT: B 884 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8569 (mmm) REVERT: C 137 PHE cc_start: 0.8511 (p90) cc_final: 0.8110 (p90) REVERT: C 151 MET cc_start: 0.7007 (mmt) cc_final: 0.6479 (mmt) REVERT: C 685 SER cc_start: 0.7848 (OUTLIER) cc_final: 0.7438 (m) outliers start: 30 outliers final: 7 residues processed: 273 average time/residue: 1.4862 time to fit residues: 464.0367 Evaluate side-chains 170 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 160 time to evaluate : 2.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 589 ASN Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 589 ASN Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 884 MET Chi-restraints excluded: chain C residue 626 ASN Chi-restraints excluded: chain C residue 685 SER 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: 1.9990 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 A 786 GLN A 917 GLN B 626 ASN C 721 ASN C 786 GLN C 917 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 25698 Z= 0.193 Angle : 0.558 17.727 34935 Z= 0.291 Chirality : 0.048 0.361 4029 Planarity : 0.004 0.061 4458 Dihedral : 7.728 67.190 4373 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.67 % Allowed : 6.01 % Favored : 92.32 % 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: -0.48 (0.14), residues: 3081 helix: 0.89 (0.20), residues: 711 sheet: 1.07 (0.19), residues: 690 loop : -1.55 (0.13), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 868 HIS 0.004 0.001 HIS A1046 PHE 0.013 0.001 PHE C 870 TYR 0.017 0.001 TYR A1120 ARG 0.006 0.000 ARG A 544 *********************** 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 229 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 184 time to evaluate : 2.775 Fit side-chains REVERT: B 518 ASP cc_start: 0.8067 (OUTLIER) cc_final: 0.7769 (t0) REVERT: C 130 PHE cc_start: 0.7758 (OUTLIER) cc_final: 0.5440 (p90) REVERT: C 137 PHE cc_start: 0.8319 (p90) cc_final: 0.7990 (p90) REVERT: C 151 MET cc_start: 0.6682 (mmt) cc_final: 0.6336 (mmt) REVERT: C 827 ASN cc_start: 0.7497 (OUTLIER) cc_final: 0.7213 (p0) outliers start: 45 outliers final: 16 residues processed: 209 average time/residue: 1.2354 time to fit residues: 304.9430 Evaluate side-chains 173 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 154 time to evaluate : 2.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 827 ASN Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 768 LYS Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain C residue 130 PHE Chi-restraints excluded: chain C residue 162 GLU Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 626 ASN Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 827 ASN Chi-restraints excluded: chain C residue 966 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 155 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 233 optimal weight: 0.9980 chunk 191 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 281 optimal weight: 3.9990 chunk 303 optimal weight: 5.9990 chunk 250 optimal weight: 0.6980 chunk 278 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 225 optimal weight: 0.9980 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 HIS A 626 ASN B 626 ASN C 721 ASN C 786 GLN C 917 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 25698 Z= 0.359 Angle : 0.677 19.348 34935 Z= 0.351 Chirality : 0.052 0.450 4029 Planarity : 0.005 0.052 4458 Dihedral : 7.672 61.769 4362 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.93 % Allowed : 8.28 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.14), residues: 3081 helix: 1.10 (0.20), residues: 675 sheet: 1.05 (0.19), residues: 678 loop : -1.61 (0.12), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 868 HIS 0.006 0.001 HIS A1046 PHE 0.020 0.002 PHE A 870 TYR 0.023 0.002 TYR B1049 ARG 0.005 0.001 ARG A1021 *********************** REFINEMENT MACRO_CYCLE 3 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 227 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 175 time to evaluate : 3.092 Fit side-chains REVERT: A 709 MET cc_start: 0.9288 (OUTLIER) cc_final: 0.9008 (mtp) REVERT: A 816 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.7229 (tpp) REVERT: B 816 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.7454 (tpp) REVERT: C 130 PHE cc_start: 0.7968 (OUTLIER) cc_final: 0.5580 (p90) REVERT: C 137 PHE cc_start: 0.8576 (p90) cc_final: 0.8229 (p90) REVERT: C 151 MET cc_start: 0.6651 (mmt) cc_final: 0.6450 (mmt) REVERT: C 827 ASN cc_start: 0.7528 (OUTLIER) cc_final: 0.7243 (p0) outliers start: 52 outliers final: 26 residues processed: 207 average time/residue: 1.2273 time to fit residues: 299.2057 Evaluate side-chains 190 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 159 time to evaluate : 2.