Starting phenix.real_space_refine on Sat Jul 27 04:52:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xod_33345/07_2024/7xod_33345.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xod_33345/07_2024/7xod_33345.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xod_33345/07_2024/7xod_33345.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xod_33345/07_2024/7xod_33345.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xod_33345/07_2024/7xod_33345.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xod_33345/07_2024/7xod_33345.cif" } resolution = 3.27 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= 0.022 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 151 5.16 5 C 22977 2.51 5 N 5979 2.21 5 O 7066 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 ARG 237": "NH1" <-> "NH2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A ARG 346": "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 GLU 471": "OE1" <-> "OE2" Residue "A ARG 493": "NH1" <-> "NH2" Residue "A ARG 498": "NH1" <-> "NH2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A ARG 577": "NH1" <-> "NH2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A ARG 765": "NH1" <-> "NH2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A GLU 868": "OE1" <-> "OE2" Residue "A ARG 905": "NH1" <-> "NH2" Residue "A ARG 983": "NH1" <-> "NH2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A ARG 995": "NH1" <-> "NH2" Residue "A ARG 1000": "NH1" <-> "NH2" Residue "A ARG 1014": "NH1" <-> "NH2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A ARG 1019": "NH1" <-> "NH2" Residue "A ARG 1039": "NH1" <-> "NH2" Residue "A ARG 1091": "NH1" <-> "NH2" Residue "A GLU 1111": "OE1" <-> "OE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B ARG 44": "NH1" <-> "NH2" Residue "B GLU 96": "OE1" <-> "OE2" Residue "B ARG 102": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 273": "NH1" <-> "NH2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B ARG 457": "NH1" <-> "NH2" Residue "B ARG 466": "NH1" <-> "NH2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "B ARG 493": "NH1" <-> "NH2" Residue "B ARG 498": "NH1" <-> "NH2" Residue "B ARG 567": "NH1" <-> "NH2" Residue "B ARG 577": "NH1" <-> "NH2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B ARG 765": "NH1" <-> "NH2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B GLU 868": "OE1" <-> "OE2" Residue "B ARG 905": "NH1" <-> "NH2" Residue "B ARG 983": "NH1" <-> "NH2" Residue "B GLU 990": "OE1" <-> "OE2" Residue "B ARG 995": "NH1" <-> "NH2" Residue "B ARG 1000": "NH1" <-> "NH2" Residue "B ARG 1014": "NH1" <-> "NH2" Residue "B ARG 1019": "NH1" <-> "NH2" Residue "B ARG 1039": "NH1" <-> "NH2" Residue "B ARG 1091": "NH1" <-> "NH2" Residue "C ARG 34": "NH1" <-> "NH2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 GLU 406": "OE1" <-> "OE2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "C GLU 471": "OE1" <-> "OE2" 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 583": "OE1" <-> "OE2" Residue "C GLU 619": "OE1" <-> "OE2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C GLU 702": "OE1" <-> "OE2" Residue "C ARG 765": "NH1" <-> "NH2" Residue "C ARG 815": "NH1" <-> "NH2" 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 GLU 1017": "OE1" <-> "OE2" Residue "C ARG 1019": "NH1" <-> "NH2" Residue "C ARG 1039": "NH1" <-> "NH2" Residue "C ARG 1091": "NH1" <-> "NH2" Residue "C GLU 1092": "OE1" <-> "OE2" Residue "X GLU 10": "OE1" <-> "OE2" Residue "X GLU 46": "OE1" <-> "OE2" Residue "X ARG 50": "NH1" <-> "NH2" Residue "X ARG 67": "NH1" <-> "NH2" Residue "X GLU 74": "OE1" <-> "OE2" Residue "X ARG 87": "NH1" <-> "NH2" Residue "Y ARG 18": "NH1" <-> "NH2" Residue "Y ARG 24": "NH1" <-> "NH2" Residue "Y GLU 55": "OE1" <-> "OE2" Residue "Y ARG 61": "NH1" <-> "NH2" Residue "Y GLU 81": "OE1" <-> "OE2" Residue "Y GLU 123": "OE1" <-> "OE2" Residue "Y ARG 142": "NH1" <-> "NH2" Residue "Y GLU 161": "OE1" <-> "OE2" Residue "Y GLU 165": "OE1" <-> "OE2" Residue "Y GLU 187": "OE1" <-> "OE2" Residue "Y ARG 211": "NH1" <-> "NH2" Residue "Y GLU 213": "OE1" <-> "OE2" 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 GLU 55": "OE1" <-> "OE2" Residue "Z ARG 61": "NH1" <-> "NH2" Residue "Z ARG 62": "NH1" <-> "NH2" Residue "Z ARG 81": "NH1" <-> "NH2" Residue "Z GLU 98": "OE1" <-> "OE2" Residue "U ARG 38": "NH1" <-> "NH2" Residue "U ARG 67": "NH1" <-> "NH2" Residue "U GLU 74": "OE1" <-> "OE2" Residue "U GLU 82": "OE1" <-> "OE2" Residue "U ARG 87": "NH1" <-> "NH2" Residue "U GLU 107": "OE1" <-> "OE2" Residue "U GLU 222": "OE1" <-> "OE2" Residue "V ARG 18": "NH1" <-> "NH2" Residue "V ARG 24": "NH1" <-> "NH2" Residue "V ARG 61": "NH1" <-> "NH2" Residue "V GLU 105": "OE1" <-> "OE2" Residue "V ARG 108": "NH1" <-> "NH2" Residue "V ARG 142": "NH1" <-> "NH2" Residue "V GLU 161": "OE1" <-> "OE2" Residue "V ARG 211": "NH1" <-> "NH2" Residue "V GLU 213": "OE1" <-> "OE2" Residue "W ARG 28": "NH1" <-> "NH2" Residue "W ARG 36": "NH1" <-> "NH2" Residue "W ARG 40": "NH1" <-> "NH2" Residue "W ARG 47": "NH1" <-> "NH2" Residue "W GLU 53": "OE1" <-> "OE2" Residue "W ARG 54": "NH1" <-> "NH2" Residue "W ARG 61": "NH1" <-> "NH2" Residue "W ARG 62": "NH1" <-> "NH2" Residue "W ARG 76": "NH1" <-> "NH2" Residue "W ARG 81": "NH1" <-> "NH2" Residue "R GLU 10": "OE1" <-> "OE2" Residue "R GLU 46": "OE1" <-> "OE2" Residue "R ARG 50": "NH1" <-> "NH2" Residue "R ARG 67": "NH1" <-> "NH2" Residue "R GLU 74": "OE1" <-> "OE2" Residue "R GLU 82": "OE1" <-> "OE2" Residue "R ARG 87": "NH1" <-> "NH2" Residue "R GLU 107": "OE1" <-> "OE2" Residue "S ARG 18": "NH1" <-> "NH2" Residue "S ARG 24": "NH1" <-> "NH2" Residue "S ARG 61": "NH1" <-> "NH2" Residue "S ARG 108": "NH1" <-> "NH2" Residue "S ARG 142": "NH1" <-> "NH2" Residue "S GLU 161": "OE1" <-> "OE2" Residue "S GLU 165": "OE1" <-> "OE2" Residue "S GLU 187": "OE1" <-> "OE2" Residue "S ARG 211": "NH1" <-> "NH2" Residue "T ARG 28": "NH1" <-> "NH2" Residue "T ARG 36": "NH1" <-> "NH2" Residue "T ARG 40": "NH1" <-> "NH2" Residue "T ARG 47": "NH1" <-> "NH2" Residue "T ARG 54": "NH1" <-> "NH2" Residue "T ARG 61": "NH1" <-> "NH2" Residue "T ARG 62": "NH1" <-> "NH2" Residue "T ARG 76": "NH1" <-> "NH2" Residue "T ARG 81": "NH1" <-> "NH2" Residue "T GLU 98": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 36173 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 7685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 7685 Classifications: {'peptide': 1026} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PTRANS': 56, 'TRANS': 969} Chain breaks: 7 Unresolved non-hydrogen bonds: 349 Unresolved non-hydrogen angles: 426 Unresolved non-hydrogen dihedrals: 291 Unresolved non-hydrogen chiralities: 22 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': 6} Unresolved non-hydrogen planarities: 183 Chain: "B" Number of atoms: 7681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 7681 Classifications: {'peptide': 1025} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 56, 'TRANS': 968} Chain breaks: 7 Unresolved non-hydrogen bonds: 345 Unresolved non-hydrogen angles: 422 Unresolved non-hydrogen dihedrals: 287 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 5, 'ASN:plan1': 5, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 186 Chain: "C" Number of atoms: 7709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7709 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 7 Unresolved non-hydrogen bonds: 307 Unresolved non-hydrogen angles: 377 Unresolved non-hydrogen dihedrals: 247 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 10, 'TYR:plan': 2, 'ASN:plan1': 9, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 191 Chain: "X" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1633 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 211} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "Y" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1622 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 201} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "Z" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 921 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "U" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1641 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 11, 'TRANS': 212} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "V" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1611 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 200} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "W" 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: "R" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1652 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 212} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "S" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1622 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 201} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "T" 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: 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 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: 19.22, per 1000 atoms: 0.53 Number of scatterers: 36173 At special positions: 0 Unit cell: (222.48, 167.272, 231.544, 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 151 16.00 O 7066 8.00 N 5979 7.00 C 22977 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, 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=1.68 