Starting phenix.real_space_refine on Sat Apr 13 12:59:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sg4_25105/04_2024/7sg4_25105_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sg4_25105/04_2024/7sg4_25105.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sg4_25105/04_2024/7sg4_25105.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sg4_25105/04_2024/7sg4_25105.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sg4_25105/04_2024/7sg4_25105_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sg4_25105/04_2024/7sg4_25105_neut.pdb" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.149 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 149 5.16 5 C 18210 2.51 5 N 4743 2.21 5 O 5607 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 385": "OD1" <-> "OD2" Residue "A TYR 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 870": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 870": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 28709 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1095, 8525 Classifications: {'peptide': 1095} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 1038} Chain: "B" Number of atoms: 8525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1095, 8525 Classifications: {'peptide': 1095} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 1038} Chain: "C" Number of atoms: 8525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1095, 8525 Classifications: {'peptide': 1095} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 1038} Chain: "H" Number of atoms: 1239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1239 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 161} Link IDs: {'PTRANS': 12, 'TRANS': 219} Unresolved non-hydrogen bonds: 535 Unresolved non-hydrogen angles: 700 Unresolved non-hydrogen dihedrals: 443 Unresolved non-hydrogen chiralities: 62 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 9, 'TYR:plan': 9, 'ASN:plan1': 7, 'TRP:plan': 4, 'HIS:plan': 4, 'PHE:plan': 5, 'GLU:plan': 6, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 291 Chain: "L" Number of atoms: 1237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1237 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 141} Link IDs: {'PTRANS': 11, 'TRANS': 208} Unresolved non-hydrogen bonds: 499 Unresolved non-hydrogen angles: 638 Unresolved non-hydrogen dihedrals: 416 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 2, 'TYR:plan': 8, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 7, 'GLU:plan': 12, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 299 Chain: "A" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Chain: "B" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "C" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Time building chain proxies: 14.70, per 1000 atoms: 0.51 Number of scatterers: 28709 At special positions: 0 Unit cell: (150.12, 143.64, 218.16, 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 149 16.00 O 5607 8.00 N 4743 7.00 C 18210 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.04 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 288 " distance=2.02 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 348 " distance=2.03 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS A 419 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.02 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.04 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.02 Simple disulfide: pdb=" SG CYS A1064 " - pdb=" SG CYS A1108 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.04 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 288 " distance=2.02 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 348 " distance=2.04 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 419 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 511 " distance=2.04 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.04 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.01 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=2.01 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 348 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 474 " distance=2.04 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " 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 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.02 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 A1301 " - " ASN A 65 " " NAG A1302 " - " ASN A 109 " " NAG A1303 " - " ASN A1116 " " NAG A1304 " - " ASN A1080 " " NAG A1305 " - " ASN A1056 " " NAG A1306 " - " ASN A 783 " " NAG A1307 " - " ASN A 699 " " NAG A1308 " - " ASN A 691 " " NAG A1309 " - " ASN A 602 " " NAG A1310 " - " ASN A 589 " " NAG A1311 " - " ASN A 357 " " NAG A1312 " - " ASN A 330 " " NAG A1313 " - " ASN A 318 " " NAG A1314 " - " ASN A 269 " " NAG A1315 " - " ASN A 227 " " NAG A1316 " - " ASN A 158 " " NAG B1301 " - " ASN B 65 " " NAG B1302 " - " ASN B 109 " " NAG B1303 " - " ASN B1116 " " NAG B1304 " - " ASN B1080 " " NAG B1305 " - " ASN B1056 " " NAG B1306 " - " ASN B 783 " " NAG B1307 " - " ASN B 699 " " NAG B1308 " - " ASN B 691 " " NAG B1309 " - " ASN B 602 " " NAG B1310 " - " ASN B 589 " " NAG B1311 " - " ASN B 357 " " NAG B1312 " - " ASN B 330 " " NAG B1313 " - " ASN B 318 " " NAG B1314 " - " ASN B 269 " " NAG B1315 " - " ASN B 227 " " NAG C1301 " - " ASN C 65 " " NAG C1302 " - " ASN C 109 " " NAG C1303 " - " ASN C1116 " " NAG C1304 " - " ASN C1080 " " NAG C1305 " - " ASN C1056 " " NAG C1306 " - " ASN C 783 " " NAG C1307 " - " ASN C 699 " " NAG C1308 " - " ASN C 691 " " NAG C1309 " - " ASN C 602 " " NAG C1310 " - " ASN C 589 " " NAG C1311 " - " ASN C 357 " " NAG C1312 " - " ASN C 330 " " NAG C1313 " - " ASN C 318 " " NAG C1314 " - " ASN C 269 " " NAG C1315 " - " ASN C 227 " " NAG C1316 " - " ASN C 158 " Time building additional restraints: 10.97 Conformation dependent library (CDL) restraints added in 5.4 seconds 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6986 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 54 sheets defined 24.1% alpha, 24.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.34 Creating SS restraints... Processing helix chain 'A' and resid 169 through 174 Processing helix chain 'A' and resid 281 through 290 Processing helix chain 'A' and resid 324 through 330 removed outlier: 4.366A pdb=" N VAL A 328 " --> pdb=" O PRO A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 358 Processing helix chain 'A' and resid 370 through 375 Processing helix chain 'A' and resid 390 through 397 removed outlier: 3.534A pdb=" N ARG A 395 " --> pdb=" O ASP A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 606 Processing helix chain 'A' and resid 664 through 670 removed outlier: 3.857A pdb=" N SER A 668 " --> pdb=" O LEU A 665 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N THR A 669 " --> pdb=" O LEU A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 726 Processing helix chain 'A' and resid 728 through 736 removed outlier: 3.987A pdb=" N LEU A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 739 No H-bonds generated for 'chain 'A' and resid 737 through 739' Processing helix chain 'A' and resid 740 through 765 removed outlier: 3.667A pdb=" N ASN A 746 " --> pdb=" O CYS A 742 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN A 756 " --> pdb=" O ILE A 752 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ASP A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 807 Processing helix chain 'A' and resid 848 through 867 Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 879 through 891 Processing helix chain 'A' and resid 895 through 900 removed outlier: 3.564A pdb=" N TYR A 899 " --> pdb=" O GLN A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 923 Processing helix chain 'A' and resid 924 through 926 No H-bonds generated for 'chain 'A' and resid 924 through 926' Processing helix chain 'A' and resid 927 through 950 removed outlier: 3.693A pdb=" N VAL A 934 " --> pdb=" O LEU A 930 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN A 937 " --> pdb=" O VAL A 933 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU A 948 " --> pdb=" O LEU A 944 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N SER A 949 " --> pdb=" O VAL A 945 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER A 950 " --> pdb=" O LYS A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 966 removed outlier: 3.554A pdb=" N LEU A 966 " --> pdb=" O ILE A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 1015 removed outlier: 4.467A pdb=" N VAL A 973 " --> pdb=" O PRO A 969 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER A1003 " --> pdb=" O GLU A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1128 Processing helix chain 'B' and resid 167 through 173 removed outlier: 4.474A pdb=" N VAL B 172 " --> pdb=" O SER B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 