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 640 GLU Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 816 MET Chi-restraints excluded: chain A residue 827 ASN Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 816 MET Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 130 PHE Chi-restraints excluded: chain C residue 306 ARG Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain C residue 827 ASN Chi-restraints excluded: chain C residue 848 THR Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 966 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 277 optimal weight: 3.9990 chunk 211 optimal weight: 0.8980 chunk 145 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 134 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 282 optimal weight: 0.5980 chunk 298 optimal weight: 2.9990 chunk 147 optimal weight: 0.7980 chunk 267 optimal weight: 2.9990 chunk 80 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 181 HIS A 626 ASN B 626 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 25698 Z= 0.168 Angle : 0.545 20.269 34935 Z= 0.280 Chirality : 0.046 0.334 4029 Planarity : 0.004 0.048 4458 Dihedral : 6.998 55.316 4360 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.78 % Allowed : 9.50 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.03 % 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: -0.25 (0.14), residues: 3081 helix: 1.43 (0.20), residues: 687 sheet: 1.10 (0.19), residues: 678 loop : -1.46 (0.12), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 868 HIS 0.004 0.001 HIS A 181 PHE 0.009 0.001 PHE B 870 TYR 0.016 0.001 TYR B1049 ARG 0.004 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 4 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 223 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 175 time to evaluate : 2.981 Fit side-chains REVERT: A 708 VAL cc_start: 0.9079 (OUTLIER) cc_final: 0.8812 (t) REVERT: A 851 MET cc_start: 0.8716 (mtt) cc_final: 0.8293 (mtt) REVERT: B 130 PHE cc_start: 0.7767 (OUTLIER) cc_final: 0.6777 (p90) REVERT: B 518 ASP cc_start: 0.8146 (OUTLIER) cc_final: 0.7732 (t0) REVERT: B 884 MET cc_start: 0.8796 (tpt) cc_final: 0.8111 (tpt) REVERT: C 130 PHE cc_start: 0.7903 (OUTLIER) cc_final: 0.5443 (p90) REVERT: C 137 PHE cc_start: 0.8583 (p90) cc_final: 0.8328 (p90) REVERT: C 322 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8075 (tm) REVERT: C 827 ASN cc_start: 0.7544 (OUTLIER) cc_final: 0.7263 (p0) outliers start: 48 outliers final: 26 residues processed: 209 average time/residue: 1.2170 time to fit residues: 301.2492 Evaluate side-chains 192 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 160 time to evaluate : 2.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 827 ASN Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain B residue 130 PHE Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 827 ASN Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 130 PHE Chi-restraints excluded: chain C residue 162 GLU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 589 ASN Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain C residue 827 ASN Chi-restraints excluded: chain C residue 848 THR Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 1108 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 248 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 222 optimal weight: 0.4980 chunk 123 optimal weight: 5.9990 chunk 254 optimal weight: 3.9990 chunk 206 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 152 optimal weight: 3.9990 chunk 268 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 626 ASN B 626 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.079 25698 Z= 0.492 Angle : 0.774 22.109 34935 Z= 0.396 Chirality : 0.056 0.512 4029 Planarity : 0.005 0.046 4458 Dihedral : 7.637 59.970 4360 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.78 % Allowed : 9.50 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.36 % 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: -0.53 (0.14), residues: 3081 helix: 0.94 (0.20), residues: 693 sheet: 1.00 (0.19), residues: 672 loop : -1.54 (0.12), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 868 HIS 0.007 0.001 HIS A1046 PHE 0.025 0.002 PHE A 870 TYR 0.025 0.003 TYR B1049 ARG 0.008 0.001 ARG A1021 *********************** REFINEMENT MACRO_CYCLE 5 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 248 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 173 time to evaluate : 2.918 Fit side-chains REVERT: A 130 PHE cc_start: 0.8078 (OUTLIER) cc_final: 0.7067 (p90) REVERT: A 708 VAL cc_start: 0.9069 (OUTLIER) cc_final: 0.8784 (t) REVERT: A 816 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.7326 (tpp) REVERT: B 708 VAL cc_start: 0.9098 (OUTLIER) cc_final: 0.8799 (t) REVERT: B 792 LEU cc_start: 0.8345 (tt) cc_final: 0.8135 (tp) REVERT: B 816 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.8102 (ttp) REVERT: C 130 PHE cc_start: 0.8128 (OUTLIER) cc_final: 0.6180 (p90) REVERT: C 827 ASN cc_start: 0.7726 (OUTLIER) cc_final: 0.7419 (p0) outliers start: 75 outliers final: 43 residues processed: 227 average time/residue: 1.2219 time to fit residues: 327.5594 Evaluate side-chains 212 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 162 time to evaluate : 2.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 816 MET Chi-restraints excluded: chain A residue 827 ASN Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain B residue 130 PHE Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 333 LYS Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 720 CYS Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 816 MET Chi-restraints excluded: chain B residue 827 ASN Chi-restraints excluded: chain B residue 848 THR Chi-restraints excluded: chain B residue 916 ILE Chi-restraints excluded: chain B residue 934 VAL Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 130 PHE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 306 ARG Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain C residue 827 ASN Chi-restraints excluded: chain C residue 848 THR Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 1108 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 100 optimal weight: 0.7980 chunk 268 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 175 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 298 optimal weight: 0.5980 chunk 248 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 98 optimal weight: 0.3980 chunk 156 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 626 ASN B 626 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 25698 Z= 0.156 Angle : 0.556 19.074 34935 Z= 0.283 Chirality : 0.046 0.330 4029 Planarity : 0.004 0.045 4458 Dihedral : 6.845 53.733 4360 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.93 % Allowed : 10.91 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.36 % 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: -0.21 (0.14), residues: 3081 helix: 1.40 (0.20), residues: 705 sheet: 1.11 (0.19), residues: 672 loop : -1.41 (0.12), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 868 HIS 0.002 0.001 HIS C1046 PHE 0.009 0.001 PHE B 909 TYR 0.020 0.001 TYR B1120 ARG 0.003 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 6 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 220 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 168 time to evaluate : 3.100 Fit side-chains REVERT: A 107 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8042 (mtm) REVERT: A 816 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.7380 (tpp) REVERT: A 851 MET cc_start: 0.8733 (mtt) cc_final: 0.8305 (mtt) REVERT: B 363 THR cc_start: 0.8491 (OUTLIER) cc_final: 0.8192 (m) REVERT: B 796 LYS cc_start: 0.8036 (mmmt) cc_final: 0.7768 (mmtm) REVERT: C 130 PHE cc_start: 0.7870 (OUTLIER) cc_final: 0.7150 (p90) REVERT: C 593 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7504 (mm-30) REVERT: C 685 SER cc_start: 0.7837 (OUTLIER) cc_final: 0.7381 (p) REVERT: C 708 VAL cc_start: 0.9071 (OUTLIER) cc_final: 0.8857 (t) REVERT: C 827 ASN cc_start: 0.7701 (OUTLIER) cc_final: 0.7403 (p0) REVERT: C 992 GLN cc_start: 0.8060 (mm110) cc_final: 0.7692 (mm110) outliers start: 52 outliers final: 19 residues processed: 206 average time/residue: 1.1658 time to fit residues: 285.2728 Evaluate side-chains 183 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 157 time to evaluate : 2.