Starting phenix.real_space_refine on Wed Mar 20 16:02:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wpd_32683/03_2024/7wpd_32683_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wpd_32683/03_2024/7wpd_32683.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wpd_32683/03_2024/7wpd_32683.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wpd_32683/03_2024/7wpd_32683.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wpd_32683/03_2024/7wpd_32683_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wpd_32683/03_2024/7wpd_32683_neut.pdb" } resolution = 3.18 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= 0.021 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 119 5.16 5 C 17734 2.51 5 N 4564 2.21 5 O 5345 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 34": "NH1" <-> "NH2" Residue "A ARG 44": "NH1" <-> "NH2" Residue "A GLU 96": "OE1" <-> "OE2" Residue "A ARG 102": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A ARG 493": "NH1" <-> "NH2" Residue "A ARG 498": "NH1" <-> "NH2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A ARG 577": "NH1" <-> "NH2" Residue "A ARG 765": "NH1" <-> "NH2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A ARG 905": "NH1" <-> "NH2" Residue "A ARG 983": "NH1" <-> "NH2" Residue "A ARG 995": "NH1" <-> "NH2" Residue "A ARG 1000": "NH1" <-> "NH2" Residue "A ARG 1014": "NH1" <-> "NH2" Residue "A ARG 1019": "NH1" <-> "NH2" Residue "A ARG 1039": "NH1" <-> "NH2" Residue "A GLU 1072": "OE1" <-> "OE2" Residue "A ARG 1091": "NH1" <-> "NH2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B ARG 44": "NH1" <-> "NH2" Residue "B ARG 102": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 273": "NH1" <-> "NH2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B ARG 408": "NH1" <-> "NH2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B ARG 457": "NH1" <-> "NH2" Residue "B ARG 466": "NH1" <-> "NH2" Residue "B ARG 493": "NH1" <-> "NH2" Residue "B ARG 498": "NH1" <-> "NH2" Residue "B ARG 509": "NH1" <-> "NH2" Residue "B ARG 567": "NH1" <-> "NH2" Residue "B ARG 577": "NH1" <-> "NH2" Residue "B GLU 619": "OE1" <-> "OE2" Residue "B GLU 725": "OE1" <-> "OE2" Residue "B ARG 765": "NH1" <-> "NH2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B GLU 819": "OE1" <-> "OE2" Residue "B ARG 905": "NH1" <-> "NH2" Residue "B GLU 918": "OE1" <-> "OE2" Residue "B ARG 983": "NH1" <-> "NH2" Residue "B ARG 1000": "NH1" <-> "NH2" Residue "B ARG 1039": "NH1" <-> "NH2" Residue "B ARG 1091": "NH1" <-> "NH2" Residue "B ARG 1107": "NH1" <-> "NH2" Residue "B GLU 1111": "OE1" <-> "OE2" Residue "C ARG 34": "NH1" <-> "NH2" Residue "C ARG 44": "NH1" <-> "NH2" Residue "C ARG 102": "NH1" <-> "NH2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C ARG 273": "NH1" <-> "NH2" Residue "C ARG 328": "NH1" <-> "NH2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 403": "NH1" <-> "NH2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "C ARG 454": "NH1" <-> "NH2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "C ARG 493": "NH1" <-> "NH2" Residue "C ARG 498": "NH1" <-> "NH2" Residue "C ARG 509": "NH1" <-> "NH2" Residue "C ARG 567": "NH1" <-> "NH2" Residue "C ARG 577": "NH1" <-> "NH2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C GLU 725": "OE1" <-> "OE2" Residue "C ARG 765": "NH1" <-> "NH2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C GLU 819": "OE1" <-> "OE2" Residue "C ARG 905": "NH1" <-> "NH2" Residue "C ARG 983": "NH1" <-> "NH2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C ARG 995": "NH1" <-> "NH2" Residue "C ARG 1000": "NH1" <-> "NH2" Residue "C ARG 1014": "NH1" <-> "NH2" Residue "C ARG 1019": "NH1" <-> "NH2" Residue "C GLU 1031": "OE1" <-> "OE2" Residue "C ARG 1039": "NH1" <-> "NH2" Residue "C ARG 1091": "NH1" <-> "NH2" Residue "X ARG 38": "NH1" <-> "NH2" Residue "X ARG 50": "NH1" <-> "NH2" Residue "X ARG 67": "NH1" <-> "NH2" Residue "X ARG 87": "NH1" <-> "NH2" Residue "Y ARG 18": "NH1" <-> "NH2" Residue "Y ARG 24": "NH1" <-> "NH2" Residue "Y ARG 61": "NH1" <-> "NH2" Residue "Y ARG 108": "NH1" <-> "NH2" Residue "Y ARG 142": "NH1" <-> "NH2" Residue "Y ARG 211": "NH1" <-> "NH2" Residue "Z ARG 28": "NH1" <-> "NH2" Residue "Z ARG 36": "NH1" <-> "NH2" Residue "Z ARG 40": "NH1" <-> "NH2" Residue "Z ARG 47": "NH1" <-> "NH2" Residue "Z ARG 54": "NH1" <-> "NH2" Residue "Z ARG 61": "NH1" <-> "NH2" Residue "Z ARG 62": "NH1" <-> "NH2" Residue "Z ARG 76": "NH1" <-> "NH2" Residue "Z ARG 81": "NH1" <-> "NH2" Residue "Z GLU 98": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 27762 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 7677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7677 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PTRANS': 52, 'TRANS': 971} Chain breaks: 7 Unresolved non-hydrogen bonds: 354 Unresolved non-hydrogen angles: 432 Unresolved non-hydrogen dihedrals: 295 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 5, 'ASN:plan1': 5, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 193 Chain: "B" Number of atoms: 7642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7642 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 971} Chain breaks: 7 Unresolved non-hydrogen bonds: 380 Unresolved non-hydrogen angles: 459 Unresolved non-hydrogen dihedrals: 316 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 7, 'ASP:plan': 13, 'PHE:plan': 2, 'GLU:plan': 14, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 226 Chain: "C" Number of atoms: 7702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 7702 Classifications: {'peptide': 1022} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 969} Chain breaks: 7 Unresolved non-hydrogen bonds: 311 Unresolved non-hydrogen angles: 382 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 10, 'TYR:plan': 2, 'ASN:plan1': 9, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 189 Chain: "X" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1665 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 212} Chain: "Y" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1633 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 201} Chain: "Z" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 925 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 13.86, per 1000 atoms: 0.50 Number of scatterers: 27762 At special positions: 0 Unit cell: (191.992, 136.784, 206.824, 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 119 16.00 O 5345 8.00 N 4564 7.00 C 17734 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS X 22 " - pdb=" SG CYS X 96 " distance=2.03 Simple disulfide: pdb=" SG CYS X 150 " - pdb=" SG CYS X 206 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 23 " - pdb=" SG CYS Y 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 134 " - pdb=" SG CYS Y 194 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 31 " - pdb=" SG CYS Z 105 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A1301 " - " ASN A1074 " " NAG A1302 " - " ASN A 234 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A1134 " " NAG A1305 " - " ASN A1098 " " NAG A1306 " - " ASN A 801 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 616 " " NAG A1310 " - " ASN A 603 " " NAG A1311 " - " ASN A 331 " " NAG B1301 " - " ASN B 603 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 657 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B1134 " " NAG B1306 " - " ASN B 234 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B1098 " " NAG B1309 " - " ASN B 801 " " NAG B1310 " - " ASN B 616 " " NAG C1301 " - " ASN C 657 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C1074 " " NAG C1306 " - " ASN C1134 " " NAG C1307 " - " ASN C1098 " " NAG C1308 " - " ASN C 165 " " NAG C1309 " - " ASN C 616 " " NAG C1310 " - " ASN C 709 " " NAG C1311 " - " ASN C 801 " " NAG C1312 " - " ASN C 282 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN C 717 " Time building additional restraints: 11.92 Conformation dependent library (CDL) restraints added in 5.4 seconds 7148 Ramachandran restraints generated. 3574 Oldfield, 0 Emsley, 3574 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6782 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 59 sheets defined 23.0% alpha, 30.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.72 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 345 removed outlier: 3.736A pdb=" N THR A 345 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 403 through 408 removed outlier: 4.317A pdb=" N ARG A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.794A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.346A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 968 removed outlier: 4.222A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER A 968 " --> pdb=" O LYS A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.558A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.962A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.148A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.772A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 365 through 370' Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.623A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 4.033A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.579A pdb=" N GLU B 619 " --> pdb=" O ASN B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 removed outlier: 3.896A pdb=" N CYS B 743 " --> pdb=" O THR B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 removed outlier: 4.365A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.545A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.683A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 885 through 890 removed outlier: 3.738A pdb=" N PHE B 888 " --> pdb=" O GLY B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.755A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.446A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.465A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 removed outlier: 3.551A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 