290 Processing helix chain 'B' and resid 325 through 330 Processing helix chain 'B' and resid 351 through 358 removed outlier: 4.143A pdb=" N LEU B 355 " --> pdb=" O ASP B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 375 removed outlier: 3.680A pdb=" N ASN B 375 " --> pdb=" O ALA B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 397 Processing helix chain 'B' and resid 403 through 410 removed outlier: 4.246A pdb=" N TYR B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 607 removed outlier: 3.627A pdb=" N VAL B 606 " --> pdb=" O ASN B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 621 removed outlier: 3.929A pdb=" N ARG B 620 " --> pdb=" O PRO B 617 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE B 621 " --> pdb=" O ALA B 618 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 617 through 621' Processing helix chain 'B' and resid 664 through 672 removed outlier: 6.731A pdb=" N THR B 669 " --> pdb=" O LEU B 666 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LYS B 672 " --> pdb=" O THR B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 726 Processing helix chain 'B' and resid 728 through 736 removed outlier: 3.653A pdb=" N LEU B 736 " --> pdb=" O ALA B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 739 No H-bonds generated for 'chain 'B' and resid 737 through 739' Processing helix chain 'B' and resid 740 through 765 removed outlier: 3.757A pdb=" N ASN B 746 " --> pdb=" O CYS B 742 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASP B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG B 758 " --> pdb=" O ALA B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 808 removed outlier: 3.622A pdb=" N LEU B 803 " --> pdb=" O PHE B 799 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL B 808 " --> pdb=" O LEU B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 867 removed outlier: 3.629A pdb=" N GLY B 867 " --> pdb=" O THR B 863 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 873 removed outlier: 3.861A pdb=" N ALA B 872 " --> pdb=" O TRP B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 891 Processing helix chain 'B' and resid 895 through 900 Processing helix chain 'B' and resid 901 through 923 Processing helix chain 'B' and resid 924 through 926 No H-bonds generated for 'chain 'B' and resid 924 through 926' Processing helix chain 'B' and resid 927 through 950 removed outlier: 3.527A pdb=" N VAL B 933 " --> pdb=" O LYS B 929 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B 934 " --> pdb=" O LEU B 930 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN B 937 " --> pdb=" O VAL B 933 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU B 948 " --> pdb=" O LEU B 944 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N SER B 949 " --> pdb=" O VAL B 945 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER B 950 " --> pdb=" O LYS B 946 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 966 Processing helix chain 'B' and resid 967 through 1015 removed outlier: 4.289A pdb=" N VAL B 973 " --> pdb=" O PRO B 969 " (cutoff:3.500A) Processing helix chain 'B' and resid 1123 through 1128 Processing helix chain 'C' and resid 131 through 135 removed outlier: 4.359A pdb=" N ASP C 134 " --> pdb=" O GLU C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 174 Processing helix chain 'C' and resid 281 through 291 Processing helix chain 'C' and resid 325 through 331 removed outlier: 3.503A pdb=" N PHE C 329 " --> pdb=" O PHE C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 357 removed outlier: 4.301A pdb=" N LEU C 355 " --> pdb=" O ASP C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 375 Processing helix chain 'C' and resid 390 through 396 Processing helix chain 'C' and resid 403 through 408 removed outlier: 3.644A pdb=" N TYR C 408 " --> pdb=" O VAL C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 428 No H-bonds generated for 'chain 'C' and resid 426 through 428' Processing helix chain 'C' and resid 602 through 607 removed outlier: 3.690A pdb=" N SER C 607 " --> pdb=" O CYS C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 668 Processing helix chain 'C' and resid 719 through 726 Processing helix chain 'C' and resid 728 through 735 Processing helix chain 'C' and resid 736 through 739 Processing helix chain 'C' and resid 740 through 765 removed outlier: 3.507A pdb=" N GLN C 756 " --> pdb=" O ILE C 752 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ASP C 757 " --> pdb=" O ALA C 753 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG C 758 " --> pdb=" O ALA C 754 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 808 removed outlier: 3.670A pdb=" N VAL C 808 " --> pdb=" O LEU C 804 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 867 removed outlier: 3.659A pdb=" N GLY C 867 " --> pdb=" O THR C 863 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 873 removed outlier: 3.685A pdb=" N ALA C 872 " --> pdb=" O TRP C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 879 through 891 Processing helix chain 'C' and resid 895 through 900 Processing helix chain 'C' and resid 901 through 923 Processing helix chain 'C' and resid 924 through 926 No H-bonds generated for 'chain 'C' and resid 924 through 926' Processing helix chain 'C' and resid 927 through 947 removed outlier: 3.800A pdb=" N VAL C 933 " --> pdb=" O LYS C 929 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL C 934 " --> pdb=" O LEU C 930 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN C 937 " --> pdb=" O VAL C 933 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 966 removed outlier: 3.522A pdb=" N ILE C 962 " --> pdb=" O VAL C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 1015 removed outlier: 4.160A pdb=" N VAL C 973 " --> pdb=" O PRO C 969 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU C 978 " --> pdb=" O GLN C 974 " (cutoff:3.500A) Processing helix chain 'C' and resid 1123 through 1128 Processing helix chain 'H' and resid 25 through 30 removed outlier: 3.751A pdb=" N THR H 28 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 67 Processing helix chain 'H' and resid 73 through 76 Processing helix chain 'H' and resid 127 through 132 Processing helix chain 'H' and resid 133 through 135 No H-bonds generated for 'chain 'H' and resid 133 through 135' Processing helix chain 'H' and resid 200 through 204 Processing helix chain 'L' and resid 48 through 52 removed outlier: 4.443A pdb=" N SER L 52 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 Processing helix chain 'L' and resid 123 through 131 removed outlier: 6.593A pdb=" N GLY L 128 " --> pdb=" O LEU L 125 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N THR L 129 " --> pdb=" O LYS L 126 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA L 130 " --> pdb=" O SER L 127 " (cutoff:3.500A) Processing helix chain 'L' and resid 149 through 153 Processing helix chain 'L' and resid 182 through 184 No H-bonds generated for 'chain 'L' and resid 182 through 184' Processing helix chain 'L' and resid 185 through 190 Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 41 removed outlier: 7.015A pdb=" N VAL A 40 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N THR A 215 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N TYR A 200 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL A 196 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS A 221 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N LEU A 194 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS A 181 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ALA A 251 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR A 252 " --> pdb=" O PHE A 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 59 removed outlier: 3.686A pdb=" N ASP A 274 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AA4, first strand: chain 'A' and resid 298 through 306 removed outlier: 5.388A pdb=" N ILE A 299 " --> pdb=" O THR A 585 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N THR A 585 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N GLN A 301 " --> pdb=" O VAL A 583 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL A 583 " --> pdb=" O GLN A 301 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER A 303 " --> pdb=" O VAL A 581 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLY A 580 " --> pdb=" O GLN A 599 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 314 removed outlier: 6.294A pdb=" N GLY A 311 " --> pdb=" O ASN A 526 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N ASN A 528 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL A 313 " --> pdb=" O ASN A 528 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ASP A 560 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLY A 552 " --> pdb=" O ASP A 560 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 