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=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 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 738 " - pdb=" SG CYS A 760 " 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=2.38 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.15 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=2.23 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=2.03 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=1.88 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 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 96 " distance=2.03 Simple disulfide: pdb=" SG CYS U 150 " - pdb=" SG CYS U 206 " distance=2.03 Simple disulfide: pdb=" SG CYS V 23 " - pdb=" SG CYS V 88 " distance=2.03 Simple disulfide: pdb=" SG CYS V 134 " - pdb=" SG CYS V 194 " distance=1.99 Simple disulfide: pdb=" SG CYS W 31 " - pdb=" SG CYS W 105 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 96 " distance=2.38 Simple disulfide: pdb=" SG CYS R 150 " - pdb=" SG CYS R 206 " distance=2.03 Simple disulfide: pdb=" SG CYS S 23 " - pdb=" SG CYS S 88 " distance=2.04 Simple disulfide: pdb=" SG CYS S 134 " - pdb=" SG CYS S 194 " distance=2.03 Simple disulfide: pdb=" SG CYS T 31 " - pdb=" SG CYS T 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 A1098 " " NAG A1305 " - " ASN A 801 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A 616 " " NAG A1309 " - " ASN A 603 " " NAG A1310 " - " ASN A 331 " " NAG A1311 " - " ASN A 165 " " NAG B1301 " - " ASN B1074 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B1098 " " NAG B1305 " - " ASN B 801 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 603 " " NAG B1310 " - " ASN B 331 " " NAG B1311 " - " ASN B 165 " " NAG B1312 " - " ASN B1134 " " 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 B 717 " Time building additional restraints: 15.05 Conformation dependent library (CDL) restraints added in 6.7 seconds 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8812 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 77 sheets defined 19.8% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.77 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.754A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.900A pdb=" N HIS A 505 " --> pdb=" O GLY A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 571 No H-bonds generated for 'chain 'A' and resid 569 through 571' Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.675A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) 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 removed outlier: 3.524A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) 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 891 removed outlier: 3.594A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.159A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.882A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.540A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.553A pdb=" N LEU A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.731A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 344 Processing helix chain 'B' and resid 383 through 390 Processing helix chain 'B' and resid 403 through 407 removed outlier: 3.564A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 removed outlier: 4.016A pdb=" N ASN B 422 " --> pdb=" O ILE B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.532A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.508A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.552A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.589A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 918 removed outlier: 3.905A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.770A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.757A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.857A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.464A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.767A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 571 No H-bonds generated for 'chain 'C' and resid 569 through 571' Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.676A 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 754 removed outlier: 3.518A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.468A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.702A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.661A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.010A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.876A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.711A 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 976 through 983 removed outlier: 3.519A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.996A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 