384 through 388 removed outlier: 3.629A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 384 through 388' Processing helix chain 'C' and resid 404 through 410 removed outlier: 4.042A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.971A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.530A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.971A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.535A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.711A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.781A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.634A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.868A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1127 through 1129 No H-bonds generated for 'chain 'C' and resid 1127 through 1129' Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 4.241A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'X' and resid 28 through 32 Processing helix chain 'X' and resid 62 through 65 removed outlier: 3.543A pdb=" N GLN X 65 " --> pdb=" O GLN X 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 62 through 65' Processing helix chain 'X' and resid 87 through 91 Processing helix chain 'X' and resid 137 through 141 Processing helix chain 'X' and resid 166 through 168 No H-bonds generated for 'chain 'X' and resid 166 through 168' Processing helix chain 'Y' and resid 79 through 83 Processing helix chain 'Y' and resid 121 through 126 Processing helix chain 'Y' and resid 150 through 153 Processing helix chain 'Y' and resid 183 through 189 removed outlier: 3.594A pdb=" N HIS Y 189 " --> pdb=" O ASP Y 185 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.973A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA A 264 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.116A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.198A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 134 through 135 removed outlier: 7.402A pdb=" N GLN A 134 " --> pdb=" O SER A 162 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.205A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.699A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY A 431 " --> pdb=" O TYR A 380 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.760A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 539 through 541 removed outlier: 5.018A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR A 572 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.682A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 removed outlier: 6.787A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.834A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.834A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.154A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 789 removed outlier: 6.380A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.767A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.694A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.513A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.755A pdb=" N ARG B 237 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE B 106 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.536A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.564A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 357 through 358 removed outlier: 4.094A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ALA B 435 " --> pdb=" O PHE B 375 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 357 through 358 removed outlier: 4.094A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.665A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.255A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.834A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AD2, first strand: chain 'B' and resid 712 through 719 removed outlier: 6.927A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 712 through 719 removed outlier: 6.927A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.316A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.800A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1094 through 1096 Processing sheet with id=AD7, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.607A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.249A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.247A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.283A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.054A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR C 572 " --> pdb=" O ASP C 568 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP C 574 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.882A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.812A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.597A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.531A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.531A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.268A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.941A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'X' and resid 3 through 6 removed outlier: 3.570A pdb=" N GLN X 3 " --> pdb=" O SER X 25 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU X 83 " --> pdb=" O VAL X 18 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL X 20 " --> pdb=" O MET X 81 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET X 81 " --> pdb=" O VAL X 20 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'X' and resid 10 through 11 removed outlier: 3.823A pdb=" N THR X 120 " --> pdb=" O GLU X 10 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL X 119 " --> pdb=" O ALA X 92 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ILE X 34 " --> pdb=" O ARG X 50 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ARG X 50 " --> pdb=" O ILE X 34 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N TRP X 36 " --> pdb=" O MET X 48 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'X' and resid 130 through 133 removed outlier: 3.572A pdb=" N PHE X 132 " --> pdb=" O LEU X 151 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N CYS X 150 " --> pdb=" O SER X 190 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER X 190 " --> pdb=" O CYS X 150 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N TYR X 186 " --> pdb=" O ASP X 154 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'X' and resid 130 through 133 removed outlier: 3.572A pdb=" N PHE X 132 " --> pdb=" O LEU X 151 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N CYS X 150 " --> pdb=" O SER X 190 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER X 190 " --> pdb=" O CYS X 150 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N TYR X 186 " --> pdb=" O ASP X 154 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N SER X 187 " --> pdb=" O ALA X 178 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ALA X 178 " --> pdb=" O SER X 187 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N SER X 189 " --> pdb=" O PHE X 176 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'X' and resid 161 through 164 Processing sheet with id=AF8, first strand: chain 'Y' and resid 5 through 7 removed outlier: 3.809A pdb=" N SER Y 7 " --> pdb=" O THR Y 22 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR Y 22 " --> pdb=" O SER Y 7 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N THR Y 69 " --> pdb=" O ALA Y 25 " (cutoff:3.500A) removed outlier: 10.136A pdb=" N GLN Y 27 " --> pdb=" O SER Y 67 " (cutoff:3.500A) removed outlier: 9.723A pdb=" N SER Y 67 " --> pdb=" O GLN Y 27 " (cutoff:3.500A) removed outlier: 11.462A pdb=" N ILE Y 29 " --> pdb=" O SER Y 65 " (cutoff:3.500A) removed outlier: 11.212A pdb=" N SER Y 65 " --> pdb=" O ILE Y 29 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Y' and resid 10 through 12 removed outlier: 3.772A pdb=" N LEU Y 33 " --> pdb=" O TYR Y 49 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N TYR Y 49 " --> pdb=" O LEU Y 33 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N TRP Y 35 " --> pdb=" O LEU Y 47 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP Y 50 " --> pdb=" O ASN Y 53 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Y' and resid 10 through 12 removed outlier: 3.551A pdb=" N GLN Y 90 " --> pdb=" O THR Y 97 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR Y 97 " --> pdb=" O GLN Y 90 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Y' and resid 114 through 118 removed outlier: 5.706A pdb=" N TYR Y 173 " --> pdb=" O ASN Y 138 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'Y' and resid 145 through 148 removed outlier: 4.868A pdb=" N LYS Y 145 " --> pdb=" O THR Y 197 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N THR Y 197 " --> pdb=" O LYS Y 145 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'Z' and resid 14 through 17 removed outlier: 3.876A pdb=" N GLN Z 14 " --> pdb=" O ALA Z 32 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU Z 29 " --> pdb=" O LEU Z 90 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU Z 90 " --> pdb=" O LEU Z 29 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Z' and resid 19 through 21 removed outlier: 3.727A pdb=" N THR Z 127 " --> pdb=" O GLY Z 19 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N TRP Z 120 " --> pdb=" O ILE Z 107 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE Z 107 " --> pdb=" O TRP Z 120 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN Z 122 " --> pdb=" O CYS Z 105 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA Z 42 " --> pdb=" O ASP Z 108 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N MET Z 43 " --> pdb=" O VAL Z 59 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL Z 59 " --> pdb=" O MET Z 43 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N TRP Z 45 " --> pdb=" O VAL Z 57 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL Z 59 " --> pdb=" O PHE Z 68 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE Z 68 " --> pdb=" O VAL Z 59 " (cutoff:3.500A) 1158 hydrogen bonds defined for protein. 