Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 28 20:10:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sg4_25105/04_2023/7sg4_25105_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sg4_25105/04_2023/7sg4_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_2023/7sg4_25105.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sg4_25105/04_2023/7sg4_25105.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sg4_25105/04_2023/7sg4_25105_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sg4_25105/04_2023/7sg4_25105_neut.pdb" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.149 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: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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 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 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 chiralities: 16 Time building chain proxies: 15.19, per 1000 atoms: 0.53 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: 10.68 Conformation dependent library (CDL) restraints added in 4.1 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: 2.35 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: 12.29 Time building geometry restraints manager: 11.57 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: 15748 17.86 - 35.72: 1121 35.72 - 53.57: 164 53.57 - 71.43: 47 71.43 - 89.29: 23 Dihedral angle restraints: 17103 sinusoidal: 6234 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 17100 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: 1.360 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: 8.470 Check model and map are aligned: 0.450 Set scattering table: 0.240 Process input model: 71.520 Find NCS groups from input model: 1.840 Set up NCS constraints: 0.140 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.880 ------------------------------------------------------------------------------- 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 : 13.285 89.288 9988 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 % 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 *********************** 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 : 3.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 26 residues processed: 154 average time/residue: 0.3883 time to fit residues: 100.3113 Evaluate side-chains 102 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 76 time to evaluate : 3.331 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 26 outliers final: 1 residues processed: 26 average time/residue: 0.3368 time to fit residues: 19.1652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 156 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 chunk 150 optimal weight: 8.9990 chunk 291 optimal weight: 0.9990 chunk 112 optimal weight: 10.0000 chunk 177 optimal weight: 5.9990 chunk 217 optimal weight: 9.9990 chunk 337 optimal weight: 10.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 B 786 GLN L 31 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2038 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= 0.225 Angle : 0.749 10.354 40039 Z= 0.402 Chirality : 0.050 0.466 4696 Planarity : 0.005 0.053 5182 Dihedral : 7.236 40.653 3994 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.65 % Favored : 91.98 % Rotamer Outliers : 1.19 % 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: 0.96 (0.20), residues: 715 sheet: -0.47 (0.19), residues: 684 loop : -1.50 (0.12), residues: 2328 *********************** 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 122 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 87 time to evaluate : 3.478 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 outliers start: 35 outliers final: 20 residues processed: 115 average time/residue: 0.4000 time to fit residues: 79.7030 Evaluate side-chains 98 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 78 time to evaluate : 3.305 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 20 outliers final: 1 residues processed: 20 average time/residue: 0.2912 time to fit residues: 15.0299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 187 optimal weight: 20.0000 chunk 104 optimal weight: 4.9990 chunk 281 optimal weight: 9.9990 chunk 230 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 338 optimal weight: 40.0000 chunk 365 optimal weight: 20.0000 chunk 301 optimal weight: 8.9990 chunk 335 optimal weight: 50.0000 chunk 115 optimal weight: 9.9990 chunk 271 optimal weight: 2.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 896 ASN B 230 ASN B 835 GLN B 896 ASN B1117 ASN ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.055 29357 Z= 0.415 Angle : 0.763 8.905 40039 Z= 0.401 Chirality : 0.051 0.488 4696 Planarity : 0.005 0.050 5182 Dihedral : 6.777 37.659 3994 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.18 % Favored : 90.53 % Rotamer Outliers : 1.40 % 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: -1.15 (0.14), residues: 3727 helix: 1.10 (0.19), residues: 728 sheet: -0.53 (0.19), residues: 692 loop : -1.52 (0.13), residues: 2307 *********************** 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 123 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 82 time to evaluate : 3.