341 through 345 removed outlier: 3.814A pdb=" N ASN A 381 " --> pdb=" O GLU A 502 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR A 363 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 348 through 349 removed outlier: 6.714A pdb=" N CYS A 348 " --> pdb=" O CYS A 511 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 435 through 439 removed outlier: 7.862A pdb=" N TYR A 438 " --> pdb=" O TYR A 481 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 640 through 641 removed outlier: 6.133A pdb=" N GLU A 640 " --> pdb=" O ALA A 676 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N THR A 678 " --> pdb=" O GLU A 640 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 684 through 685 Processing sheet with id=AB2, first strand: chain 'A' and resid 693 through 710 removed outlier: 6.630A pdb=" N GLN A1053 " --> pdb=" O THR A 698 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N PHE A 700 " --> pdb=" O PRO A1051 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE A 702 " --> pdb=" O TYR A1049 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N TYR A1049 " --> pdb=" O ILE A 702 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILE A 704 " --> pdb=" O VAL A1047 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL A1047 " --> pdb=" O ILE A 704 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR A 706 " --> pdb=" O LEU A1045 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU A1045 " --> pdb=" O THR A 706 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL A 708 " --> pdb=" O VAL A1043 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL A1043 " --> pdb=" O VAL A 708 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N GLY A1041 " --> pdb=" O PRO A 710 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N TYR A1049 " --> pdb=" O HIS A1030 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N HIS A1030 " --> pdb=" O TYR A1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 693 through 710 removed outlier: 6.630A pdb=" N GLN A1053 " --> pdb=" O THR A 698 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N PHE A 700 " --> pdb=" O PRO A1051 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE A 702 " --> pdb=" O TYR A1049 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N TYR A1049 " --> pdb=" O ILE A 702 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILE A 704 " --> pdb=" O VAL A1047 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL A1047 " --> pdb=" O ILE A 704 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR A 706 " --> pdb=" O LEU A1045 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU A1045 " --> pdb=" O THR A 706 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL A 708 " --> pdb=" O VAL A1043 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL A1043 " --> pdb=" O VAL A 708 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N GLY A1041 " --> pdb=" O PRO A 710 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N THR A1058 " --> pdb=" O PHE A1079 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 716 through 718 Processing sheet with id=AB5, first strand: chain 'A' and resid 769 through 771 Processing sheet with id=AB6, first strand: chain 'A' and resid 778 through 779 Processing sheet with id=AB7, first strand: chain 'A' and resid 1102 through 1105 removed outlier: 3.625A pdb=" N ALA A1069 " --> pdb=" O SER A1105 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 40 through 41 removed outlier: 7.030A pdb=" N VAL B 40 " --> pdb=" O LEU B 216 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N THR B 215 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N TYR B 200 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL B 196 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LYS B 221 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N LEU B 194 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR B 252 " --> pdb=" O PHE B 69 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 51 through 59 removed outlier: 3.895A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 81 through 82 Processing sheet with id=AC2, first strand: chain 'B' and resid 298 through 306 removed outlier: 5.389A pdb=" N ILE B 299 " --> pdb=" O THR B 585 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N THR B 585 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N GLN B 301 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL B 583 " --> pdb=" O GLN B 301 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER B 303 " --> pdb=" O VAL B 581 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N GLY B 580 " --> pdb=" O GLN B 599 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 314 removed outlier: 6.548A pdb=" N GLY B 311 " --> pdb=" O ASN B 526 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N ASN B 528 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL B 313 " --> pdb=" O ASN B 528 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ASP B 560 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLY B 552 " --> pdb=" O ASP B 560 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 341 through 345 removed outlier: 3.816A pdb=" N ASN B 381 " --> pdb=" O GLU B 502 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR B 363 " --> pdb=" O ALA B 422 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 378 through 379 Processing sheet with id=AC6, first strand: chain 'B' and resid 640 through 641 removed outlier: 6.029A pdb=" N GLU B 640 " --> pdb=" O ALA B 676 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N THR B 678 " --> pdb=" O GLU B 640 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE B 656 " --> pdb=" O ILE B 652 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 683 through 685 removed outlier: 6.815A pdb=" N ALA B 683 " --> pdb=" O MET C 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 693 through 710 removed outlier: 6.381A pdb=" N GLN B1053 " --> pdb=" O THR B 698 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N PHE B 700 " --> pdb=" O PRO B1051 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE B 702 " --> pdb=" O TYR B1049 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N TYR B1049 " --> pdb=" O ILE B 702 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE B 704 " --> pdb=" O VAL B1047 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL B1047 " --> pdb=" O ILE B 704 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR B 706 " --> pdb=" O LEU B1045 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU B1045 " --> pdb=" O THR B 706 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL B 708 " --> pdb=" O VAL B1043 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL B1043 " --> pdb=" O VAL B 708 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLY B1041 " --> pdb=" O PRO B 710 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N TYR B1049 " --> pdb=" O HIS B1030 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N HIS B1030 " --> pdb=" O TYR B1049 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 693 through 710 removed outlier: 6.381A pdb=" N GLN B1053 " --> pdb=" O THR B 698 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N PHE B 700 " --> pdb=" O PRO B1051 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE B 702 " --> pdb=" O TYR B1049 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N TYR B1049 " --> pdb=" O ILE B 702 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE B 704 " --> pdb=" O VAL B1047 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL B1047 " --> pdb=" O ILE B 704 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR B 706 " --> pdb=" O LEU B1045 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU B1045 " --> pdb=" O THR B 706 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL B 708 " --> pdb=" O VAL B1043 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL B1043 " --> pdb=" O VAL B 708 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLY B1041 " --> pdb=" O PRO B 710 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR B1058 " --> pdb=" O PHE B1079 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA B1060 " --> pdb=" O PHE B1077 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N PHE B1077 " --> pdb=" O ALA B1060 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 716 through 718 Processing sheet with id=AD2, first strand: chain 'B' and resid 778 through 779 Processing sheet with id=AD3, first strand: chain 'B' and resid 1102 through 1105 removed outlier: 3.821A pdb=" N ALA B1069 " --> pdb=" O SER B1105 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 40 through 41 removed outlier: 7.019A pdb=" N VAL C 40 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N THR C 215 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N TYR C 200 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL C 196 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LYS C 221 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N LEU C 194 " --> pdb=" O LYS C 221 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS C 181 " --> pdb=" O GLU C 93 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 51 through 59 removed outlier: 3.502A pdb=" N PHE C 59 " --> pdb=" O LYS C 258 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP C 274 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 81 through 82 removed outlier: 6.681A pdb=" N VAL C 123 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE C 164 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE C 125 " --> pdb=" O GLU C 162 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLU C 162 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ALA C 127 " --> pdb=" O THR C 160 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 298 through 306 removed outlier: 5.345A pdb=" N ILE C 299 " --> pdb=" O THR C 585 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N THR C 585 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N GLN C 301 " --> pdb=" O VAL C 583 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N VAL C 583 " --> pdb=" O GLN C 301 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER C 303 " --> pdb=" O VAL C 581 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N GLY C 580 " --> pdb=" O GLN C 599 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 314 removed outlier: 6.676A pdb=" N GLY C 311 " --> pdb=" O ASN C 526 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N ASN C 528 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL C 313 " --> pdb=" O ASN C 528 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ASP C 560 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLY C 552 " --> pdb=" O ASP C 560 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 341 through 345 removed outlier: 3.906A pdb=" N GLU C 341 " --> pdb=" O SER C 386 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.029A pdb=" N CYS C 348 " --> pdb=" O CYS C 511 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'C' and resid 640 through 641 removed outlier: 6.150A pdb=" N GLU C 640 " --> pdb=" O ALA C 676 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N THR C 678 " --> pdb=" O GLU C 640 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 693 through 710 removed outlier: 7.032A pdb=" N GLN C1053 " --> pdb=" O THR C 698 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N PHE C 700 " --> pdb=" O PRO C1051 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE C 702 " --> pdb=" O TYR C1049 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N TYR C1049 " --> pdb=" O ILE C 702 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE C 704 " --> pdb=" O VAL C1047 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL C1047 " --> pdb=" O ILE C 704 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N THR C 706 " --> pdb=" O LEU C1045 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LEU C1045 " --> pdb=" O THR C 706 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL C 708 " --> pdb=" O VAL C1043 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL C1043 " --> pdb=" O VAL C 708 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLY C1041 " --> pdb=" O PRO C 710 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N TYR C1049 " --> pdb=" O HIS C1030 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N HIS C1030 " --> pdb=" O TYR C1049 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 693 through 710 removed outlier: 7.032A pdb=" N GLN C1053 " --> pdb=" O THR C 698 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N PHE C 700 " --> pdb=" O PRO C1051 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE C 702 " --> pdb=" O TYR C1049 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N TYR C1049 " --> pdb=" O ILE C 702 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE C 704 " --> pdb=" O VAL C1047 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL C1047 " --> pdb=" O ILE C 704 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N THR C 706 " --> pdb=" O LEU C1045 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LEU C1045 " --> pdb=" O THR C 706 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL C 708 " --> pdb=" O VAL C1043 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL C1043 " --> pdb=" O VAL C 708 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLY C1041 " --> pdb=" O PRO C 710 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N THR C1058 " --> pdb=" O PHE C1079 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 715 through 718 removed outlier: 4.478A pdb=" N LYS C 715 " --> pdb=" O LEU C 843 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 778 through 779 Processing sheet with id=AE7, first strand: chain 'C' and resid 1102 through 1105 removed outlier: 3.609A pdb=" N ALA C1069 " --> pdb=" O SER C1105 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 5 through 7 removed outlier: 4.050A pdb=" N VAL H 20 " --> pdb=" O LEU H 80 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ILE H 78 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AF1, first strand: chain 'H' and resid 57 through 59 removed outlier: 4.113A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 121 through 122 Processing sheet with id=AF3, first strand: chain 'H' and resid 137 through 139 Processing sheet with id=AF4, first strand: chain 'H' and resid 154 through 155 removed outlier: 3.518A pdb=" N TRP H 154 " --> pdb=" O ILE H 195 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 169 through 171 removed outlier: 3.905A pdb=" N LEU H 175 " --> pdb=" O GLN H 171 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 66 through 67 Processing sheet with id=AF7, first strand: chain 'L' and resid 33 through 37 Processing sheet with id=AF8, first strand: chain 'L' and resid 133 through 137 removed outlier: 5.977A pdb=" N THR L 172 " --> pdb=" O GLN L 166 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLN L 166 " --> pdb=" O THR L 172 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 144 through 146 removed outlier: 3.535A pdb=" N CYS L 194 " --> pdb=" O LYS L 207 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS L 207 " --> pdb=" O CYS L 194 " (cutoff:3.500A) 1040 hydrogen bonds defined for protein. 2799 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: 12.33 Time building geometry restraints manager: 11.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7979 1.34 - 1.46: 5312 1.46 - 1.58: 15863 1.58 - 1.70: 0 1.70 - 1.83: 203 Bond restraints: 29357 Sorted by residual: bond pdb=" CA ASN B 626 " pdb=" C ASN B 626 " ideal model delta sigma weight residual 1.520 1.566 -0.047 1.12e-02 7.97e+03 1.73e+01 bond pdb=" N GLY B 625 " pdb=" CA GLY B 625 " ideal model delta sigma weight residual 1.446 1.491 -0.045 1.11e-02 8.12e+03 1.64e+01 bond pdb=" CA PRO A 469 " pdb=" C PRO A 469 " ideal model delta sigma weight residual 1.517 1.553 -0.036 9.30e-03 1.16e+04 1.52e+01 bond pdb=" CA VAL H 109 " pdb=" CB VAL H 109 " ideal model delta sigma weight residual 1.553 1.525 0.028 7.40e-03 1.83e+04 1.43e+01 bond pdb=" C5 NAG A1309 " pdb=" O5 NAG A1309 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.41e+01 ... (remaining 29352 not shown) Histogram of bond angle deviations from ideal: 97.67 - 105.31: 629 105.31 - 112.95: 13931 112.95 - 120.60: 15136 120.60 - 128.24: 10211 128.24 - 135.88: 132 Bond angle restraints: 40039 Sorted by residual: angle pdb=" CA VAL C 66 " pdb=" CB VAL C 66 " pdb=" CG1 VAL C 66 " ideal model delta sigma weight residual 110.40 132.27 -21.87 1.70e+00 3.46e-01 1.66e+02 angle pdb=" N PRO A 470 " pdb=" CA PRO A 470 " pdb=" C PRO A 470 " ideal model delta sigma weight residual 112.47 133.86 -21.39 2.06e+00 2.36e-01 1.08e+02 angle pdb=" N PRO B 470 " pdb=" CA PRO B 470 " pdb=" C PRO B 470 " ideal model delta sigma weight residual 112.47 132.61 -20.14 2.06e+00 2.36e-01 9.56e+01 angle pdb=" N PRO C 470 " pdb=" CA PRO C 470 " pdb=" C PRO C 470 " ideal model delta sigma weight residual 112.47 132.25 -19.78 2.06e+00 2.36e-01 9.22e+01 angle pdb=" CA PHE B 545 " pdb=" CB PHE B 545 " pdb=" CG PHE B 545 " ideal model delta sigma weight residual 113.80 121.90 -8.10 1.00e+00 1.00e+00 6.56e+01 ... (remaining 40034 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 16651 17.86 - 35.72: 1171 35.72 - 53.57: 191 53.57 - 71.43: 54 71.43 - 89.29: 23 Dihedral angle restraints: 18090 sinusoidal: 7221 harmonic: 10869 Sorted by residual: dihedral pdb=" N PRO A 470 " pdb=" C PRO A 470 " pdb=" CA PRO A 470 " pdb=" CB PRO A 470 " ideal model delta harmonic sigma weight residual 115.10 151.21 -36.11 0 2.50e+00 1.60e-01 2.09e+02 dihedral pdb=" N PRO B 470 " pdb=" C PRO B 470 " pdb=" CA PRO B 470 " pdb=" CB PRO B 470 " ideal model delta harmonic sigma weight residual 115.10 151.14 -36.04 0 2.50e+00 1.60e-01 2.08e+02 dihedral pdb=" N PRO C 470 " pdb=" C PRO C 470 " pdb=" CA PRO C 470 " pdb=" CB PRO C 470 " ideal model delta harmonic sigma weight residual 115.10 150.94 -35.84 0 2.50e+00 1.60e-01 2.06e+02 ... (remaining 18087 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.319: 4648 0.319 - 0.639: 38 0.639 - 0.958: 1 0.958 - 1.278: 0 1.278 - 1.597: 9 Chirality restraints: 4696 Sorted by residual: chirality pdb=" CA PRO A 470 " pdb=" N PRO A 470 " pdb=" C PRO A 470 " pdb=" CB PRO A 470 " both_signs ideal model delta sigma weight residual False 2.72 1.12 1.60 2.00e-01 2.50e+01 6.38e+01 chirality pdb=" CA PRO B 470 " pdb=" N PRO B 470 " pdb=" C PRO B 470 " pdb=" CB PRO B 470 " both_signs ideal model delta sigma weight residual False 2.72 1.14 1.58 2.00e-01 2.50e+01 6.25e+01 chirality pdb=" CA PRO C 470 " pdb=" N PRO C 470 " pdb=" C PRO C 470 " pdb=" CB PRO C 470 " both_signs ideal model delta sigma weight residual False 2.72 1.15 1.57 2.00e-01 2.50e+01 6.17e+01 ... (remaining 4693 not shown) Planarity restraints: 5229 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 158 " -0.147 2.00e-02 2.50e+03 1.49e-01 2.76e+02 pdb=" CG ASN A 158 " 0.105 2.00e-02 2.50e+03 pdb=" OD1 ASN A 158 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN A 158 " 0.216 2.00e-02 2.50e+03 pdb=" C1 NAG A1316 " -0.176 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 109 " 0.138 2.00e-02 2.50e+03 1.45e-01 2.62e+02 pdb=" CG ASN C 109 " -0.086 2.00e-02 2.50e+03 pdb=" OD1 ASN C 109 " -0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN C 109 " -0.219 2.00e-02 2.50e+03 pdb=" C1 NAG C1302 " 0.173 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 868 " 0.191 2.00e-02 2.50e+03 1.02e-01 2.61e+02 pdb=" CG TRP A 868 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP A 868 " -0.078 2.00e-02 2.50e+03 pdb=" CD2 TRP A 868 " -0.064 2.00e-02 2.50e+03 pdb=" NE1 TRP A 868 " -0.081 2.00e-02 2.50e+03 pdb=" CE2 TRP A 868 " 0.012 2.00e-02 2.50e+03 pdb=" CE3 TRP A 868 " -0.131 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 868 " 0.140 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 868 " -0.067 2.00e-02 2.50e+03 pdb=" CH2 TRP A 868 " 0.095 2.00e-02 2.50e+03 ... (remaining 5226 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.01: 15221 3.01 - 3.48: 29130 3.48 - 3.95: 47335 3.95 - 4.43: 53028 4.43 - 4.90: 86469 Nonbonded interactions: 231183 Sorted by model distance: nonbonded pdb=" OD1 ASP A 554 " pdb=" OG SER A 556 " model vdw 2.531 2.440 nonbonded pdb=" OH TYR B 383 " pdb=" OE1 GLU B 502 " model vdw 2.542 2.440 nonbonded pdb=" OE1 GLU A 294 " pdb=" OG1 THR A 588 " model vdw 2.552 2.440 nonbonded pdb=" OE1 GLU B 294 " pdb=" OG1 THR B 588 " model vdw 2.555 2.440 nonbonded pdb=" OE1 GLU C 294 " pdb=" OG1 THR C 588 " model vdw 2.556 2.440 ... (remaining 231178 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 35 through 1129 or resid 1301 through 1315)) selection = chain 'B' selection = (chain 'C' and (resid 35 through 1129 or resid 1301 through 1315)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.710 Check model and map are aligned: 0.410 Set scattering table: 0.260 Process input model: 74.920 Find NCS groups from input model: 1.880 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 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 : 0.014 0.075 29357 Z= 0.890 Angle : 1.911 21.874 40039 Z= 1.256 Chirality : 0.123 1.597 4696 Planarity : 0.015 0.167 5182 Dihedral : 13.177 89.288 10975 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 0.22 Ramachandran Plot: Outliers : 1.58 % Allowed : 9.53 % Favored : 88.89 % Rotamer: Outliers : 2.01 % Allowed : 4.85 % Favored : 93.14 % Cbeta Deviations : 0.86 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % 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: -2.14 (0.12), residues: 3727 helix: -1.15 (0.16), residues: 725 sheet: -0.08 (0.21), residues: 517 loop : -1.92 (0.11), residues: 2485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.191 0.031 TRP A 868 HIS 0.010 0.003 HIS C 445 PHE 0.141 0.015 PHE C 47 TYR 0.219 0.025 TYR L 92 ARG 0.016 0.001 ARG A 495 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 96 time to evaluate : 3.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 382 VAL cc_start: 0.8552 (OUTLIER) cc_final: 0.8220 (t) REVERT: B 884 MET cc_start: 0.9119 (mmm) cc_final: 0.8808 (tpt) REVERT: B 1032 MET cc_start: 0.8552 (ptp) cc_final: 0.8248 (ptp) REVERT: C 379 PHE cc_start: 0.8493 (m-80) cc_final: 0.8139 (m-80) REVERT: H 100 SER cc_start: 0.6666 (p) cc_final: 0.6392 (m) outliers start: 59 outliers final: 26 residues processed: 154 average time/residue: 0.4033 time to fit residues: 104.6530 Evaluate side-chains 104 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 77 time to evaluate : 3.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 481 TYR Chi-restraints excluded: chain A residue 560 ASP Chi-restraints excluded: chain A residue 619 TRP Chi-restraints excluded: chain A residue 661 HIS Chi-restraints excluded: chain A residue 742 CYS Chi-restraints excluded: chain A residue 1056 ASN Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 661 HIS Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 441 ARG Chi-restraints excluded: chain C residue 560 ASP Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain L residue 194 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 0.9990 chunk 281 optimal weight: 10.0000 chunk 156 optimal weight: 0.0570 chunk 96 optimal weight: 1.9990 chunk 190 optimal weight: 4.9990 chunk 150 optimal weight: 20.0000 chunk 291 optimal weight: 0.9990 chunk 112 optimal weight: 9.9990 chunk 177 optimal weight: 5.9990 chunk 217 optimal weight: 8.9990 chunk 337 optimal weight: 9.9990 overall best weight: 1.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 178 ASN A 214 ASN A 409 ASN A 479 ASN A 721 ASN B 112 GLN ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 ASN B 737 GLN L 31 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29357 Z= 0.214 Angle : 0.746 8.426 40039 Z= 0.399 Chirality : 0.050 0.450 4696 Planarity : 0.005 0.053 5182 Dihedral : 8.657 59.681 5030 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.57 % Favored : 92.06 % Rotamer: Outliers : 1.71 % Allowed : 6.69 % Favored : 91.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.53 % Twisted General : 0.20 % 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: -1.17 (0.13), residues: 3727 helix: 0.94 (0.19), residues: 715 sheet: -0.46 (0.19), residues: 682 loop : -1.50 (0.12), residues: 2330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 423 HIS 0.004 0.001 HIS B1065 PHE 0.028 0.002 PHE A 451 TYR 0.023 0.002 TYR A 484 ARG 0.007 0.001 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 87 time to evaluate : 3.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8034 (m-30) cc_final: 0.7556 (t70) REVERT: A 190 LYS cc_start: 0.8483 (pttt) cc_final: 0.8069 (pttp) REVERT: A 374 LEU cc_start: 0.7539 (mt) cc_final: 0.7212 (mp) REVERT: A 770 MET cc_start: 0.8738 (mmm) cc_final: 0.8516 (mmp) REVERT: A 816 MET cc_start: 0.3194 (ttt) cc_final: 0.2978 (ttm) REVERT: B 107 MET cc_start: 0.7935 (mpp) cc_final: 0.7670 (mmm) REVERT: B 151 MET cc_start: 0.2523 (mmt) cc_final: 0.1892 (mmp) REVERT: B 476 TRP cc_start: 0.6241 (OUTLIER) cc_final: 0.6025 (t60) REVERT: B 884 MET cc_start: 0.9019 (mmm) cc_final: 0.8743 (tpt) REVERT: C 816 MET cc_start: 0.0311 (mtt) cc_final: -0.0077 (mpp) REVERT: H 100 SER cc_start: 0.7257 (p) cc_final: 0.7031 (m) REVERT: L 27 GLN cc_start: 0.8168 (mm-40) cc_final: 0.7454 (pm20) outliers start: 50 outliers final: 34 residues processed: 130 average time/residue: 0.4080 time to fit residues: 88.9651 Evaluate side-chains 115 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 80 time to evaluate : 3.