3141 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: 13.75 Time building geometry restraints manager: 12.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 8875 1.35 - 1.47: 7202 1.47 - 1.58: 12176 1.58 - 1.70: 0 1.70 - 1.82: 148 Bond restraints: 28401 Sorted by residual: bond pdb=" N LYS A 969 " pdb=" CA LYS A 969 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.33e-02 5.65e+03 6.91e+00 bond pdb=" N GLN Z 10 " pdb=" CA GLN Z 10 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.90e-02 2.77e+03 4.43e+00 bond pdb=" CA ASN A 481 " pdb=" CB ASN A 481 " ideal model delta sigma weight residual 1.526 1.557 -0.031 1.76e-02 3.23e+03 3.14e+00 bond pdb=" N ALA C 27 " pdb=" CA ALA C 27 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.00e+00 bond pdb=" N ALA B 27 " pdb=" CA ALA B 27 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.99e+00 ... (remaining 28396 not shown) Histogram of bond angle deviations from ideal: 100.07 - 106.90: 862 106.90 - 113.73: 15678 113.73 - 120.55: 10622 120.55 - 127.38: 11337 127.38 - 134.21: 276 Bond angle restraints: 38775 Sorted by residual: angle pdb=" CA CYS A 291 " pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " ideal model delta sigma weight residual 114.40 134.21 -19.81 2.30e+00 1.89e-01 7.42e+01 angle pdb=" OG1 THR X 28 " pdb=" CB THR X 28 " pdb=" CG2 THR X 28 " ideal model delta sigma weight residual 109.30 120.51 -11.21 2.00e+00 2.50e-01 3.14e+01 angle pdb=" OG1 THR X 126 " pdb=" CB THR X 126 " pdb=" CG2 THR X 126 " ideal model delta sigma weight residual 109.30 120.51 -11.21 2.00e+00 2.50e-01 3.14e+01 angle pdb=" CG1 ILE Y 117 " pdb=" CB ILE Y 117 " pdb=" CG2 ILE Y 117 " ideal model delta sigma weight residual 110.70 126.01 -15.31 3.00e+00 1.11e-01 2.60e+01 angle pdb=" CG1 ILE X 112 " pdb=" CB ILE X 112 " pdb=" CG2 ILE X 112 " ideal model delta sigma weight residual 110.70 125.97 -15.27 3.00e+00 1.11e-01 2.59e+01 ... (remaining 38770 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 15989 17.99 - 35.99: 1012 35.99 - 53.98: 175 53.98 - 71.97: 51 71.97 - 89.96: 18 Dihedral angle restraints: 17245 sinusoidal: 6705 harmonic: 10540 Sorted by residual: dihedral pdb=" CB CYS C 743 " pdb=" SG CYS C 743 " pdb=" SG CYS C 749 " pdb=" CB CYS C 749 " ideal model delta sinusoidal sigma weight residual 93.00 179.45 -86.45 1 1.00e+01 1.00e-02 9.01e+01 dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual -86.00 -172.21 86.21 1 1.00e+01 1.00e-02 8.97e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual -86.00 -170.65 84.65 1 1.00e+01 1.00e-02 8.71e+01 ... (remaining 17242 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.336: 4556 0.336 - 0.673: 22 0.673 - 1.009: 0 1.009 - 1.346: 1 1.346 - 1.682: 7 Chirality restraints: 4586 Sorted by residual: chirality pdb=" CG LEU Z 29 " pdb=" CB LEU Z 29 " pdb=" CD1 LEU Z 29 " pdb=" CD2 LEU Z 29 " both_signs ideal model delta sigma weight residual False -2.59 -0.91 -1.68 2.00e-01 2.50e+01 7.07e+01 chirality pdb=" CB ILE Y 117 " pdb=" CA ILE Y 117 " pdb=" CG1 ILE Y 117 " pdb=" CG2 ILE Y 117 " both_signs ideal model delta sigma weight residual False 2.64 0.99 1.65 2.00e-01 2.50e+01 6.82e+01 chirality pdb=" CB ILE X 112 " pdb=" CA ILE X 112 " pdb=" CG1 ILE X 112 " pdb=" CG2 ILE X 112 " both_signs ideal model delta sigma weight residual False 2.64 1.01 1.64 2.00e-01 2.50e+01 6.69e+01 ... (remaining 4583 not shown) Planarity restraints: 5002 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A1134 " 0.075 2.00e-02 2.50e+03 1.65e-01 3.41e+02 pdb=" CG ASN A1134 " -0.043 2.00e-02 2.50e+03 pdb=" OD1 ASN A1134 " 0.092 2.00e-02 2.50e+03 pdb=" ND2 ASN A1134 " -0.299 2.00e-02 2.50e+03 pdb=" C1 NAG A1304 " 0.175 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 806 " 0.042 5.00e-02 4.00e+02 6.37e-02 6.50e+00 pdb=" N PRO B 807 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO B 807 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 807 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A1078 " 0.032 5.00e-02 4.00e+02 4.82e-02 3.71e+00 pdb=" N PRO A1079 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A1079 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A1079 " 0.027 5.00e-02 4.00e+02 ... (remaining 4999 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 104 2.47 - 3.08: 19702 3.08 - 3.69: 40324 3.69 - 4.29: 59101 4.29 - 4.90: 99936 Nonbonded interactions: 219167 Sorted by model distance: nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 1.866 2.440 nonbonded pdb=" O ILE B 742 " pdb=" NH1 ARG B1000 " model vdw 1.936 2.520 nonbonded pdb=" O TYR Y 49 " pdb=" OH TYR Y 91 " model vdw 1.986 2.440 nonbonded pdb=" OD1 ASP Z 108 " pdb=" OG SER Z 116 " model vdw 2.026 2.440 nonbonded pdb=" OE2 GLU C 298 " pdb=" OG1 THR C 315 " model vdw 2.058 2.440 ... (remaining 219162 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 27 through 39 or (resid 40 and (name N or name CA or name \ C or name O or name CB )) or resid 41 through 45 or (resid 46 and (name N or nam \ e CA or name C or name O or name CB )) or resid 47 through 51 or (resid 52 throu \ gh 53 and (name N or name CA or name C or name O or name CB )) or resid 54 throu \ gh 68 or resid 81 through 86 or (resid 87 and (name N or name CA or name C or na \ me O or name CB )) or resid 88 through 95 or (resid 96 through 98 and (name N or \ name CA or name C or name O or name CB )) or resid 99 through 114 or (resid 115 \ and (name N or name CA or name C or name O or name CB )) or resid 116 through 1 \ 23 or (resid 124 and (name N or name CA or name C or name O or name CB )) or res \ id 125 through 133 or (resid 134 and (name N or name CA or name C or name O or n \ ame CB )) or resid 135 or (resid 136 through 138 and (name N or name CA or name \ C or name O or name CB )) or resid 139 through 142 or resid 158 through 160 or ( \ resid 161 through 164 and (name N or name CA or name C or name O or name CB )) o \ r resid 165 through 194 or (resid 195 and (name N or name CA or name C or name O \ or name CB )) or resid 196 through 205 or (resid 206 and (name N or name CA or \ name C or name O or name CB )) or resid 207 through 209 or (resid 210 and (name \ N or name CA or name C or name O or name CB )) or resid 215 through 244 or (resi \ d 245 through 246 and (name N or name CA or name C or name O or name CB )) or re \ sid 247 through 253 or (resid 254 and (name N or name CA or name C or name O or \ name CB )) or resid 255 through 280 or (resid 281 and (name N or name CA or name \ C or name O or name CB )) or resid 282 through 286 or (resid 287 through 288 an \ d (name N or name CA or name C or name O or name CB )) or resid 289 through 308 \ or (resid 309 through 310 and (name N or name CA or name C or name O or name CB \ )) or resid 311 through 318 or (resid 319 and (name N or name CA or name C or na \ me O or name CB )) or resid 320 through 323 or (resid 324 and (name N or name CA \ or name C or name O or name CB )) or resid 325 through 331 or (resid 332 and (n \ ame N or name CA or name C or name O or name CB )) or resid 333 through 355 or ( \ resid 356 through 357 and (name N or name CA or name C or name O or name CB )) o \ r resid 358 through 385 or (resid 386 and (name N or name CA or name C or name O \ or name CB )) or resid 387 or (resid 388 and (name N or name CA or name C or na \ me O or name CB )) or resid 389 through 404 or (resid 405 through 406 and (name \ N or name CA or name C or name O or name CB )) or resid 407 through 440 or (resi \ d 441 through 442 and (name N or name CA or name C or name O or name CB )) or re \ sid 443 through 458 or (resid 459 and (name N or name CA or name C or name O or \ name CB )) or resid 460 through 531 or (resid 532 and (name N or name CA or name \ C or name O or name CB )) or resid 533 through 536 or (resid 537 and (name N or \ name CA or name C or name O or name CB )) or resid 538 through 553 or (resid 55 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 555 or (resi \ d 556 through 558 and (name N or name CA or name C or name O or name CB )) or re \ sid 559 through 563 or (resid 564 and (name N or name CA or name C or name O or \ name CB )) or resid 565 through 570 or (resid 571 through 572 and (name N or nam \ e CA or name C or name O or name CB )) or resid 573 through 612 or (resid 613 an \ d (name N or name CA or name C or name O or name CB )) or resid 614 through 620 \ or resid 641 through 676 or (resid 690 and (name N or name CA or name C or name \ O or name CB )) or resid 691 through 736 or (resid 737 and (name N or name CA or \ name C or name O or name CB )) or resid 738 through 744 or (resid 745 and (name \ N or name CA or name C or name O or name CB )) or resid 746 through 747 or (res \ id 748 and (name N or name CA or name C or name O or name CB )) or resid 749 thr \ ough 775 or (resid 776 and (name N or name CA or name C or name O or name CB )) \ or resid 777 through 778 or (resid 779 through 780 and (name N or name CA or nam \ e C or name O or name CB )) or resid 781 through 810 or (resid 811 and (name N o \ r name CA or name C or name O or name CB )) or resid 812 through 827 or (resid 8 \ 28 and (name N or name CA or name C or name O or name CB )) or (resid 855 and (n \ ame N or name CA or name C or name O or name CB )) or resid 856 through 867 or ( \ resid 868 and (name N or name CA or name C or name O or name CB )) or resid 869 \ through 938 or (resid 939 through 944 and (name N or name CA or name C or name O \ or name CB )) or resid 945 through 984 or (resid 985 and (name N or name CA or \ name C or name O or name CB )) or resid 986 through 987 or (resid 988 through 98 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 990 through \ 994 or (resid 995 and (name N or name CA or name C or name O or name CB )) or re \ sid 996 through 1013 or (resid 1014 through 1016 and (name N or name CA or name \ C or name O or name CB )) or resid 1017 through 1018 or (resid 1019 through 1020 \ and (name N