3.717A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'X' and resid 87 through 91 removed outlier: 3.712A pdb=" N THR X 91 " --> pdb=" O SER X 88 " (cutoff:3.500A) Processing helix chain 'X' and resid 137 through 141 removed outlier: 3.554A pdb=" N SER X 140 " --> pdb=" O SER X 137 " (cutoff:3.500A) Processing helix chain 'X' and resid 166 through 171 removed outlier: 3.587A pdb=" N LEU X 169 " --> pdb=" O SER X 166 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR X 170 " --> pdb=" O GLY X 167 " (cutoff:3.500A) Processing helix chain 'X' and resid 197 through 199 No H-bonds generated for 'chain 'X' and resid 197 through 199' Processing helix chain 'Y' and resid 79 through 83 Processing helix chain 'Y' and resid 121 through 128 removed outlier: 3.634A pdb=" N LEU Y 125 " --> pdb=" O SER Y 121 " (cutoff:3.500A) Processing helix chain 'Y' and resid 149 through 153 Processing helix chain 'Y' and resid 183 through 189 removed outlier: 3.821A pdb=" N HIS Y 189 " --> pdb=" O ASP Y 185 " (cutoff:3.500A) Processing helix chain 'Z' and resid 38 through 41 Processing helix chain 'Z' and resid 71 through 74 removed outlier: 3.633A pdb=" N GLN Z 74 " --> pdb=" O ASP Z 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 71 through 74' Processing helix chain 'U' and resid 87 through 91 removed outlier: 3.595A pdb=" N THR U 91 " --> pdb=" O SER U 88 " (cutoff:3.500A) Processing helix chain 'U' and resid 100 through 103 removed outlier: 3.673A pdb=" N SER U 103 " --> pdb=" O ALA U 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 100 through 103' Processing helix chain 'U' and resid 137 through 141 Processing helix chain 'U' and resid 197 through 199 No H-bonds generated for 'chain 'U' and resid 197 through 199' Processing helix chain 'V' and resid 79 through 83 removed outlier: 3.737A pdb=" N ILE V 83 " --> pdb=" O PRO V 80 " (cutoff:3.500A) Processing helix chain 'V' and resid 121 through 126 Processing helix chain 'V' and resid 150 through 153 Processing helix chain 'V' and resid 183 through 189 removed outlier: 4.000A pdb=" N HIS V 189 " --> pdb=" O ASP V 185 " (cutoff:3.500A) Processing helix chain 'W' and resid 37 through 41 Processing helix chain 'W' and resid 96 through 100 Processing helix chain 'R' and resid 28 through 32 Processing helix chain 'R' and resid 87 through 91 removed outlier: 3.851A pdb=" N THR R 91 " --> pdb=" O SER R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 195 through 199 Processing helix chain 'S' and resid 121 through 128 removed outlier: 3.606A pdb=" N LEU S 125 " --> pdb=" O SER S 121 " (cutoff:3.500A) Processing helix chain 'S' and resid 149 through 153 Processing helix chain 'S' and resid 182 through 189 removed outlier: 3.769A pdb=" N TYR S 186 " --> pdb=" O SER S 182 " (cutoff:3.500A) Processing helix chain 'T' and resid 37 through 41 removed outlier: 4.234A pdb=" N ARG T 40 " --> pdb=" O THR T 37 " (cutoff:3.500A) Processing helix chain 'T' and resid 71 through 75 removed outlier: 4.078A pdb=" N GLN T 74 " --> pdb=" O ASP T 71 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N GLY T 75 " --> pdb=" O SER T 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 71 through 75' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.844A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.200A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.495A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.382A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.622A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.232A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.051A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.617A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.968A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 703 through 704 removed outlier: 7.303A 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: 6.722A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 789 removed outlier: 6.507A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.913A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.439A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.397A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.421A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.987A 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: 3.594A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.585A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.746A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N THR B 573 " --> pdb=" O ASP B 568 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ASP B 568 " --> pdb=" O THR B 573 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.631A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 