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 16 residues processed: 116 average time/residue: 0.3778 time to fit residues: 77.3966 Evaluate side-chains 94 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 78 time to evaluate : 3.565 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 16 outliers final: 1 residues processed: 16 average time/residue: 0.2888 time to fit residues: 13.2141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 334 optimal weight: 50.0000 chunk 254 optimal weight: 30.0000 chunk 175 optimal weight: 0.9990 chunk 37 optimal weight: 50.0000 chunk 161 optimal weight: 8.9990 chunk 227 optimal weight: 8.9990 chunk 339 optimal weight: 50.0000 chunk 359 optimal weight: 50.0000 chunk 177 optimal weight: 8.9990 chunk 321 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 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 178 ASN A 445 HIS A 896 ASN C 381 ASN C 661 HIS C 838 ASN ** H 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 29357 Z= 0.347 Angle : 0.689 8.994 40039 Z= 0.362 Chirality : 0.049 0.480 4696 Planarity : 0.005 0.053 5182 Dihedral : 6.395 35.750 3994 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.85 % Favored : 90.85 % Rotamer Outliers : 1.43 % 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: -1.10 (0.14), residues: 3727 helix: 1.45 (0.20), residues: 715 sheet: -0.70 (0.19), residues: 700 loop : -1.52 (0.13), residues: 2312 *********************** 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 117 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 75 time to evaluate : 3.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 14 residues processed: 112 average time/residue: 0.4018 time to fit residues: 78.8144 Evaluate side-chains 84 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 70 time to evaluate : 3.441 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 14 outliers final: 1 residues processed: 14 average time/residue: 0.2869 time to fit residues: 12.0015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 299 optimal weight: 1.9990 chunk 204 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 267 optimal weight: 1.9990 chunk 148 optimal weight: 50.0000 chunk 306 optimal weight: 6.9990 chunk 248 optimal weight: 50.0000 chunk 0 optimal weight: 10.0000 chunk 183 optimal weight: 4.9990 chunk 322 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 896 ASN B 661 HIS C1088 GLN ** H 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 29357 Z= 0.229 Angle : 0.639 13.840 40039 Z= 0.334 Chirality : 0.047 0.420 4696 Planarity : 0.004 0.062 5182 Dihedral : 6.028 34.475 3994 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.77 % Favored : 90.98 % Rotamer Outliers : 0.89 % 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: -0.94 (0.14), residues: 3727 helix: 1.70 (0.20), residues: 727 sheet: -0.56 (0.19), residues: 733 loop : -1.51 (0.13), residues: 2267 *********************** 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 101 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 75 time to evaluate : 3.439 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 8 residues processed: 97 average time/residue: 0.3764 time to fit residues: 65.3126 Evaluate side-chains 79 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 71 time to evaluate : 3.378 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.2905 time to fit residues: 8.6845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 120 optimal weight: 30.0000 chunk 323 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 chunk 211 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 359 optimal weight: 50.0000 chunk 298 optimal weight: 10.0000 chunk 166 optimal weight: 6.9990 chunk 29 optimal weight: 0.0020 chunk 119 optimal weight: 4.9990 chunk 188 optimal weight: 0.8980 overall best weight: 2.7794 ------------------------------------------------------------------------------- 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 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 838 ASN B 661 HIS ** 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: 0.8035 moved from start: 0.3449 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= 0.217 Angle : 0.616 11.432 40039 Z= 0.321 Chirality : 0.046 0.381 4696 Planarity : 0.004 0.063 5182 Dihedral : 5.785 32.645 3994 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.83 % Favored : 90.93 % Rotamer Outliers : 0.75 % 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: 1.93 (0.20), residues: 721 sheet: -0.55 (0.19), residues: 722 loop : -1.46 (0.13), residues: 2284 *********************** 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 98 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 76 time to evaluate : 3.474 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 10 residues processed: 94 average time/residue: 0.3953 time to fit residues: 65.2722 Evaluate side-chains 83 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 73 time to evaluate : 3.396 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 10 average time/residue: 0.2701 time to fit residues: 9.7035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 347 optimal weight: 50.0000 chunk 40 optimal weight: 20.0000 chunk 205 optimal weight: 5.9990 chunk 262 optimal weight: 0.0670 chunk 203 optimal weight: 5.9990 chunk 302 optimal weight: 4.9990 chunk 200 optimal weight: 6.9990 chunk 358 optimal weight: 0.9980 chunk 224 optimal weight: 4.9990 chunk 218 optimal weight: 10.0000 chunk 165 optimal weight: 4.9990 overall best weight: 3.2124 ------------------------------------------------------------------------------- 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 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 661 HIS B 733 ASN B 883 GLN ** 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: 0.8042 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 29357 Z= 0.235 Angle : 0.603 11.827 40039 Z= 0.316 Chirality : 0.046 0.378 4696 Planarity : 0.004 0.063 5182 Dihedral : 5.679 42.126 3994 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.77 % Favored : 90.98 % Rotamer Outliers : 0.78 % 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: -0.83 (0.14), residues: 3727 helix: 1.99 (0.20), residues: 721 sheet: -0.56 (0.19), residues: 722 loop : -1.46 (0.13), residues: 2284 *********************** 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 100 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 77 time to evaluate : 3.270 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 8 residues processed: 97 average time/residue: 0.3858 time to fit residues: 66.9668 Evaluate side-chains 83 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 75 time to evaluate : 3.414 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.2723 time to fit residues: 8.6908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 214 optimal weight: 7.9990 chunk 108 optimal weight: 7.9990 chunk 70 optimal weight: 0.9980 chunk 69 optimal weight: 7.9990 chunk 227 optimal weight: 6.9990 chunk 244 optimal weight: 0.4980 chunk 177 optimal weight: 8.9990 chunk 33 optimal weight: 20.0000 chunk 281 optimal weight: 9.9990 overall best weight: 4.