or name CA or name C or name O or name CB )) or resid 1021 through \ 1037 or (resid 1038 and (name N or name CA or name C or name O or name CB )) or \ resid 1039 through 1050 or (resid 1051 and (name N or name CA or name C or name \ O or name CB )) or resid 1052 through 1091 or (resid 1092 and (name N or name CA \ or name C or name O or name CB )) or resid 1093 through 1110 or (resid 1111 and \ (name N or name CA or name C or name O or name CB )) or resid 1112 through 1143 \ or (resid 1144 through 1146 and (name N or name CA or name C or name O or name \ CB )) or resid 1301 through 1310)) selection = (chain 'B' and (resid 27 through 39 or (resid 40 and (name N or name CA or name \ C or name O or name CB )) or resid 41 through 51 or (resid 52 through 53 and (na \ me N or name CA or name C or name O or name CB )) or resid 54 through 67 or (res \ id 68 and (name N or name CA or name C or name O or name CB )) or resid 81 throu \ gh 86 or (resid 87 and (name N or name CA or name C or name O or name CB )) or r \ esid 88 through 107 or (resid 108 through 113 and (name N or name CA or name C o \ r name O or name CB )) or resid 114 or (resid 115 and (name N or name CA or name \ C or name O or name CB )) or resid 116 through 120 or (resid 121 through 124 an \ d (name N or name CA or name C or name O or name CB )) or resid 125 through 160 \ or (resid 161 through 164 and (name N or name CA or name C or name O or name CB \ )) or resid 165 through 194 or (resid 195 and (name N or name CA or name C or na \ me O or name CB )) or resid 196 through 199 or (resid 200 and (name N or name CA \ or name C or name O or name CB )) or resid 201 through 217 or (resid 218 and (n \ ame N or name CA or name C or name O or name CB )) or resid 219 through 223 or ( \ resid 224 and (name N or name CA or name C or name O or name CB )) or resid 225 \ through 248 or (resid 249 through 250 and (name N or name CA or name C or name O \ or name CB )) or resid 251 through 253 or (resid 254 and (name N or name CA or \ name C or name O or name CB )) or resid 255 through 320 or (resid 321 and (name \ N or name CA or name C or name O or name CB )) or resid 322 or (resid 323 throug \ h 324 and (name N or name CA or name C or name O or name CB )) or resid 325 thro \ ugh 331 or (resid 332 and (name N or name CA or name C or name O or name CB )) o \ r resid 333 through 356 or (resid 357 and (name N or name CA or name C or name O \ or name CB )) or resid 358 through 402 or (resid 403 and (name N or name CA or \ name C or name O or name CB )) or resid 404 or (resid 405 through 406 and (name \ N or name CA or name C or name O or name CB )) or resid 407 or (resid 408 and (n \ ame N or name CA or name C or name O or name CB )) or resid 409 through 414 or ( \ resid 415 and (name N or name CA or name C or name O or name CB )) or resid 416 \ through 423 or (resid 424 and (name N or name CA or name C or name O or name CB \ )) or resid 425 through 444 or (resid 445 and (name N or name CA or name C or na \ me O or name CB )) or resid 446 through 457 or (resid 458 through 459 and (name \ N or name CA or name C or name O or name CB )) or resid 460 through 464 or (resi \ d 465 and (name N or name CA or name C or name O or name CB )) or resid 466 thro \ ugh 486 or (resid 487 and (name N or name CA or name C or name O or name CB )) o \ r resid 488 through 499 or (resid 500 and (name N or name CA or name C or name O \ or name CB )) or resid 501 through 508 or (resid 509 and (name N or name CA or \ name C or name O or name CB )) or resid 510 through 563 or (resid 564 and (name \ N or name CA or name C or name O or name CB )) or resid 565 through 568 or (resi \ d 569 through 572 and (name N or name CA or name C or name O or name CB )) or re \ sid 573 through 579 or (resid 580 and (name N or name CA or name C or name O or \ name CB )) or resid 581 through 617 or (resid 618 and (name N or name CA or name \ C or name O or name CB )) or resid 619 through 620 or resid 641 through 739 or \ (resid 740 and (name N or name CA or name C or name O or name CB )) or resid 741 \ through 747 or (resid 748 and (name N or name CA or name C or name O or name CB \ )) or resid 749 through 807 or (resid 808 and (name N or name CA or name C or n \ ame O or name CB )) or resid 809 through 818 or (resid 819 and (name N or name C \ A or name C or name O or name CB )) or resid 820 through 824 or (resid 825 and ( \ name N or name CA or name C or name O or name CB )) or resid 826 through 828 or \ resid 855 through 917 or (resid 918 and (name N or name CA or name C or name O o \ r name CB )) or resid 919 through 920 or (resid 921 and (name N or name CA or na \ me C or name O or name CB )) or resid 922 through 932 or (resid 933 and (name N \ or name CA or name C or name O or name CB )) or resid 934 through 935 or (resid \ 936 and (name N or name CA or name C or name O or name CB )) or resid 937 throug \ h 940 or (resid 941 through 944 and (name N or name CA or name C or name O or na \ me CB )) or resid 945 through 946 or (resid 947 and (name N or name CA or name C \ or name O or name CB )) or resid 948 through 963 or (resid 964 and (name N or n \ ame CA or name C or name O or name CB )) or resid 965 through 1050 or (resid 105 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 1052 through \ 1106 or (resid 1107 and (name N or name CA or name C or name O or name CB )) or \ resid 1108 through 1110 or (resid 1111 and (name N or name CA or name C or name \ O or name CB )) or resid 1112 through 1137 or (resid 1138 and (name N or name C \ A or name C or name O or name CB )) or resid 1139 through 1143 or (resid 1144 th \ rough 1146 and (name N or name CA or name C or name O or name CB )) or resid 130 \ 1 through 1310)) selection = (chain 'C' and (resid 27 through 67 or (resid 68 and (name N or name CA or name \ C or name O or name CB )) or resid 81 through 95 or (resid 96 through 98 and (na \ me N or name CA or name C or name O or name CB )) or resid 99 through 107 or (re \ sid 108 through 113 and (name N or name CA or name C or name O or name CB )) or \ resid 114 through 123 or (resid 124 and (name N or name CA or name C or name O o \ r name CB )) or resid 125 through 135 or (resid 136 through 138 and (name N or n \ ame CA or name C or name O or name CB )) or resid 139 through 142 or resid 158 t \ hrough 175 or (resid 176 through 187 and (name N or name CA or name C or name O \ or name CB )) or resid 188 through 199 or (resid 200 and (name N or name CA or n \ ame C or name O or name CB )) or resid 201 through 205 or (resid 206 and (name N \ or name CA or name C or name O or name CB )) or resid 207 through 217 or (resid \ 218 and (name N or name CA or name C or name O or name CB )) or resid 219 throu \ gh 223 or (resid 224 and (name N or name CA or name C or name O or name CB )) or \ resid 225 through 244 or (resid 245 through 246 and (name N or name CA or name \ C or name O or name CB )) or resid 247 through 248 or (resid 249 through 250 and \ (name N or name CA or name C or name O or name CB )) or resid 251 through 280 o \ r (resid 281 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 82 through 286 or (resid 287 through 288 and (name N or name CA or name C or nam \ e O or name CB )) or resid 289 through 303 or (resid 304 and (name N or name CA \ or name C or name O or name CB )) or resid 305 through 308 or (resid 309 through \ 310 and (name N or name CA or name C or name O or name CB )) or resid 311 throu \ gh 320 or (resid 321 and (name N or name CA or name C or name O or name CB )) or \ resid 322 through 323 or (resid 324 and (name N or name CA or name C or name O \ or name CB )) or resid 325 through 345 or (resid 346 and (name N or name CA or n \ ame C or name O or name CB )) or resid 347 through 368 or (resid 369 and (name N \ or name CA or name C or name O or name CB )) or resid 370 through 385 or (resid \ 386 and (name N or name CA or name C or name O or name CB )) or resid 387 throu \ gh 402 or (resid 403 and (name N or name CA or name C or name O or name CB )) or \ (resid 404 through 406 and (name N or name CA or name C or name O or name CB )) \ or resid 407 or (resid 408 and (name N or name CA or name C or name O or name C \ B )) or resid 409 through 423 or (resid 424 and (name N or name CA or name C or \ name O or name CB )) or resid 425 through 427 or (resid 428 and (name N or name \ CA or name C or name O or name CB )) or resid 429 through 438 or (resid 439 and \ (name N or name CA or name C or name O or name CB )) or resid 440 or (resid 441 \ through 442 and (name N or name CA or name C or name O or name CB )) or resid 44 \ 3 or (resid 444 through 445 and (name N or name CA or name C or name O or name C \ B )) or resid 446 through 461 or (resid 462 and (name N or name CA or name C or \ name O or name CB )) or resid 463 through 508 or (resid 509 and (name N or name \ CA or name C or name O or name CB )) or resid 510 through 531 or (resid 532 and \ (name N or name CA or name C or name O or name CB )) or resid 533 through 536 or \ (resid 537 and (name N or name CA or name C or name O or name CB )) or resid 53 \ 8 through 556 or (resid 557 through 558 and (name N or name CA or name C or name \ O or name CB )) or resid 559 through 568 or (resid 569 through 572 and (name N \ or name CA or name C or name O or name CB )) or resid 573 through 612 or (resid \ 613 and (name N or name CA or name C or name O or name CB )) or resid 614 throug \ h 662 or (resid 663 and (name N or name CA or name C or name O or name CB )) or \ resid 664 through 701 or (resid 702 and (name N or name CA or name C or name O o \ r name CB )) or resid 703 through 736 or (resid 737 and (name N or name CA or na \ me C or name O or name CB )) or resid 738 through 739 or (resid 740 and (name N \ or name CA or name C or name O or name CB )) or resid 741 through 744 or (resid \ 745 and (name N or name CA or name C or name O or name CB )) or resid 746 