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 481 TYR Chi-restraints excluded: chain A residue 619 TRP Chi-restraints excluded: chain A residue 661 HIS Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 476 TRP Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 661 HIS Chi-restraints excluded: chain B residue 720 CYS Chi-restraints excluded: chain B residue 832 ILE Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 416 PHE Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 441 ARG Chi-restraints excluded: chain C residue 619 TRP Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 742 CYS Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 194 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 187 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 281 optimal weight: 10.0000 chunk 230 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 338 optimal weight: 50.0000 chunk 365 optimal weight: 9.9990 chunk 301 optimal weight: 10.0000 chunk 335 optimal weight: 5.9990 chunk 115 optimal weight: 8.9990 chunk 271 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 896 ASN ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 786 GLN B 835 GLN B 896 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 29357 Z= 0.318 Angle : 0.709 11.823 40039 Z= 0.375 Chirality : 0.049 0.453 4696 Planarity : 0.004 0.048 5182 Dihedral : 8.108 59.901 5017 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.80 % Favored : 90.90 % Rotamer: Outliers : 2.08 % Allowed : 7.34 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.05 (0.14), residues: 3727 helix: 1.21 (0.20), residues: 732 sheet: -0.44 (0.19), residues: 708 loop : -1.49 (0.13), residues: 2287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 423 HIS 0.006 0.001 HIS A1046 PHE 0.029 0.002 PHE B 545 TYR 0.031 0.002 TYR A 622 ARG 0.004 0.000 ARG A 829 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 81 time to evaluate : 3.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 THR cc_start: 0.3895 (OUTLIER) cc_final: 0.3245 (m) REVERT: A 166 ASP cc_start: 0.8261 (m-30) cc_final: 0.7734 (t0) REVERT: A 190 LYS cc_start: 0.8482 (pttt) cc_final: 0.8197 (pttp) REVERT: A 352 TYR cc_start: 0.7324 (t80) cc_final: 0.7090 (t80) REVERT: A 374 LEU cc_start: 0.7813 (mt) cc_final: 0.7584 (mt) REVERT: A 816 MET cc_start: 0.3374 (ttt) cc_final: 0.3146 (ttm) REVERT: B 107 MET cc_start: 0.8229 (mpp) cc_final: 0.7975 (mmm) REVERT: B 476 TRP cc_start: 0.5999 (OUTLIER) cc_final: 0.5713 (t60) REVERT: B 884 MET cc_start: 0.9046 (mmm) cc_final: 0.8646 (tpt) REVERT: C 816 MET cc_start: 0.0237 (mtt) cc_final: -0.0077 (mpp) REVERT: L 27 GLN cc_start: 0.8293 (mm-40) cc_final: 0.7723 (pm20) outliers start: 61 outliers final: 36 residues processed: 134 average time/residue: 0.3978 time to fit residues: 92.2488 Evaluate side-chains 115 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 77 time to evaluate : 3.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 436 TYR Chi-restraints excluded: chain A residue 481 TYR Chi-restraints excluded: chain A residue 619 TRP Chi-restraints excluded: chain A residue 838 ASN Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 476 TRP Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 720 CYS Chi-restraints excluded: chain B residue 835 GLN Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 416 PHE Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 441 ARG Chi-restraints excluded: chain C residue 619 TRP Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 742 CYS Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain L residue 36 TYR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 194 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 334 optimal weight: 5.9990 chunk 254 optimal weight: 9.9990 chunk 175 optimal weight: 0.8980 chunk 37 optimal weight: 50.0000 chunk 161 optimal weight: 10.0000 chunk 227 optimal weight: 0.4980 chunk 339 optimal weight: 6.9990 chunk 359 optimal weight: 40.0000 chunk 177 optimal weight: 10.0000 chunk 321 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 overall best weight: 4.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN A 445 HIS A 661 HIS B 835 GLN C 381 ASN C 661 HIS ** H 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 29357 Z= 0.288 Angle : 0.661 8.690 40039 Z= 0.349 Chirality : 0.048 0.517 4696 Planarity : 0.004 0.051 5182 Dihedral : 7.810 59.012 5012 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.67 % Favored : 91.07 % Rotamer: Outliers : 2.01 % Allowed : 8.16 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.97 (0.14), residues: 3727 helix: 1.48 (0.20), residues: 727 sheet: -0.51 (0.19), residues: 722 loop : -1.46 (0.13), residues: 2278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 423 HIS 0.005 0.001 HIS A 181 PHE 0.025 0.002 PHE B 545 TYR 0.028 0.002 TYR A 622 ARG 0.004 0.000 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 78 time to evaluate : 3.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8252 (m-30) cc_final: 0.7721 (t0) REVERT: A 190 LYS cc_start: 0.8470 (pttt) cc_final: 0.8207 (pttp) REVERT: A 245 TRP cc_start: 0.2952 (OUTLIER) cc_final: 0.2663 (m-90) REVERT: A 334 PHE cc_start: 0.3082 (OUTLIER) cc_final: 0.2368 (m-10) REVERT: A 352 TYR cc_start: 0.7373 (t80) cc_final: 0.7163 (t80) REVERT: A 374 LEU cc_start: 0.7904 (mt) cc_final: 0.7589 (mt) REVERT: A 816 MET cc_start: 0.3474 (ttt) cc_final: 0.3188 (ttm) REVERT: B 373 LYS cc_start: 0.8922 (mmmt) cc_final: 0.8686 (mmmt) REVERT: B 476 TRP cc_start: 0.6083 (OUTLIER) cc_final: 0.5749 (t60) REVERT: B 884 MET cc_start: 0.9027 (mmm) cc_final: 0.8657 (tpt) REVERT: C 379 PHE cc_start: 0.8578 (m-80) cc_final: 0.8037 (t80) REVERT: C 816 MET cc_start: 0.0132 (mtt) cc_final: -0.0241 (mpp) REVERT: H 140 CYS cc_start: 0.7060 (OUTLIER) cc_final: 0.6682 (t) REVERT: L 27 GLN cc_start: 0.8462 (mm-40) cc_final: 0.7856 (pm20) outliers start: 59 outliers final: 35 residues processed: 129 average time/residue: 0.3930 time to fit residues: 86.5216 Evaluate side-chains 115 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 76 time to evaluate : 3.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 245 TRP Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 436 TYR Chi-restraints excluded: chain A residue 619 TRP Chi-restraints excluded: chain A residue 661 HIS Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 476 TRP Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 661 HIS Chi-restraints excluded: chain B residue 720 CYS Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1118 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 416 PHE Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 441 ARG Chi-restraints excluded: chain C residue 619 TRP Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 742 CYS Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 140 CYS Chi-restraints excluded: chain L residue 36 TYR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 194 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 299 optimal weight: 0.0020 chunk 204 optimal weight: 0.9980 chunk 5 optimal weight: 8.9990 chunk 267 optimal weight: 7.9990 chunk 148 optimal weight: 20.0000 chunk 306 optimal weight: 6.9990 chunk 248 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 183 optimal weight: 2.9990 chunk 322 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 overall best weight: 2.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 838 ASN C1088 GLN ** H 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29357 Z= 0.207 Angle : 0.621 14.375 40039 Z= 0.326 Chirality : 0.047 0.463 4696 Planarity : 0.004 0.058 5182 Dihedral : 7.524 59.266 5008 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.45 % Favored : 91.28 % Rotamer: Outliers : 1.71 % Allowed : 8.91 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.86 (0.14), residues: 3727 helix: 1.72 (0.20), residues: 727 sheet: -0.50 (0.19), residues: 732 loop : -1.43 (0.13), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 423 HIS 0.026 0.001 HIS A 661 PHE 0.034 0.001 PHE A 168 TYR 0.024 0.001 TYR A 622 ARG 0.004 0.000 ARG B 449 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 79 time to evaluate : 3.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8127 (m-30) cc_final: 0.7661 (t0) REVERT: A 190 LYS cc_start: 0.8460 (pttt) cc_final: 0.8207 (pttp) REVERT: A 245 TRP cc_start: 0.3044 (OUTLIER) cc_final: 0.2753 (m-90) REVERT: A 334 PHE cc_start: 0.2975 (OUTLIER) cc_final: 0.2179 (m-10) REVERT: A 816 MET cc_start: 0.3379 (ttt) cc_final: 0.3068 (ttm) REVERT: B 37 MET cc_start: 0.8969 (mmm) cc_final: 0.8743 (mmm) REVERT: B 373 LYS cc_start: 0.8870 (mmmt) cc_final: 0.8615 (mmmt) REVERT: B 476 TRP cc_start: 0.6123 (OUTLIER) cc_final: 0.5776 (t60) REVERT: B 884 MET cc_start: 0.8986 (mmm) cc_final: 0.8627 (tpt) REVERT: C 816 MET cc_start: -0.0006 (mtt) cc_final: -0.0394 (mpp) REVERT: H 140 CYS cc_start: 0.7049 (OUTLIER) cc_final: 0.6672 (t) REVERT: L 27 GLN cc_start: 0.8486 (mm-40) cc_final: 0.7914 (pm20) outliers start: 50 outliers final: 34 residues processed: 123 average time/residue: 0.4095 time to fit residues: 85.0434 Evaluate side-chains 112 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 74 time to evaluate : 3.