3.982A pdb=" N CYS B 525 " --> pdb=" O CYS B 361 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE B 392 " --> pdb=" O VAL B 524 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.054A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.535A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 735 removed outlier: 4.116A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.541A pdb=" N SER B1123 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD4, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.886A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 63 through 66 removed outlier: 3.612A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.674A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.674A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.345A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.074A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.020A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.894A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.894A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.230A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.507A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'X' and resid 3 through 6 removed outlier: 3.873A pdb=" N THR X 69 " --> pdb=" O GLU X 82 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'X' and resid 10 through 12 removed outlier: 6.411A pdb=" N GLU X 10 " --> pdb=" O THR X 120 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ILE X 34 " --> pdb=" O ARG X 50 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ARG X 50 " --> pdb=" O ILE X 34 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TRP X 36 " --> pdb=" O MET X 48 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'X' and resid 130 through 132 removed outlier: 4.154A pdb=" N PHE X 132 " --> pdb=" O LEU X 151 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LEU X 151 " --> pdb=" O PHE X 132 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N TYR X 186 " --> pdb=" O ASP X 154 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N SER X 189 " --> pdb=" O PHE X 176 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE X 176 " --> pdb=" O SER X 189 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'X' and resid 161 through 164 Processing sheet with id=AF2, first strand: chain 'Y' and resid 4 through 5 removed outlier: 5.109A pdb=" N THR Y 69 " --> pdb=" O ALA Y 25 " (cutoff:3.500A) removed outlier: 10.425A pdb=" N GLN Y 27 " --> pdb=" O SER Y 67 " (cutoff:3.500A) removed outlier: 9.572A pdb=" N SER Y 67 " --> pdb=" O GLN Y 27 " (cutoff:3.500A) removed outlier: 11.104A pdb=" N ILE Y 29 " --> pdb=" O SER Y 65 " (cutoff:3.500A) removed outlier: 10.922A pdb=" N SER Y 65 " --> pdb=" O ILE Y 29 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Y' and resid 45 through 48 removed outlier: 6.148A pdb=" N TRP Y 35 " --> pdb=" O LEU Y 47 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN Y 38 " --> pdb=" O THR Y 85 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN Y 90 " --> pdb=" O THR Y 97 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N THR Y 97 " --> pdb=" O GLN Y 90 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Y' and resid 45 through 48 removed outlier: 6.148A pdb=" N TRP Y 35 " --> pdb=" O LEU Y 47 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN Y 38 " --> pdb=" O THR Y 85 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Y' and resid 114 through 118 removed outlier: 3.815A pdb=" N ASN Y 138 " --> pdb=" O TYR Y 173 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N TYR Y 173 " --> pdb=" O ASN Y 138 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Y' and resid 191 through 196 Processing sheet with id=AF7, first strand: chain 'Z' and resid 14 through 16 removed outlier: 3.558A pdb=" N SER Z 30 " --> pdb=" O SER Z 16 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR Z 78 " --> pdb=" O GLN Z 91 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Z' and resid 19 through 21 removed outlier: 6.090A pdb=" N GLY Z 19 " --> pdb=" O THR Z 127 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N TRP Z 120 " --> pdb=" O ILE Z 107 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE Z 107 " --> pdb=" O TRP Z 120 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN Z 122 " --> pdb=" O CYS Z 105 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Z' and resid 58 through 59 Processing sheet with id=AG1, first strand: chain 'U' and resid 5 through 6 removed outlier: 3.955A pdb=" N VAL U 5 " --> pdb=" O LYS U 23 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR U 78 " --> pdb=" O ASP U 73 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'U' and