throug \ h 775 or (resid 776 and (name N or name CA or name C or name O or name CB )) or \ resid 777 through 778 or (resid 779 through 780 and (name N or name CA or name C \ or name O or name CB )) or resid 781 through 794 or (resid 795 and (name N or n \ ame CA or name C or name O or name CB )) or resid 796 through 807 or (resid 808 \ and (name N or name CA or name C or name O or name CB )) or resid 809 through 81 \ 0 or (resid 811 and (name N or name CA or name C or name O or name CB )) or resi \ d 812 through 818 or (resid 819 and (name N or name CA or name C or name O or na \ me CB )) or resid 820 through 824 or (resid 825 and (name N or name CA or name C \ or name O or name CB )) or resid 826 through 828 or (resid 855 and (name N or n \ ame CA or name C or name O or name CB )) or resid 856 through 867 or (resid 868 \ and (name N or name CA or name C or name O or name CB )) or resid 869 through 91 \ 7 or (resid 918 and (name N or name CA or name C or name O or name CB )) or resi \ d 919 through 938 or (resid 939 through 944 and (name N or name CA or name C or \ name O or name CB )) or resid 945 through 946 or (resid 947 and (name N or name \ CA or name C or name O or name CB )) or resid 948 through 963 or (resid 964 and \ (name N or name CA or name C or name O or name CB )) or resid 965 through 994 or \ (resid 995 and (name N or name CA or name C or name O or name CB )) or resid 99 \ 6 through 1013 or (resid 1014 through 1016 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1017 through 1018 or (resid 1019 through 1020 and ( \ name N or name CA or name C or name O or name CB )) or resid 1021 through 1072 o \ r (resid 1073 and (name N or name CA or name C or name O or name CB )) or resid \ 1074 through 1091 or (resid 1092 and (name N or name CA or name C or name O or n \ ame CB )) or resid 1093 through 1137 or (resid 1138 and (name N or name CA or na \ me C or name O or name CB )) or resid 1139 through 1140 or (resid 1141 through 1 \ 142 and (name N or name CA or name C or name O or name CB )) or resid 1143 throu \ gh 1145 or (resid 1146 and (name N or name CA or name C or name O or name CB )) \ or resid 1301 through 1310)) } ncs_group { reference = chain 'D' selection = chain 'E' } 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: 5.050 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: 23.450 Check model and map are aligned: 0.440 Set scattering table: 0.270 Process input model: 79.020 Find NCS groups from input model: 2.060 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6582 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 : 0.003 0.047 28401 Z= 0.181 Angle : 0.562 19.807 38775 Z= 0.289 Chirality : 0.081 1.682 4586 Planarity : 0.003 0.064 4967 Dihedral : 12.298 89.963 10334 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.03 % Allowed : 0.21 % Favored : 99.76 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.14), residues: 3574 helix: 2.41 (0.21), residues: 661 sheet: 1.04 (0.17), residues: 915 loop : -0.33 (0.14), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP X 106 HIS 0.003 0.000 HIS A 954 PHE 0.008 0.001 PHE A 592 TYR 0.008 0.001 TYR C1067 ARG 0.010 0.001 ARG B1000 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7148 Ramachandran restraints generated. 3574 Oldfield, 0 Emsley, 3574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7148 Ramachandran restraints generated. 3574 Oldfield, 0 Emsley, 3574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 422 time to evaluate : 3.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 737 ASP cc_start: 0.7064 (t0) cc_final: 0.6843 (t0) REVERT: A 807 PRO cc_start: 0.7154 (Cg_endo) cc_final: 0.6902 (Cg_exo) REVERT: A 977 LEU cc_start: 0.7897 (mm) cc_final: 0.7674 (mm) REVERT: A 993 ILE cc_start: 0.8239 (mm) cc_final: 0.7970 (mt) REVERT: A 1017 GLU cc_start: 0.7205 (tm-30) cc_final: 0.6981 (tm-30) REVERT: B 583 GLU cc_start: 0.6752 (tp30) cc_final: 0.6498 (tp30) REVERT: B 584 ILE cc_start: 0.6759 (mp) cc_final: 0.5930 (mp) REVERT: B 858 LEU cc_start: 0.8371 (mt) cc_final: 0.8150 (mp) REVERT: B 1127 ASP cc_start: 0.7201 (t70) cc_final: 0.6989 (t0) REVERT: C 574 ASP cc_start: 0.6884 (t70) cc_final: 0.6313 (t0) REVERT: C 655 TYR cc_start: 0.7404 (t80) cc_final: 0.6897 (t80) REVERT: C 825 LYS cc_start: 0.8819 (mtpp) cc_final: 0.8477 (mmtm) REVERT: C 1019 ARG cc_start: 0.7230 (tpt170) cc_final: 0.6891 (tpt-90) REVERT: C 1130 ILE cc_start: 0.7878 (mt) cc_final: 0.7648 (mt) REVERT: Y 4 MET cc_start: 0.4428 (ptp) cc_final: 0.2917 (tmm) outliers start: 1 outliers final: 0 residues processed: 422 average time/residue: 0.3839 time to fit residues: 256.7470 Evaluate side-chains 375 residues out of total 3152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 375 time to evaluate : 3.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 304 optimal weight: 0.0370 chunk 273 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 93 optimal weight: 0.3980 chunk 184 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 282 optimal weight: 0.4980 chunk 109 optimal weight: 0.0050 chunk 172 optimal weight: 0.6980 chunk 210 optimal weight: 5.9990 chunk 327 optimal weight: 0.8980 overall best weight: 0.3272 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN B 343 ASN ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 787 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 ASN Y 79 GLN ** Z 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28401 Z= 0.178 Angle : 0.559 11.592 38775 Z= 0.294 Chirality : 0.046 0.400 4586 Planarity : 0.004 0.053 4967 Dihedral : 4.816 58.923 4637 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.63 % Allowed : 6.21 % Favored : 93.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.14), residues: 3574 helix: 2.31 (0.21), residues: 662 sheet: 0.97 (0.17), residues: 878 loop : -0.29 (0.14), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP X 106 HIS 0.003 0.001 HIS C 207 PHE 0.024 0.001 PHE A 643 TYR 0.023 0.001 TYR C1067 ARG 0.005 0.000 ARG C 328 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7148 Ramachandran restraints generated. 3574 Oldfield, 0 Emsley, 3574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7148 Ramachandran restraints generated. 3574 Oldfield, 0 Emsley, 3574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 399 time to evaluate : 2.973 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 656 VAL cc_start: 0.8477 (t) cc_final: 0.8171 (m) REVERT: A 993 ILE cc_start: 0.8335 (mm) cc_final: 0.8062 (mm) REVERT: B 52 GLN cc_start: 0.7229 (tm-30) cc_final: 0.7029 (tm-30) REVERT: B 92 PHE cc_start: 0.8135 (t80) cc_final: 0.7712 (t80) REVERT: B 547 LYS cc_start: 0.7788 (tptp) cc_final: 0.7488 (tptp) REVERT: B 703 ASN cc_start: 0.7315 (p0) cc_final: 0.6980 (p0) REVERT: B 936 ASP cc_start: 0.7076 (t70) cc_final: 0.6813 (t0) REVERT: B 966 LEU cc_start: 0.8688 (tp) cc_final: 0.8479 (tp) REVERT: C 266 TYR cc_start: 0.7756 (m-80) cc_final: 0.7190 (m-10) REVERT: C 712 ILE cc_start: 0.7562 (mt) cc_final: 0.7137 (tt) REVERT: C 878 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8021 (mt) REVERT: C 902 MET cc_start: 0.7511 (tpt) cc_final: 0.7068 (tpt) REVERT: C 934 ILE cc_start: 0.8176 (mm) cc_final: 0.7956 (tt) REVERT: C 1133 VAL cc_start: 0.7990 (m) cc_final: 0.7747 (m) outliers start: 18 outliers final: 10 residues processed: 404 average time/residue: 0.3822 time to fit residues: 249.6587 Evaluate side-chains 384 residues out of total 3152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 373 time to evaluate : 2.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 954 HIS Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain X residue 109 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 182 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 chunk 272 optimal weight: 0.0370 chunk 223 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 328 optimal weight: 6.9990 chunk 354 optimal weight: 1.9990 chunk 292 optimal weight: 0.9980 chunk 325 optimal weight: 10.0000 chunk 111 optimal weight: 4.9990 chunk 263 optimal weight: 0.7980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 544 ASN ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B 914 ASN B 955 ASN C 422 ASN C 926 GLN ** Z 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 28401 Z= 0.241 Angle : 0.556 9.062 38775 Z= 0.291 Chirality : 0.046 0.262 4586 Planarity : 0.004 0.049 4967 Dihedral : 4.706 58.105 4637 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.47 % Allowed : 8.93 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.14), residues: 3574 helix: 1.94 (0.20), residues: 678 sheet: 0.83 (0.17), residues: 895 loop : -0.45 (0.14), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP X 106 HIS 0.007 0.001 HIS B1058 PHE 0.024 0.002 PHE A1089 TYR 0.027 0.001 TYR C1067 ARG 0.007 0.000 ARG C 328 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7148 Ramachandran restraints generated. 3574 Oldfield, 0 Emsley, 3574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7148 Ramachandran restraints generated. 3574 Oldfield, 0 Emsley, 3574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 3152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 410 time to evaluate : 2.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 541 PHE cc_start: 0.7627 (p90) cc_final: 0.7317 (p90) REVERT: A 655 TYR cc_start: 0.6788 (t80) cc_final: 0.6436 (t80) REVERT: A 656 VAL cc_start: 0.8595 (t) cc_final: 0.8321 (m) REVERT: A 821 LEU cc_start: 0.7772 (mp) cc_final: 0.7472 (mp) REVERT: A 993 ILE cc_start: 0.8347 (mm) cc_final: 0.8027 (mt) REVERT: A 1005 GLN cc_start: 0.7960 (tp-100) cc_final: 0.7752 (tp40) REVERT: B 52 GLN cc_start: 0.7315 (tm-30) cc_final: 0.7104 (tm-30) REVERT: B 547 LYS cc_start: 0.7943 (tptp) cc_final: 0.7616 (tptp) REVERT: B 936 ASP cc_start: 0.7140 (t70) cc_final: 0.6923 (t0) REVERT: C 287 ASP cc_start: 0.6792 (t0) cc_final: 0.6428 (t70) REVERT: C 878 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8208 (mt) REVERT: C 902 MET cc_start: 0.7524 (tpt) cc_final: 0.7132 (tpt) REVERT: C 961 THR cc_start: 0.8673 (t) cc_final: 0.8336 (p) REVERT: C 1139 ASP cc_start: 0.7073 (t70) cc_final: 0.6650 (t70) outliers start: 42 outliers final: 34 residues processed: 429 average time/residue: 0.3870 time to fit residues: 268.5146 Evaluate side-chains 424 residues out of total 3152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 389 time to evaluate : 2.