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 816 MET Chi-restraints excluded: chain A residue 827 ASN Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain C residue 130 PHE Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 685 SER Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 720 CYS Chi-restraints excluded: chain C residue 827 ASN Chi-restraints excluded: chain C residue 848 THR Chi-restraints excluded: chain C residue 1108 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 288 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 218 optimal weight: 0.8980 chunk 169 optimal weight: 1.9990 chunk 251 optimal weight: 0.0050 chunk 166 optimal weight: 0.8980 chunk 297 optimal weight: 1.9990 chunk 186 optimal weight: 3.9990 chunk 181 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 626 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25698 Z= 0.213 Angle : 0.594 18.458 34935 Z= 0.301 Chirality : 0.048 0.348 4029 Planarity : 0.004 0.045 4458 Dihedral : 6.723 53.902 4358 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.08 % Allowed : 11.28 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.36 % 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: -0.17 (0.14), residues: 3081 helix: 1.34 (0.20), residues: 714 sheet: 1.13 (0.19), residues: 672 loop : -1.36 (0.13), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 868 HIS 0.004 0.001 HIS A1046 PHE 0.012 0.001 PHE B 870 TYR 0.021 0.001 TYR A1120 ARG 0.005 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 7 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 221 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 165 time to evaluate : 3.050 Fit side-chains REVERT: A 816 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.7405 (tpp) REVERT: A 851 MET cc_start: 0.8776 (mtt) cc_final: 0.8311 (mtt) REVERT: B 130 PHE cc_start: 0.7851 (OUTLIER) cc_final: 0.7393 (p90) REVERT: B 792 LEU cc_start: 0.8327 (tt) cc_final: 0.8104 (tp) REVERT: B 796 LYS cc_start: 0.8077 (mmmt) cc_final: 0.7853 (mmtm) REVERT: B 884 MET cc_start: 0.8806 (tpt) cc_final: 0.8247 (tpt) REVERT: C 130 PHE cc_start: 0.7831 (OUTLIER) cc_final: 0.7030 (p90) REVERT: C 685 SER cc_start: 0.7781 (OUTLIER) cc_final: 0.7328 (p) REVERT: C 708 VAL cc_start: 0.9080 (OUTLIER) cc_final: 0.8835 (t) REVERT: C 827 ASN cc_start: 0.7721 (OUTLIER) cc_final: 0.7430 (p0) outliers start: 56 outliers final: 34 residues processed: 212 average time/residue: 1.2294 time to fit residues: 308.6662 Evaluate side-chains 202 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 162 time to evaluate : 2.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 640 GLU Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 816 MET Chi-restraints excluded: chain A residue 827 ASN Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain B residue 130 PHE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 720 CYS Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 848 THR Chi-restraints excluded: chain C residue 130 PHE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 589 ASN Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 685 SER Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 720 CYS Chi-restraints excluded: chain C residue 827 ASN Chi-restraints excluded: chain C residue 848 THR Chi-restraints excluded: chain C residue 972 GLU Chi-restraints excluded: chain C residue 1108 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 184 optimal weight: 0.6980 chunk 118 optimal weight: 0.9980 chunk 177 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 189 optimal weight: 4.9990 chunk 202 optimal weight: 6.9990 chunk 147 optimal weight: 2.9990 chunk 27 optimal weight: 0.4980 chunk 234 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 626 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 25698 Z= 0.159 Angle : 0.550 17.909 34935 Z= 0.280 Chirality : 0.046 0.314 4029 Planarity : 0.004 0.045 4458 Dihedral : 6.391 51.809 4358 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.89 % Allowed : 11.73 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.36 % 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: -0.06 (0.14), residues: 3081 helix: 1.64 (0.21), residues: 696 sheet: 1.09 (0.19), residues: 717 loop : -1.38 (0.13), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 868 HIS 0.003 0.001 HIS A 181 PHE 0.009 0.001 PHE A 137 TYR 0.020 0.001 TYR B1120 ARG 0.005 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 8 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 213 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 162 time to evaluate : 3.015 Fit side-chains REVERT: A 588 THR cc_start: 0.8523 (m) cc_final: 0.8243 (m) REVERT: A 685 SER cc_start: 0.7733 (OUTLIER) cc_final: 0.7299 (p) REVERT: A 816 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.7410 (tpp) REVERT: A 851 MET cc_start: 0.8721 (mtt) cc_final: 0.8265 (mtt) REVERT: B 130 PHE cc_start: 0.7830 (OUTLIER) cc_final: 0.7049 (p90) REVERT: B 363 THR cc_start: 0.8396 (OUTLIER) cc_final: 0.8070 (m) REVERT: B 792 LEU cc_start: 0.8317 (tt) cc_final: 0.8098 (tp) REVERT: B 884 MET cc_start: 0.8848 (tpt) cc_final: 0.8339 (tpt) REVERT: C 130 PHE cc_start: 0.7862 (OUTLIER) cc_final: 0.7138 (p90) REVERT: C 685 SER cc_start: 0.7739 (OUTLIER) cc_final: 0.7290 (p) REVERT: C 708 VAL cc_start: 0.9076 (OUTLIER) cc_final: 0.8873 (t) REVERT: C 827 ASN cc_start: 0.7710 (OUTLIER) cc_final: 0.7422 (p0) outliers start: 51 outliers final: 30 residues processed: 201 average time/residue: 1.1983 time to fit residues: 284.7577 Evaluate side-chains 193 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 155 time to evaluate : 2.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 816 MET Chi-restraints excluded: chain A residue 827 ASN Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 999 GLU Chi-restraints excluded: chain B residue 130 PHE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 720 CYS Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 827 ASN Chi-restraints excluded: chain B residue 848 THR Chi-restraints excluded: chain C residue 130 PHE Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 685 SER Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 720 CYS Chi-restraints excluded: chain C residue 827 ASN Chi-restraints excluded: chain C residue 848 THR Chi-restraints excluded: chain C residue 1108 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 270 optimal weight: 0.8980 chunk 285 optimal weight: 3.9990 chunk 260 optimal weight: 1.9990 chunk 277 optimal weight: 4.9990 chunk 167 optimal weight: 4.9990 chunk 120 optimal weight: 0.0070 chunk 217 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 250 optimal weight: 0.9990 chunk 262 optimal weight: 0.5980 chunk 276 optimal weight: 0.6980 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 626 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 25698 Z= 0.148 Angle : 0.535 19.238 34935 Z= 0.272 Chirality : 0.046 0.300 4029 Planarity : 0.003 0.045 4458 Dihedral : 6.155 50.420 4358 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.67 % Allowed : 12.25 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: 0.01 (0.14), residues: 3081 helix: 1.75 (0.21), residues: 696 sheet: 1.06 (0.19), residues: 723 loop : -1.31 (0.13), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 868 HIS 0.003 0.001 HIS A 181 PHE 0.008 0.001 PHE B 909 TYR 0.021 0.001 TYR A1120 ARG 0.005 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 9 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 203 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 158 time to evaluate : 2.970 Fit side-chains REVERT: A 588 THR cc_start: 0.8446 (m) cc_final: 0.8171 (m) REVERT: A 685 SER cc_start: 0.7811 (OUTLIER) cc_final: 0.7301 (p) REVERT: A 816 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.7411 (tpp) REVERT: A 851 MET cc_start: 0.8709 (mtt) cc_final: 0.8275 (mtt) REVERT: B 130 PHE cc_start: 0.7756 (OUTLIER) cc_final: 0.6898 (p90) REVERT: B 267 ASP cc_start: 0.7874 (m-30) cc_final: 0.7606 (m-30) REVERT: B 363 THR cc_start: 0.8371 (OUTLIER) cc_final: 0.8063 (m) REVERT: B 792 LEU cc_start: 0.8372 (tt) cc_final: 0.8164 (tp) REVERT: B 884 MET cc_start: 0.8853 (tpt) cc_final: 0.8335 (tpt) REVERT: C 130 PHE cc_start: 0.7892 (OUTLIER) cc_final: 0.7133 (p90) REVERT: C 685 SER cc_start: 0.7728 (OUTLIER) cc_final: 0.7282 (p) REVERT: C 827 ASN cc_start: 0.7696 (OUTLIER) cc_final: 0.7420 (p0) outliers start: 45 outliers final: 31 residues processed: 192 average time/residue: 1.1930 time to fit residues: 272.9120 Evaluate side-chains 191 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 153 time to evaluate : 2.