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 245 TRP Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 436 TYR Chi-restraints excluded: chain A residue 619 TRP Chi-restraints excluded: chain A residue 661 HIS Chi-restraints excluded: chain A residue 838 ASN Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 476 TRP Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 661 HIS Chi-restraints excluded: chain B residue 720 CYS Chi-restraints excluded: chain B residue 832 ILE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 416 PHE Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 441 ARG Chi-restraints excluded: chain C residue 619 TRP Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 742 CYS Chi-restraints excluded: chain C residue 832 ILE Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 140 CYS Chi-restraints excluded: chain L residue 36 TYR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 194 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 120 optimal weight: 40.0000 chunk 323 optimal weight: 8.9990 chunk 71 optimal weight: 6.9990 chunk 211 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 359 optimal weight: 20.0000 chunk 298 optimal weight: 9.9990 chunk 166 optimal weight: 5.9990 chunk 29 optimal weight: 0.0010 chunk 119 optimal weight: 20.0000 chunk 188 optimal weight: 0.0870 overall best weight: 1.9568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 HIS ** H 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 29 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29357 Z= 0.177 Angle : 0.595 11.751 40039 Z= 0.312 Chirality : 0.046 0.487 4696 Planarity : 0.004 0.065 5182 Dihedral : 7.296 59.429 5008 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.51 % Favored : 91.23 % Rotamer: Outliers : 1.88 % Allowed : 9.49 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.78 (0.14), residues: 3727 helix: 1.92 (0.20), residues: 726 sheet: -0.40 (0.19), residues: 743 loop : -1.45 (0.13), residues: 2258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 423 HIS 0.007 0.001 HIS A 661 PHE 0.019 0.001 PHE C 545 TYR 0.021 0.001 TYR C 622 ARG 0.004 0.000 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 77 time to evaluate : 3.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8014 (m-30) cc_final: 0.7554 (t70) REVERT: A 190 LYS cc_start: 0.8446 (pttt) cc_final: 0.8179 (pttp) REVERT: A 245 TRP cc_start: 0.2958 (OUTLIER) cc_final: 0.2637 (m-90) REVERT: A 334 PHE cc_start: 0.3091 (OUTLIER) cc_final: 0.2209 (m-10) REVERT: A 410 TYR cc_start: 0.2541 (OUTLIER) cc_final: 0.2250 (p90) REVERT: A 417 MET cc_start: 0.6797 (tpp) cc_final: 0.6521 (tpt) REVERT: B 144 MET cc_start: -0.0994 (tmm) cc_final: -0.2362 (ttp) REVERT: B 373 LYS cc_start: 0.8838 (mmmt) cc_final: 0.8569 (mmmt) REVERT: B 476 TRP cc_start: 0.6350 (OUTLIER) cc_final: 0.6045 (t60) REVERT: B 884 MET cc_start: 0.8970 (mmm) cc_final: 0.8582 (tpt) REVERT: C 379 PHE cc_start: 0.8560 (m-80) cc_final: 0.8093 (t80) REVERT: C 816 MET cc_start: -0.0214 (mtt) cc_final: -0.0576 (mpp) REVERT: H 140 CYS cc_start: 0.6988 (OUTLIER) cc_final: 0.6585 (t) REVERT: L 27 GLN cc_start: 0.8455 (mm-40) cc_final: 0.7953 (pm20) outliers start: 55 outliers final: 35 residues processed: 126 average time/residue: 0.3949 time to fit residues: 85.8318 Evaluate side-chains 114 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 74 time to evaluate : 3.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 245 TRP Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 436 TYR Chi-restraints excluded: chain A residue 619 TRP Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 476 TRP Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 661 HIS Chi-restraints excluded: chain B residue 720 CYS Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 416 PHE Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 441 ARG Chi-restraints excluded: chain C residue 619 TRP Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 742 CYS Chi-restraints excluded: chain C residue 832 ILE Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 140 CYS Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain L residue 36 TYR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 194 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 347 optimal weight: 20.0000 chunk 40 optimal weight: 9.9990 chunk 205 optimal weight: 0.1980 chunk 262 optimal weight: 9.9990 chunk 203 optimal weight: 5.9990 chunk 302 optimal weight: 0.8980 chunk 200 optimal weight: 10.0000 chunk 358 optimal weight: 8.9990 chunk 224 optimal weight: 3.9990 chunk 218 optimal weight: 9.9990 chunk 165 optimal weight: 7.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 ASN ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 ASN B 230 ASN ** H 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 29357 Z= 0.272 Angle : 0.617 9.632 40039 Z= 0.324 Chirality : 0.046 0.385 4696 Planarity : 0.004 0.064 5182 Dihedral : 7.310 59.224 5008 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.91 % Favored : 90.85 % Rotamer: Outliers : 1.88 % Allowed : 9.93 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.79 (0.14), residues: 3727 helix: 1.87 (0.20), residues: 726 sheet: -0.46 (0.19), residues: 722 loop : -1.41 (0.13), residues: 2279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 245 HIS 0.006 0.001 HIS A 181 PHE 0.024 0.001 PHE C 545 TYR 0.028 0.001 TYR A 622 ARG 0.004 0.000 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 77 time to evaluate : 3.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 LYS cc_start: 0.8455 (pttt) cc_final: 0.8200 (pttp) REVERT: A 245 TRP cc_start: 0.3109 (OUTLIER) cc_final: 0.2780 (m-90) REVERT: A 334 PHE cc_start: 0.3285 (OUTLIER) cc_final: 0.2399 (m-10) REVERT: A 622 TYR cc_start: -0.2326 (OUTLIER) cc_final: -0.4081 (m-80) REVERT: B 373 LYS cc_start: 0.8811 (mmmt) cc_final: 0.8527 (mmmt) REVERT: B 476 TRP cc_start: 0.6426 (OUTLIER) cc_final: 0.6111 (t60) REVERT: B 884 MET cc_start: 0.8971 (mmm) cc_final: 0.8650 (tpt) REVERT: C 151 MET cc_start: 0.3155 (mmt) cc_final: 0.2905 (mmp) REVERT: C 379 PHE cc_start: 0.8567 (m-80) cc_final: 0.7905 (t80) REVERT: C 816 MET cc_start: -0.0222 (mtt) cc_final: -0.0619 (mpp) REVERT: H 140 CYS cc_start: 0.6972 (OUTLIER) cc_final: 0.6548 (t) REVERT: L 27 GLN cc_start: 0.8506 (mm-40) cc_final: 0.7963 (pm20) outliers start: 55 outliers final: 38 residues processed: 127 average time/residue: 0.3947 time to fit residues: 85.7252 Evaluate side-chains 120 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 77 time to evaluate : 3.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 245 TRP Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 436 TYR Chi-restraints excluded: chain A residue 619 TRP Chi-restraints excluded: chain A residue 622 TYR Chi-restraints excluded: chain A residue 838 ASN Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 476 TRP Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 661 HIS Chi-restraints excluded: chain B residue 720 CYS Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 149 HIS Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 441 ARG Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 619 TRP Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 742 CYS Chi-restraints excluded: chain C residue 832 ILE Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 140 CYS Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain L residue 36 TYR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 194 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 221 optimal weight: 9.9990 chunk 143 optimal weight: 40.0000 chunk 214 optimal weight: 6.9990 chunk 108 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 227 optimal weight: 4.9990 chunk 244 optimal weight: 2.9990 chunk 177 optimal weight: 5.9990 chunk 33 optimal weight: 20.0000 chunk 281 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 HIS B 733 ASN B 835 GLN ** C 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 29357 Z= 0.349 Angle : 0.655 10.497 40039 Z= 0.342 Chirality : 0.048 0.515 4696 Planarity : 0.005 0.066 5182 Dihedral : 7.494 59.752 5008 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.31 % Favored : 90.45 % Rotamer: Outliers : 1.77 % Allowed : 10.27 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.92 (0.14), residues: 3727 helix: 1.70 (0.20), residues: 734 sheet: -0.59 (0.19), residues: 738 loop : -1.48 (0.13), residues: 2255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 423 HIS 0.007 0.001 HIS A 181 PHE 0.027 0.002 PHE C 545 TYR 0.035 0.002 TYR A 622 ARG 0.005 0.000 ARG C 48 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 73 time to evaluate : 3.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 LYS cc_start: 0.8463 (pttt) cc_final: 0.8201 (pttp) REVERT: A 245 TRP cc_start: 0.3261 (OUTLIER) cc_final: 0.2888 (m-90) REVERT: A 545 PHE cc_start: 0.7302 (OUTLIER) cc_final: 0.6952 (p90) REVERT: A 622 TYR cc_start: -0.2193 (OUTLIER) cc_final: -0.4320 (m-80) REVERT: B 144 MET cc_start: -0.0390 (tmm) cc_final: -0.2065 (ttp) REVERT: B 373 LYS cc_start: 0.8765 (mmmt) cc_final: 0.8493 (mmmt) REVERT: B 476 TRP cc_start: 0.6314 (OUTLIER) cc_final: 0.6000 (t60) REVERT: B 884 MET cc_start: 0.8987 (mmm) cc_final: 0.8643 (tpt) REVERT: C 144 MET cc_start: 0.5408 (pmm) cc_final: 0.5119 (pmm) REVERT: C 379 PHE cc_start: 0.8460 (m-80) cc_final: 0.8038 (t80) REVERT: C 816 MET cc_start: 0.0028 (mtt) cc_final: -0.0391 (mpp) REVERT: H 140 CYS cc_start: 0.6978 (OUTLIER) cc_final: 0.6568 (t) REVERT: L 27 GLN cc_start: 0.8526 (mm-40) cc_final: 0.7953 (pm20) outliers start: 52 outliers final: 35 residues processed: 122 average time/residue: 0.3897 time to fit residues: 81.6798 Evaluate side-chains 113 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 73 time to evaluate : 3.