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 954 HIS Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain X residue 109 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 324 optimal weight: 3.9990 chunk 246 optimal weight: 8.9990 chunk 170 optimal weight: 0.9980 chunk 36 optimal weight: 10.0000 chunk 156 optimal weight: 1.9990 chunk 220 optimal weight: 4.9990 chunk 329 optimal weight: 0.0270 chunk 348 optimal weight: 50.0000 chunk 172 optimal weight: 0.6980 chunk 312 optimal weight: 0.9980 chunk 94 optimal weight: 0.6980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6767 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 28401 Z= 0.240 Angle : 0.542 8.716 38775 Z= 0.285 Chirality : 0.045 0.350 4586 Planarity : 0.004 0.046 4967 Dihedral : 4.722 57.360 4637 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.99 % Allowed : 10.85 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.14), residues: 3574 helix: 1.87 (0.20), residues: 674 sheet: 0.76 (0.17), residues: 895 loop : -0.49 (0.14), residues: 2005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP X 106 HIS 0.006 0.001 HIS B1058 PHE 0.023 0.001 PHE C 92 TYR 0.025 0.001 TYR C1067 ARG 0.005 0.000 ARG B 577 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7148 Ramachandran restraints generated. 3574 Oldfield, 0 Emsley, 3574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7148 Ramachandran restraints generated. 3574 Oldfield, 0 Emsley, 3574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 407 time to evaluate : 2.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 535 LYS cc_start: 0.7484 (mtmm) cc_final: 0.7280 (pttp) REVERT: A 541 PHE cc_start: 0.7661 (p90) cc_final: 0.7258 (p90) REVERT: A 656 VAL cc_start: 0.8483 (t) cc_final: 0.8263 (m) REVERT: A 776 LYS cc_start: 0.8226 (tttm) cc_final: 0.7928 (ttmm) REVERT: A 821 LEU cc_start: 0.7761 (mp) cc_final: 0.7549 (mp) REVERT: A 993 ILE cc_start: 0.8391 (mm) cc_final: 0.8064 (mt) REVERT: A 1005 GLN cc_start: 0.7992 (tp40) cc_final: 0.7739 (tp40) REVERT: A 1010 GLN cc_start: 0.8106 (mm-40) cc_final: 0.7870 (mm-40) REVERT: A 1139 ASP cc_start: 0.7779 (OUTLIER) cc_final: 0.7405 (p0) REVERT: B 52 GLN cc_start: 0.7339 (tm-30) cc_final: 0.7111 (tm-30) REVERT: B 547 LYS cc_start: 0.7941 (tptp) cc_final: 0.7607 (tptp) REVERT: B 703 ASN cc_start: 0.7458 (p0) cc_final: 0.6841 (p0) REVERT: B 709 ASN cc_start: 0.6390 (OUTLIER) cc_final: 0.6173 (m110) REVERT: B 931 ILE cc_start: 0.7577 (mm) cc_final: 0.7134 (mt) REVERT: B 961 THR cc_start: 0.8387 (OUTLIER) cc_final: 0.8131 (t) REVERT: C 712 ILE cc_start: 0.7569 (mt) cc_final: 0.6992 (tt) REVERT: C 750 SER cc_start: 0.8222 (t) cc_final: 0.7881 (m) REVERT: C 878 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8207 (mt) REVERT: C 902 MET cc_start: 0.7551 (tpt) cc_final: 0.7155 (tpt) REVERT: C 961 THR cc_start: 0.8619 (t) cc_final: 0.8306 (p) REVERT: C 1029 MET cc_start: 0.8604 (tpp) cc_final: 0.8296 (tpp) REVERT: C 1068 VAL cc_start: 0.6637 (t) cc_final: 0.5635 (p) REVERT: Y 4 MET cc_start: 0.4577 (ptp) cc_final: 0.3102 (tpt) outliers start: 57 outliers final: 40 residues processed: 432 average time/residue: 0.3897 time to fit residues: 273.2371 Evaluate side-chains 437 residues out of total 3152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 393 time to evaluate : 2.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 954 HIS Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain X residue 109 VAL Chi-restraints excluded: chain Z residue 43 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 290 optimal weight: 0.7980 chunk 198 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 259 optimal weight: 0.7980 chunk 143 optimal weight: 4.9990 chunk 297 optimal weight: 0.9990 chunk 241 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 178 optimal weight: 0.7980 chunk 313 optimal weight: 7.9990 chunk 88 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1125 ASN ** Z 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 28401 Z= 0.289 Angle : 0.563 9.115 38775 Z= 0.297 Chirality : 0.046 0.447 4586 Planarity : 0.004 0.048 4967 Dihedral : 4.847 56.318 4637 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.86 % Allowed : 11.03 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.14), residues: 3574 helix: 1.74 (0.20), residues: 672 sheet: 0.68 (0.17), residues: 920 loop : -0.55 (0.14), residues: 1982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP X 106 HIS 0.007 0.001 HIS B1058 PHE 0.026 0.002 PHE A 855 TYR 0.028 0.002 TYR C1067 ARG 0.005 0.000 ARG A1039 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7148 Ramachandran restraints generated. 3574 Oldfield, 0 Emsley, 3574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7148 Ramachandran restraints generated. 3574 Oldfield, 0 Emsley, 3574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 3152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 416 time to evaluate : 3.333 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: A 821 LEU cc_start: 0.7808 (mp) cc_final: 0.7555 (mp) REVERT: A 993 ILE cc_start: 0.8352 (mm) cc_final: 0.8063 (mt) REVERT: A 1005 GLN cc_start: 0.8037 (tp40) cc_final: 0.7783 (tp40) REVERT: A 1017 GLU cc_start: 0.7093 (tm-30) cc_final: 0.6815 (tm-30) REVERT: A 1031 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7617 (mt-10) REVERT: A 1139 ASP cc_start: 0.7862 (OUTLIER) cc_final: 0.7503 (p0) REVERT: B 52 GLN cc_start: 0.7388 (tm-30) cc_final: 0.7185 (tm-30) REVERT: B 552 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.8014 (mt) REVERT: B 703 ASN cc_start: 0.7514 (OUTLIER) cc_final: 0.6711 (p0) REVERT: B 709 ASN cc_start: 0.6788 (OUTLIER) cc_final: 0.6501 (m110) REVERT: B 901 GLN cc_start: 0.6487 (OUTLIER) cc_final: 0.6230 (pt0) REVERT: B 914 ASN cc_start: 0.7961 (OUTLIER) cc_final: 0.7278 (p0) REVERT: B 931 ILE cc_start: 0.7647 (mm) cc_final: 0.7218 (mt) REVERT: B 961 THR cc_start: 0.8494 (OUTLIER) cc_final: 0.8256 (t) REVERT: B 1041 ASP cc_start: 0.6820 (m-30) cc_final: 0.6580 (t70) REVERT: C 191 GLU cc_start: 0.7429 (mt-10) cc_final: 0.7195 (mt-10) REVERT: C 310 LYS cc_start: 0.8130 (ttmt) cc_final: 0.7847 (ttpt) REVERT: C 750 SER cc_start: 0.8192 (t) cc_final: 0.7757 (m) REVERT: C 878 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8258 (mt) REVERT: C 902 MET cc_start: 0.7577 (tpt) cc_final: 0.7151 (tpt) REVERT: C 923 ILE cc_start: 0.6863 (mt) cc_final: 0.6645 (tt) REVERT: C 929 SER cc_start: 0.7571 (m) cc_final: 0.7311 (t) REVERT: C 961 THR cc_start: 0.8581 (t) cc_final: 0.8285 (p) REVERT: C 1029 MET cc_start: 0.8606 (tpp) cc_final: 0.8405 (tpp) REVERT: C 1068 VAL cc_start: 0.6693 (t) cc_final: 0.5721 (p) REVERT: Y 4 MET cc_start: 0.4636 (ptp) cc_final: 0.3145 (tpt) outliers start: 82 outliers final: 52 residues processed: 460 average time/residue: 0.3815 time to fit residues: 282.8827 Evaluate side-chains 456 residues out of total 3152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 396 time to evaluate : 3.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 954 HIS Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain X residue 109 VAL Chi-restraints excluded: chain Z residue 43 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 117 optimal weight: 0.7980 chunk 314 optimal weight: 20.0000 chunk 68 optimal weight: 0.0570 chunk 204 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 349 optimal weight: 4.9990 chunk 289 optimal weight: 0.6980 chunk 161 optimal weight: 0.0010 chunk 29 optimal weight: 4.9990 chunk 115 optimal weight: 0.6980 chunk 183 optimal weight: 0.9980 overall best weight: 0.4504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 784 GLN A1135 ASN B 66 HIS B 207 HIS B 317 ASN ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1125 ASN ** Z 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6784 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28401 Z= 0.186 Angle : 0.521 9.269 38775 Z= 0.274 Chirality : 0.044 0.404 4586 Planarity : 0.004 0.047 4967 Dihedral : 4.635 56.228 4637 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.55 % Allowed : 12.39 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.14), residues: 3574 helix: 1.91 (0.20), residues: 668 sheet: 0.76 (0.17), residues: 910 loop : -0.50 (0.14), residues: 1996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP X 106 HIS 0.006 0.001 HIS B 207 PHE 0.034 0.001 PHE A 643 TYR 0.023 0.001 TYR C1067 ARG 0.009 0.000 ARG C1091 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7148 Ramachandran restraints generated. 3574 Oldfield, 0 Emsley, 3574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7148 Ramachandran restraints generated. 3574 Oldfield, 0 Emsley, 3574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 3152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 411 time to evaluate : 3.