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 661 HIS C 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: 0.8069 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.065 29357 Z= 0.335 Angle : 0.650 11.424 40039 Z= 0.339 Chirality : 0.047 0.375 4696 Planarity : 0.004 0.062 5182 Dihedral : 5.769 35.227 3994 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.23 % Favored : 90.53 % Rotamer Outliers : 0.72 % 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: -0.93 (0.14), residues: 3727 helix: 1.86 (0.20), residues: 725 sheet: -0.76 (0.19), residues: 719 loop : -1.47 (0.13), residues: 2283 *********************** 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 95 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 74 time to evaluate : 3.674 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 8 residues processed: 94 average time/residue: 0.3817 time to fit residues: 64.1638 Evaluate side-chains 81 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 73 time to evaluate : 3.705 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.2884 time to fit residues: 8.8041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 326 optimal weight: 2.9990 chunk 343 optimal weight: 9.9990 chunk 313 optimal weight: 3.9990 chunk 334 optimal weight: 40.0000 chunk 201 optimal weight: 7.9990 chunk 145 optimal weight: 20.0000 chunk 262 optimal weight: 40.0000 chunk 102 optimal weight: 1.9990 chunk 301 optimal weight: 0.8980 chunk 316 optimal weight: 5.9990 chunk 332 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS A 201 GLN ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 661 HIS C1088 GLN ** H 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 29357 Z= 0.205 Angle : 0.602 10.794 40039 Z= 0.314 Chirality : 0.046 0.461 4696 Planarity : 0.004 0.064 5182 Dihedral : 5.575 32.625 3994 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.21 % Favored : 91.57 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.85 (0.14), residues: 3727 helix: 2.01 (0.20), residues: 727 sheet: -0.60 (0.19), residues: 740 loop : -1.49 (0.13), residues: 2260 *********************** 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 86 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 77 time to evaluate : 3.690 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 85 average time/residue: 0.4075 time to fit residues: 62.0279 Evaluate side-chains 77 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 74 time to evaluate : 3.608 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.2432 time to fit residues: 5.7129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 219 optimal weight: 5.9990 chunk 353 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 167 optimal weight: 0.0980 chunk 245 optimal weight: 4.9990 chunk 370 optimal weight: 40.0000 chunk 341 optimal weight: 20.0000 chunk 295 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 227 optimal weight: 20.0000 chunk 180 optimal weight: 0.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- 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 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 661 HIS H 61 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 29357 Z= 0.198 Angle : 0.599 11.433 40039 Z= 0.310 Chirality : 0.046 0.377 4696 Planarity : 0.004 0.063 5182 Dihedral : 5.459 35.328 3994 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.88 % Favored : 90.93 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.14), residues: 3727 helix: 2.06 (0.20), residues: 725 sheet: -0.54 (0.19), residues: 743 loop : -1.50 (0.13), residues: 2259 ********************** 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 90 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 78 time to evaluate : 3.326 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 88 average time/residue: 0.3931 time to fit residues: 61.4193 Evaluate side-chains 78 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 73 time to evaluate : 3.224 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.2786 time to fit residues: 6.9134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 234 optimal weight: 6.9990 chunk 314 optimal weight: 6.9990 chunk 90 optimal weight: 7.9990 chunk 272 optimal weight: 8.9990 chunk 43 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 295 optimal weight: 0.9990 chunk 123 optimal weight: 30.0000 chunk 303 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 54 optimal weight: 0.0770 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 ASN ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.068636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.045110 restraints weight = 173100.365| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 4.79 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 29357 Z= 0.169 Angle : 0.584 11.097 40039 Z= 0.302 Chirality : 0.046 0.521 4696 Planarity : 0.004 0.064 5182 Dihedral : 5.330 30.794 3994 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.21 % Favored : 91.60 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.77 (0.14), residues: 3727 helix: 2.13 (0.21), residues: 726 sheet: -0.51 (0.19), residues: 746 loop : -1.48 (0.13), residues: 2255 =============================================================================== Job complete usr+sys time: 4216.42 seconds wall clock time: 79 minutes 39.58 seconds (4779.58 seconds total)