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 245 TRP Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 436 TYR Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 619 TRP Chi-restraints excluded: chain A residue 622 TYR Chi-restraints excluded: chain A residue 661 HIS Chi-restraints excluded: chain A residue 838 ASN Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 476 TRP Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 661 HIS Chi-restraints excluded: chain B residue 720 CYS Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 149 HIS Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 441 ARG Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 742 CYS Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 140 CYS Chi-restraints excluded: chain L residue 36 TYR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 194 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 326 optimal weight: 7.9990 chunk 343 optimal weight: 3.9990 chunk 313 optimal weight: 0.9990 chunk 334 optimal weight: 40.0000 chunk 201 optimal weight: 7.9990 chunk 145 optimal weight: 6.9990 chunk 262 optimal weight: 40.0000 chunk 102 optimal weight: 4.9990 chunk 301 optimal weight: 2.9990 chunk 316 optimal weight: 0.0970 chunk 332 optimal weight: 7.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29357 Z= 0.208 Angle : 0.601 11.066 40039 Z= 0.314 Chirality : 0.046 0.380 4696 Planarity : 0.004 0.066 5182 Dihedral : 7.335 59.768 5008 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.80 % Favored : 90.98 % Rotamer: Outliers : 1.64 % Allowed : 10.20 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.84 (0.14), residues: 3727 helix: 1.89 (0.20), residues: 734 sheet: -0.57 (0.19), residues: 731 loop : -1.46 (0.13), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 423 HIS 0.006 0.001 HIS A 181 PHE 0.021 0.001 PHE C 545 TYR 0.025 0.001 TYR A 622 ARG 0.003 0.000 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 74 time to evaluate : 3.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 TRP cc_start: 0.3156 (OUTLIER) cc_final: 0.2776 (m-90) REVERT: A 334 PHE cc_start: 0.3745 (OUTLIER) cc_final: 0.2780 (m-10) REVERT: A 622 TYR cc_start: -0.2639 (OUTLIER) cc_final: -0.4317 (m-80) REVERT: B 144 MET cc_start: -0.0151 (tmm) cc_final: -0.1751 (ttp) REVERT: B 271 THR cc_start: 0.8705 (OUTLIER) cc_final: 0.8413 (p) REVERT: B 373 LYS cc_start: 0.8777 (mmmt) cc_final: 0.8507 (mmmt) REVERT: B 476 TRP cc_start: 0.6299 (OUTLIER) cc_final: 0.5958 (t60) REVERT: B 884 MET cc_start: 0.8952 (mmm) cc_final: 0.8580 (tpt) REVERT: C 144 MET cc_start: 0.5341 (pmm) cc_final: 0.5110 (pmm) REVERT: C 379 PHE cc_start: 0.8503 (m-80) cc_final: 0.8096 (t80) REVERT: H 140 CYS cc_start: 0.6936 (OUTLIER) cc_final: 0.6516 (t) REVERT: L 27 GLN cc_start: 0.8498 (mm-40) cc_final: 0.7936 (pm20) outliers start: 48 outliers final: 34 residues processed: 118 average time/residue: 0.4033 time to fit residues: 80.6960 Evaluate side-chains 113 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 73 time to evaluate : 3.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 245 TRP Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 436 TYR Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 619 TRP Chi-restraints excluded: chain A residue 622 TYR Chi-restraints excluded: chain A residue 661 HIS Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 476 TRP Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 661 HIS Chi-restraints excluded: chain B residue 720 CYS Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 149 HIS Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 441 ARG Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 619 TRP Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 742 CYS Chi-restraints excluded: chain C residue 832 ILE Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 140 CYS Chi-restraints excluded: chain L residue 36 TYR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 194 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 219 optimal weight: 6.9990 chunk 353 optimal weight: 10.0000 chunk 215 optimal weight: 9.9990 chunk 167 optimal weight: 5.9990 chunk 245 optimal weight: 4.9990 chunk 370 optimal weight: 50.0000 chunk 341 optimal weight: 40.0000 chunk 295 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 227 optimal weight: 9.9990 chunk 180 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 HIS ** C 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 29357 Z= 0.311 Angle : 0.635 10.745 40039 Z= 0.331 Chirality : 0.047 0.491 4696 Planarity : 0.004 0.066 5182 Dihedral : 7.391 59.152 5008 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.15 % Favored : 90.64 % Rotamer: Outliers : 1.47 % Allowed : 10.44 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.90 (0.14), residues: 3727 helix: 1.74 (0.20), residues: 740 sheet: -0.54 (0.19), residues: 745 loop : -1.50 (0.13), residues: 2242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 423 HIS 0.007 0.001 HIS A 181 PHE 0.025 0.002 PHE C 545 TYR 0.030 0.002 TYR A 622 ARG 0.004 0.000 ARG C 48 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 74 time to evaluate : 3.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 TRP cc_start: 0.3283 (OUTLIER) cc_final: 0.2893 (m-90) REVERT: A 622 TYR cc_start: -0.2361 (OUTLIER) cc_final: -0.4183 (m-80) REVERT: B 144 MET cc_start: -0.0038 (tmm) cc_final: -0.1545 (ttp) REVERT: B 373 LYS cc_start: 0.8784 (mmmt) cc_final: 0.8537 (mmmt) REVERT: B 476 TRP cc_start: 0.6337 (OUTLIER) cc_final: 0.6006 (t60) REVERT: B 884 MET cc_start: 0.8978 (mmm) cc_final: 0.8639 (tpt) REVERT: H 140 CYS cc_start: 0.6939 (OUTLIER) cc_final: 0.6516 (t) REVERT: L 27 GLN cc_start: 0.8498 (mm-40) cc_final: 0.8002 (pm20) outliers start: 43 outliers final: 34 residues processed: 113 average time/residue: 0.3941 time to fit residues: 76.4044 Evaluate side-chains 110 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 72 time to evaluate : 3.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 245 TRP Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 436 TYR Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 619 TRP Chi-restraints excluded: chain A residue 622 TYR Chi-restraints excluded: chain A residue 661 HIS Chi-restraints excluded: chain A residue 894 THR Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 476 TRP Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 661 HIS Chi-restraints excluded: chain B residue 720 CYS Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 441 ARG Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 619 TRP Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 742 CYS Chi-restraints excluded: chain C residue 832 ILE Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 140 CYS Chi-restraints excluded: chain L residue 36 TYR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 194 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 234 optimal weight: 5.9990 chunk 314 optimal weight: 6.9990 chunk 90 optimal weight: 7.9990 chunk 272 optimal weight: 6.9990 chunk 43 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 295 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 chunk 303 optimal weight: 1.9990 chunk 37 optimal weight: 40.0000 chunk 54 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 HIS ** C 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 889 ASN ** H 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.068810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.044741 restraints weight = 166642.198| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 4.85 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 29357 Z= 0.280 Angle : 0.625 11.660 40039 Z= 0.325 Chirality : 0.047 0.444 4696 Planarity : 0.004 0.062 5182 Dihedral : 7.328 58.585 5008 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.96 % Favored : 90.82 % Rotamer: Outliers : 1.37 % Allowed : 10.72 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.89 (0.14), residues: 3727 helix: 1.78 (0.20), residues: 740 sheet: -0.52 (0.19), residues: 745 loop : -1.51 (0.13), residues: 2242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 423 HIS 0.017 0.001 HIS A 661 PHE 0.024 0.001 PHE C 545 TYR 0.028 0.001 TYR A 622 ARG 0.003 0.000 ARG C 48 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4707.84 seconds wall clock time: 88 minutes 19.98 seconds (5299.98 seconds total)