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 532 ASN cc_start: 0.7200 (p0) cc_final: 0.6859 (p0) REVERT: A 538 CYS cc_start: 0.5341 (t) cc_final: 0.5139 (t) REVERT: A 776 LYS cc_start: 0.8219 (tttm) cc_final: 0.7938 (ttmm) REVERT: A 993 ILE cc_start: 0.8325 (mm) cc_final: 0.8023 (mt) REVERT: A 1005 GLN cc_start: 0.8007 (tp40) cc_final: 0.7718 (tp40) REVERT: A 1010 GLN cc_start: 0.8071 (mm-40) cc_final: 0.7837 (mm-40) REVERT: A 1019 ARG cc_start: 0.7691 (ttm-80) cc_final: 0.7398 (ttm-80) REVERT: A 1139 ASP cc_start: 0.7859 (OUTLIER) cc_final: 0.7474 (p0) REVERT: B 52 GLN cc_start: 0.7428 (tm-30) cc_final: 0.7166 (tm-30) REVERT: B 552 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.8010 (mt) REVERT: B 658 ASN cc_start: 0.7374 (p0) cc_final: 0.7013 (p0) REVERT: B 703 ASN cc_start: 0.7450 (p0) cc_final: 0.6669 (p0) REVERT: B 931 ILE cc_start: 0.7634 (mm) cc_final: 0.7243 (mt) REVERT: B 961 THR cc_start: 0.8461 (OUTLIER) cc_final: 0.8210 (t) REVERT: C 190 ARG cc_start: 0.7142 (ttm110) cc_final: 0.6719 (mtt90) REVERT: C 191 GLU cc_start: 0.7371 (mt-10) cc_final: 0.7086 (mt-10) REVERT: C 750 SER cc_start: 0.8184 (t) cc_final: 0.7717 (m) REVERT: C 754 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8154 (mm) REVERT: C 878 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8185 (mt) REVERT: C 902 MET cc_start: 0.7533 (tpt) cc_final: 0.7171 (tpt) REVERT: C 929 SER cc_start: 0.7593 (m) cc_final: 0.7289 (t) REVERT: C 961 THR cc_start: 0.8556 (t) cc_final: 0.8234 (p) REVERT: C 1029 MET cc_start: 0.8606 (tpp) cc_final: 0.8388 (tpp) REVERT: X 68 VAL cc_start: 0.4821 (t) cc_final: 0.4448 (p) REVERT: Y 4 MET cc_start: 0.4656 (ptp) cc_final: 0.3133 (tpt) outliers start: 73 outliers final: 50 residues processed: 453 average time/residue: 0.3910 time to fit residues: 286.0235 Evaluate side-chains 453 residues out of total 3152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 398 time to evaluate : 2.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 954 HIS Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain X residue 73 ASP Chi-restraints excluded: chain X residue 109 VAL Chi-restraints excluded: chain Z residue 43 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 336 optimal weight: 6.9990 chunk 39 optimal weight: 0.0170 chunk 199 optimal weight: 0.3980 chunk 255 optimal weight: 0.6980 chunk 197 optimal weight: 0.7980 chunk 294 optimal weight: 1.9990 chunk 195 optimal weight: 0.4980 chunk 347 optimal weight: 20.0000 chunk 217 optimal weight: 0.9980 chunk 212 optimal weight: 20.0000 chunk 160 optimal weight: 0.8980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS B 207 HIS B 317 ASN ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1125 ASN ** Z 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28401 Z= 0.193 Angle : 0.520 8.431 38775 Z= 0.273 Chirality : 0.044 0.363 4586 Planarity : 0.004 0.047 4967 Dihedral : 4.575 56.445 4637 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.86 % Allowed : 13.12 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.14), residues: 3574 helix: 1.92 (0.20), residues: 667 sheet: 0.70 (0.17), residues: 915 loop : -0.49 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP X 106 HIS 0.017 0.001 HIS B 66 PHE 0.029 0.001 PHE A 643 TYR 0.023 0.001 TYR C1067 ARG 0.006 0.000 ARG C1091 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7148 Ramachandran restraints generated. 3574 Oldfield, 0 Emsley, 3574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7148 Ramachandran restraints generated. 3574 Oldfield, 0 Emsley, 3574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 3152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 415 time to evaluate : 3.168 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: A 31 SER cc_start: 0.6096 (OUTLIER) cc_final: 0.5849 (m) REVERT: A 532 ASN cc_start: 0.7222 (p0) cc_final: 0.6869 (p0) REVERT: A 538 CYS cc_start: 0.5287 (t) cc_final: 0.5072 (t) REVERT: A 776 LYS cc_start: 0.8213 (tttm) cc_final: 0.7902 (ttmm) REVERT: A 821 LEU cc_start: 0.7664 (mt) cc_final: 0.7436 (mp) REVERT: A 993 ILE cc_start: 0.8312 (mm) cc_final: 0.8008 (mt) REVERT: A 1005 GLN cc_start: 0.8021 (tp40) cc_final: 0.7795 (tp40) REVERT: A 1010 GLN cc_start: 0.8080 (mm-40) cc_final: 0.7849 (mm-40) REVERT: A 1017 GLU cc_start: 0.7108 (tm-30) cc_final: 0.6779 (tm-30) REVERT: A 1139 ASP cc_start: 0.7869 (OUTLIER) cc_final: 0.7495 (p0) REVERT: B 52 GLN cc_start: 0.7440 (tm-30) cc_final: 0.7169 (tm-30) REVERT: B 552 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.8026 (mt) REVERT: B 565 PHE cc_start: 0.7088 (p90) cc_final: 0.6858 (p90) REVERT: B 655 TYR cc_start: 0.7164 (t80) cc_final: 0.6896 (t80) REVERT: B 703 ASN cc_start: 0.7430 (p0) cc_final: 0.6621 (p0) REVERT: B 709 ASN cc_start: 0.6736 (OUTLIER) cc_final: 0.6192 (m-40) REVERT: B 914 ASN cc_start: 0.7904 (OUTLIER) cc_final: 0.7233 (p0) REVERT: B 931 ILE cc_start: 0.7669 (mm) cc_final: 0.7253 (mt) REVERT: B 961 THR cc_start: 0.8494 (OUTLIER) cc_final: 0.8250 (t) REVERT: C 190 ARG cc_start: 0.7128 (ttm110) cc_final: 0.6728 (mtt90) REVERT: C 191 GLU cc_start: 0.7414 (mt-10) cc_final: 0.7131 (mt-10) REVERT: C 750 SER cc_start: 0.8195 (t) cc_final: 0.7737 (m) REVERT: C 754 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8140 (mm) REVERT: C 878 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8204 (mt) REVERT: C 902 MET cc_start: 0.7538 (tpt) cc_final: 0.7162 (tpt) REVERT: C 929 SER cc_start: 0.7606 (m) cc_final: 0.7310 (t) REVERT: C 961 THR cc_start: 0.8555 (t) cc_final: 0.8246 (p) REVERT: C 1029 MET cc_start: 0.8605 (tpp) cc_final: 0.8398 (tpp) REVERT: X 68 VAL cc_start: 0.4829 (t) cc_final: 0.4447 (p) REVERT: Y 4 MET cc_start: 0.4676 (ptp) cc_final: 0.3141 (tpt) outliers start: 82 outliers final: 65 residues processed: 460 average time/residue: 0.3839 time to fit residues: 283.7157 Evaluate side-chains 483 residues out of total 3152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 410 time to evaluate : 2.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 954 HIS Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 969 LYS Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain X residue 73 ASP Chi-restraints excluded: chain X residue 109 VAL Chi-restraints excluded: chain Z residue 43 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 215 optimal weight: 0.9980 chunk 138 optimal weight: 6.9990 chunk 207 optimal weight: 0.6980 chunk 104 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 221 optimal weight: 5.9990 chunk 237 optimal weight: 6.9990 chunk 172 optimal weight: 0.9980 chunk 32 optimal weight: 7.9990 chunk 273 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 207 HIS B 317 ASN ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1125 ASN ** Z 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 28401 Z= 0.291 Angle : 0.561 10.379 38775 Z= 0.295 Chirality : 0.046 0.393 4586 Planarity : 0.004 0.048 4967 Dihedral : 4.725 57.063 4637 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.76 % Allowed : 13.82 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.14), residues: 3574 helix: 1.72 (0.20), residues: 670 sheet: 0.58 (0.16), residues: 921 loop : -0.59 (0.14), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP X 106 HIS 0.027 0.001 HIS B 66 PHE 0.031 0.002 PHE B 65 TYR 0.027 0.001 TYR C1067 ARG 0.006 0.000 ARG C1091 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7148 Ramachandran restraints generated. 3574 Oldfield, 0 Emsley, 3574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7148 Ramachandran restraints generated. 3574 Oldfield, 0 Emsley, 3574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 3152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 413 time to evaluate : 2.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 SER cc_start: 0.6087 (OUTLIER) cc_final: 0.5578 (p) REVERT: A 532 ASN cc_start: 0.7278 (p0) cc_final: 0.6927 (p0) REVERT: A 776 LYS cc_start: 0.8236 (tttm) cc_final: 0.7951 (ttmm) REVERT: A 821 LEU cc_start: 0.7717 (mt) cc_final: 0.7506 (mp) REVERT: A 993 ILE cc_start: 0.8357 (mm) cc_final: 0.8072 (mt) REVERT: A 1005 GLN cc_start: 0.8031 (tp40) cc_final: 0.7786 (tp40) REVERT: A 1017 GLU cc_start: 0.7120 (tm-30) cc_final: 0.6834 (tm-30) REVERT: A 1019 ARG cc_start: 0.7759 (ttm-80) cc_final: 0.7492 (ttm-80) REVERT: B 52 GLN cc_start: 0.7486 (tm-30) cc_final: 0.7222 (tm-30) REVERT: B 81 ASN cc_start: 0.7819 (OUTLIER) cc_final: 0.7511 (m-40) REVERT: B 552 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8033 (mt) REVERT: B 655 TYR cc_start: 0.7231 (t80) cc_final: 0.6941 (t80) REVERT: B 703 ASN cc_start: 0.7473 (OUTLIER) cc_final: 0.6614 (p0) REVERT: B 709 ASN cc_start: 0.6966 (OUTLIER) cc_final: 0.6584 (m-40) REVERT: B 914 ASN cc_start: 0.7959 (OUTLIER) cc_final: 0.7293 (p0) REVERT: B 931 ILE cc_start: 0.7664 (mm) cc_final: 0.7266 (mt) REVERT: B 961 THR cc_start: 0.8537 (OUTLIER) cc_final: 0.8306 (t) REVERT: C 190 ARG cc_start: 0.7131 (ttm110) cc_final: 0.6920 (mtt90) REVERT: C 191 GLU cc_start: 0.7473 (mt-10) cc_final: 0.7177 (mt-10) REVERT: C 287 ASP cc_start: 0.6723 (t0) cc_final: 0.6415 (t70) REVERT: C 750 SER cc_start: 0.8236 (t) cc_final: 0.7761 (m) REVERT: C 754 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8120 (mm) REVERT: C 878 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8271 (mt) REVERT: C 902 MET cc_start: 0.7556 (tpt) cc_final: 0.7193 (tpt) REVERT: C 923 ILE cc_start: 0.6920 (mt) cc_final: 0.6673 (tt) REVERT: C 929 SER cc_start: 0.7605 (m) cc_final: 0.7304 (t) REVERT: C 961 THR cc_start: 0.8568 (t) cc_final: 0.8254 (p) REVERT: C 981 PHE cc_start: 0.7205 (m-80) cc_final: 0.6959 (m-10) REVERT: C 1029 MET cc_start: 0.8612 (tpp) cc_final: 0.8409 (tpp) REVERT: X 68 VAL cc_start: 0.4913 (t) cc_final: 0.4540 (p) REVERT: Y 4 MET cc_start: 0.4727 (ptp) cc_final: 0.3231 (tpt) outliers start: 79 outliers final: 63 residues processed: 451 average time/residue: 0.3846 time to fit residues: 279.2453 Evaluate side-chains 479 residues out of total 3152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 407 time to evaluate : 2.