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 816 MET Chi-restraints excluded: chain A residue 827 ASN Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain B residue 130 PHE Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 720 CYS Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 848 THR Chi-restraints excluded: chain C residue 130 PHE Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 626 ASN Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 679 MET Chi-restraints excluded: chain C residue 685 SER Chi-restraints excluded: chain C residue 720 CYS Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain C residue 827 ASN Chi-restraints excluded: chain C residue 848 THR Chi-restraints excluded: chain C residue 1108 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 182 optimal weight: 2.9990 chunk 293 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 chunk 204 optimal weight: 0.6980 chunk 307 optimal weight: 0.8980 chunk 283 optimal weight: 0.9980 chunk 245 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 189 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 626 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25698 Z= 0.206 Angle : 0.574 19.019 34935 Z= 0.293 Chirality : 0.047 0.331 4029 Planarity : 0.004 0.046 4458 Dihedral : 6.220 50.495 4358 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.56 % Allowed : 12.51 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.36 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.14), residues: 3081 helix: 1.65 (0.21), residues: 696 sheet: 1.12 (0.19), residues: 717 loop : -1.35 (0.13), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 868 HIS 0.003 0.001 HIS C1046 PHE 0.011 0.001 PHE B 870 TYR 0.021 0.001 TYR B1120 ARG 0.005 0.000 ARG A 306 ********************** REFINEMENT MACRO_CYCLE 10 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 197 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 155 time to evaluate : 3.046 Fit side-chains REVERT: A 588 THR cc_start: 0.8524 (m) cc_final: 0.8234 (m) REVERT: A 685 SER cc_start: 0.7687 (OUTLIER) cc_final: 0.7186 (p) REVERT: A 851 MET cc_start: 0.8745 (mtt) cc_final: 0.8291 (mtt) REVERT: B 130 PHE cc_start: 0.7876 (OUTLIER) cc_final: 0.7024 (p90) REVERT: B 792 LEU cc_start: 0.8347 (tt) cc_final: 0.8147 (tp) REVERT: C 130 PHE cc_start: 0.7784 (OUTLIER) cc_final: 0.7094 (p90) REVERT: C 685 SER cc_start: 0.7711 (OUTLIER) cc_final: 0.7292 (p) REVERT: C 827 ASN cc_start: 0.7723 (OUTLIER) cc_final: 0.7441 (p0) outliers start: 42 outliers final: 35 residues processed: 187 average time/residue: 1.2205 time to fit residues: 269.3347 Evaluate side-chains 192 residues out of total 2694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 152 time to evaluate : 2.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 827 ASN Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain B residue 130 PHE Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 720 CYS Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 848 THR Chi-restraints excluded: chain C residue 130 PHE Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 626 ASN Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 679 MET Chi-restraints excluded: chain C residue 685 SER Chi-restraints excluded: chain C residue 720 CYS Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain C residue 827 ASN Chi-restraints excluded: chain C residue 848 THR Chi-restraints excluded: chain C residue 1108 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 194 optimal weight: 3.9990 chunk 261 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 226 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 245 optimal weight: 1.9990 chunk 102 optimal weight: 0.0020 chunk 252 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 626 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.116566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.089395 restraints weight = 32480.479| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.11 r_work: 0.2899 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25698 Z= 0.213 Angle : 0.575 19.185 34935 Z= 0.294 Chirality : 0.048 0.341 4029 Planarity : 0.004 0.045 4458 Dihedral : 6.259 51.213 4358 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.89 % Allowed : 12.25 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.03 % 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: -0.02 (0.14), residues: 3081 helix: 1.61 (0.20), residues: 696 sheet: 1.22 (0.19), residues: 687 loop : -1.32 (0.13), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 868 HIS 0.003 0.001 HIS A1046 PHE 0.012 0.001 PHE B 870 TYR 0.023 0.002 TYR A1120 ARG 0.005 0.000 ARG A 306 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6767.05 seconds wall clock time: 122 minutes 41.10 seconds (7361.10 seconds total)