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 954 HIS Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 969 LYS Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain X residue 73 ASP Chi-restraints excluded: chain X residue 109 VAL Chi-restraints excluded: chain Z residue 43 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 316 optimal weight: 0.5980 chunk 333 optimal weight: 2.9990 chunk 304 optimal weight: 0.8980 chunk 324 optimal weight: 20.0000 chunk 195 optimal weight: 0.0470 chunk 141 optimal weight: 50.0000 chunk 254 optimal weight: 0.7980 chunk 99 optimal weight: 0.5980 chunk 292 optimal weight: 0.9980 chunk 306 optimal weight: 4.9990 chunk 323 optimal weight: 10.0000 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 317 ASN ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN C 901 GLN ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1125 ASN ** Z 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 28401 Z= 0.217 Angle : 0.543 10.170 38775 Z= 0.284 Chirality : 0.045 0.381 4586 Planarity : 0.004 0.048 4967 Dihedral : 4.664 56.624 4637 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.65 % Allowed : 14.31 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.00 % 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: 0.29 (0.14), residues: 3574 helix: 1.80 (0.20), residues: 671 sheet: 0.65 (0.17), residues: 908 loop : -0.59 (0.14), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP X 106 HIS 0.006 0.001 HIS B 207 PHE 0.029 0.001 PHE A 643 TYR 0.024 0.001 TYR C1067 ARG 0.005 0.000 ARG C1091 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7148 Ramachandran restraints generated. 3574 Oldfield, 0 Emsley, 3574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7148 Ramachandran restraints generated. 3574 Oldfield, 0 Emsley, 3574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 3152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 409 time to evaluate : 3.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 SER cc_start: 0.6117 (OUTLIER) cc_final: 0.5898 (m) REVERT: A 206 LYS cc_start: 0.7933 (tptt) cc_final: 0.7697 (tptt) REVERT: A 532 ASN cc_start: 0.7218 (p0) cc_final: 0.6857 (p0) REVERT: A 539 VAL cc_start: 0.7783 (m) cc_final: 0.7485 (p) REVERT: A 649 CYS cc_start: 0.5449 (t) cc_final: 0.5035 (t) REVERT: A 776 LYS cc_start: 0.8219 (tttm) cc_final: 0.7930 (ttmm) REVERT: A 821 LEU cc_start: 0.7694 (mt) cc_final: 0.7454 (mp) REVERT: A 988 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.6473 (pm20) REVERT: A 993 ILE cc_start: 0.8347 (mm) cc_final: 0.8030 (mt) REVERT: A 1005 GLN cc_start: 0.8034 (tp40) cc_final: 0.7745 (tp40) REVERT: A 1017 GLU cc_start: 0.7105 (tm-30) cc_final: 0.6836 (tm-30) REVERT: A 1019 ARG cc_start: 0.7739 (ttm-80) cc_final: 0.7505 (ttm-80) REVERT: A 1031 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7649 (mt-10) REVERT: A 1139 ASP cc_start: 0.7876 (OUTLIER) cc_final: 0.7506 (p0) REVERT: B 52 GLN cc_start: 0.7465 (tm-30) cc_final: 0.7203 (tm-30) REVERT: B 81 ASN cc_start: 0.7854 (OUTLIER) cc_final: 0.7560 (m-40) REVERT: B 552 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8061 (mt) REVERT: B 584 ILE cc_start: 0.7227 (mp) cc_final: 0.6865 (pt) REVERT: B 655 TYR cc_start: 0.7192 (t80) cc_final: 0.6918 (t80) REVERT: B 703 ASN cc_start: 0.7439 (OUTLIER) cc_final: 0.6594 (p0) REVERT: B 709 ASN cc_start: 0.6976 (OUTLIER) cc_final: 0.6632 (m-40) REVERT: B 804 GLN cc_start: 0.7796 (mm-40) cc_final: 0.7493 (mm-40) REVERT: B 878 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7242 (mm) REVERT: B 931 ILE cc_start: 0.7676 (mm) cc_final: 0.7288 (mt) REVERT: B 961 THR cc_start: 0.8515 (t) cc_final: 0.8286 (t) REVERT: B 969 LYS cc_start: 0.8034 (mtpp) cc_final: 0.7774 (mtpp) REVERT: C 190 ARG cc_start: 0.7099 (ttm110) cc_final: 0.6876 (mtt90) REVERT: C 750 SER cc_start: 0.8201 (t) cc_final: 0.7791 (m) REVERT: C 878 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8222 (mt) REVERT: C 902 MET cc_start: 0.7543 (tpt) cc_final: 0.7180 (tpt) REVERT: C 929 SER cc_start: 0.7606 (m) cc_final: 0.7300 (t) REVERT: C 961 THR cc_start: 0.8547 (t) cc_final: 0.8236 (p) REVERT: X 68 VAL cc_start: 0.5024 (t) cc_final: 0.4615 (p) REVERT: Y 4 MET cc_start: 0.4750 (ptp) cc_final: 0.3253 (tpt) outliers start: 76 outliers final: 58 residues processed: 449 average time/residue: 0.3787 time to fit residues: 273.8470 Evaluate side-chains 480 residues out of total 3152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 413 time to evaluate : 2.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 954 HIS Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain X residue 73 ASP Chi-restraints excluded: chain X residue 109 VAL Chi-restraints excluded: chain Z residue 43 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 212 optimal weight: 8.9990 chunk 342 optimal weight: 0.9990 chunk 209 optimal weight: 3.9990 chunk 162 optimal weight: 0.7980 chunk 238 optimal weight: 4.9990 chunk 359 optimal weight: 30.0000 chunk 331 optimal weight: 9.9990 chunk 286 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 221 optimal weight: 5.9990 chunk 175 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS B 66 HIS B 207 HIS ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 ASN C 644 GLN C 901 GLN ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 53 ASN ** Z 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.123 28401 Z= 0.467 Angle : 0.649 9.624 38775 Z= 0.343 Chirality : 0.050 0.427 4586 Planarity : 0.005 0.049 4967 Dihedral : 5.130 57.487 4637 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.65 % Allowed : 14.86 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.00 % 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: -0.11 (0.14), residues: 3574 helix: 1.22 (0.20), residues: 675 sheet: 0.37 (0.17), residues: 929 loop : -0.75 (0.14), residues: 1970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP X 106 HIS 0.009 0.001 HIS B1058 PHE 0.042 0.002 PHE A 643 TYR 0.035 0.002 TYR C1067 ARG 0.013 0.001 ARG C 328 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7148 Ramachandran restraints generated. 3574 Oldfield, 0 Emsley, 3574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7148 Ramachandran restraints generated. 3574 Oldfield, 0 Emsley, 3574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 3152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 423 time to evaluate : 3.031 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: A 31 SER cc_start: 0.6451 (OUTLIER) cc_final: 0.6204 (m) REVERT: A 296 LEU cc_start: 0.8088 (tp) cc_final: 0.7887 (tt) REVERT: A 537 LYS cc_start: 0.8200 (ptmt) cc_final: 0.7829 (ptmm) REVERT: A 649 CYS cc_start: 0.5630 (t) cc_final: 0.5241 (t) REVERT: A 821 LEU cc_start: 0.7778 (mt) cc_final: 0.7458 (mp) REVERT: A 993 ILE cc_start: 0.8363 (mm) cc_final: 0.8088 (mt) REVERT: A 1005 GLN cc_start: 0.8063 (tp40) cc_final: 0.7786 (tp40) REVERT: A 1017 GLU cc_start: 0.7075 (tm-30) cc_final: 0.6868 (tm-30) REVERT: A 1019 ARG cc_start: 0.7778 (ttm-80) cc_final: 0.7464 (ttm-80) REVERT: B 28 TYR cc_start: 0.8185 (m-10) cc_final: 0.7982 (m-80) REVERT: B 52 GLN cc_start: 0.7512 (tm-30) cc_final: 0.7267 (tm-30) REVERT: B 552 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8084 (mt) REVERT: B 655 TYR cc_start: 0.7256 (t80) cc_final: 0.7009 (t80) REVERT: B 703 ASN cc_start: 0.7429 (OUTLIER) cc_final: 0.6469 (p0) REVERT: B 878 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.7022 (mt) REVERT: B 914 ASN cc_start: 0.8020 (OUTLIER) cc_final: 0.7379 (p0) REVERT: B 931 ILE cc_start: 0.7655 (mm) cc_final: 0.7315 (mt) REVERT: B 969 LYS cc_start: 0.8106 (mtpp) cc_final: 0.7860 (mtpp) REVERT: C 190 ARG cc_start: 0.7107 (ttm110) cc_final: 0.6892 (mtt90) REVERT: C 266 TYR cc_start: 0.7412 (m-80) cc_final: 0.7056 (m-10) REVERT: C 574 ASP cc_start: 0.7376 (t0) cc_final: 0.7150 (t0) REVERT: C 740 MET cc_start: 0.6930 (tpp) cc_final: 0.6544 (tpp) REVERT: C 750 SER cc_start: 0.8248 (t) cc_final: 0.7880 (m) REVERT: C 869 MET cc_start: 0.8256 (mtp) cc_final: 0.7987 (mtt) REVERT: C 902 MET cc_start: 0.7581 (tpt) cc_final: 0.7202 (tpt) REVERT: C 923 ILE cc_start: 0.6969 (mt) cc_final: 0.6728 (tt) REVERT: C 929 SER cc_start: 0.7556 (m) cc_final: 0.7264 (t) REVERT: C 961 THR cc_start: 0.8585 (t) cc_final: 0.8288 (p) REVERT: C 993 ILE cc_start: 0.8653 (mt) cc_final: 0.8442 (tt) REVERT: X 68 VAL cc_start: 0.5155 (t) cc_final: 0.4763 (p) REVERT: Y 4 MET cc_start: 0.4993 (ptp) cc_final: 0.3394 (tpt) outliers start: 76 outliers final: 58 residues processed: 466 average time/residue: 0.3822 time to fit residues: 283.6566 Evaluate side-chains 469 residues out of total 3152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 406 time to evaluate : 3.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 954 HIS Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain X residue 73 ASP Chi-restraints excluded: chain X residue 109 VAL Chi-restraints excluded: chain Z residue 43 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 227 optimal weight: 0.5980 chunk 305 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 chunk 264 optimal weight: 0.5980 chunk 42 optimal weight: 30.0000 chunk 79 optimal weight: 0.7980 chunk 286 optimal weight: 0.5980 chunk 120 optimal weight: 0.0770 chunk 294 optimal weight: 0.5980 chunk 36 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 641 ASN A 901 GLN B 207 HIS ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 914 ASN C 66 HIS C 314 GLN C 607 GLN C 901 GLN ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.213055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.156709 restraints weight = 45897.806| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 3.10 r_work: 0.3636 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 28401 Z= 0.203 Angle : 0.556 10.337 38775 Z= 0.292 Chirality : 0.046 0.819 4586 Planarity : 0.004 0.060 4967 Dihedral : 4.881 58.565 4637 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.27 % Allowed : 14.93 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.00 % 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: 0.14 (0.14), residues: 3574 helix: 1.73 (0.20), residues: 659 sheet: 0.55 (0.17), residues: 919 loop : -0.69 (0.14), residues: 1996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP X 106 HIS 0.020 0.001 HIS B 66 PHE 0.039 0.001 PHE A 643 TYR 0.023 0.001 TYR C1067 ARG 0.006 0.000 ARG C 328 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7979.72 seconds wall clock time: 143 minutes 37.36 seconds (8617.36 seconds total)