resid 10 through 12 removed outlier: 7.304A pdb=" N ILE U 34 " --> pdb=" O ARG U 50 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ARG U 50 " --> pdb=" O ILE U 34 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N TRP U 36 " --> pdb=" O MET U 48 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'U' and resid 130 through 133 removed outlier: 6.085A pdb=" N TYR U 186 " --> pdb=" O ASP U 154 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'U' and resid 130 through 133 removed outlier: 6.085A pdb=" N TYR U 186 " --> pdb=" O ASP U 154 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL U 179 " --> pdb=" O SER U 187 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'U' and resid 160 through 164 Processing sheet with id=AG6, first strand: chain 'V' and resid 4 through 7 Processing sheet with id=AG7, first strand: chain 'V' and resid 10 through 13 removed outlier: 3.558A pdb=" N VAL V 104 " --> pdb=" O ALA V 84 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA V 84 " --> pdb=" O VAL V 104 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LEU V 33 " --> pdb=" O TYR V 49 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N TYR V 49 " --> pdb=" O LEU V 33 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TRP V 35 " --> pdb=" O LEU V 47 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP V 50 " --> pdb=" O ASN V 53 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'V' and resid 10 through 13 removed outlier: 3.558A pdb=" N VAL V 104 " --> pdb=" O ALA V 84 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA V 84 " --> pdb=" O VAL V 104 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N THR V 97 " --> pdb=" O GLN V 90 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'V' and resid 114 through 118 removed outlier: 3.525A pdb=" N PHE V 118 " --> pdb=" O VAL V 133 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL V 133 " --> pdb=" O PHE V 118 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N TYR V 173 " --> pdb=" O ASN V 138 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'V' and resid 144 through 148 Processing sheet with id=AH2, first strand: chain 'W' and resid 12 through 14 Processing sheet with id=AH3, first strand: chain 'W' and resid 68 through 69 removed outlier: 6.796A pdb=" N PHE W 56 " --> pdb=" O ARG W 47 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ARG W 47 " --> pdb=" O PHE W 56 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA W 58 " --> pdb=" O TRP W 45 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N MET W 43 " --> pdb=" O ALA W 60 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA W 42 " --> pdb=" O ASP W 108 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'W' and resid 80 through 82 removed outlier: 3.679A pdb=" N THR W 87 " --> pdb=" O ASP W 82 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'R' and resid 3 through 6 Processing sheet with id=AH6, first strand: chain 'R' and resid 58 through 59 removed outlier: 4.219A pdb=" N GLY R 49 " --> pdb=" O TRP R 36 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'R' and resid 132 through 134 removed outlier: 3.733A pdb=" N CYS R 150 " --> pdb=" O SER R 190 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER R 190 " --> pdb=" O CYS R 150 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'R' and resid 162 through 163 Processing sheet with id=AH9, first strand: chain 'S' and resid 4 through 5 removed outlier: 3.614A pdb=" N ASP S 70 " --> pdb=" O SER S 67 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'S' and resid 10 through 13 removed outlier: 3.533A pdb=" N THR S 102 " --> pdb=" O TYR S 86 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N TRP S 35 " --> pdb=" O LEU S 47 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU S 47 " --> pdb=" O TRP S 35 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN S 37 " --> pdb=" O LYS S 45 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'S' and resid 114 through 118 removed outlier: 3.714A pdb=" N ALA S 130 " --> pdb=" O LEU S 181 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N CYS S 134 " --> pdb=" O SER S 177 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N TYR S 173 " --> pdb=" O ASN S 138 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN S 160 " --> pdb=" O THR S 178 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'S' and resid 192 through 196 removed outlier: 3.611A pdb=" N LYS S 207 " --> pdb=" O CYS S 194 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'T' and resid 13 through 16 removed outlier: 3.542A pdb=" N SER T 16 " --> pdb=" O SER T 30 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER T 30 " --> pdb=" O SER T 16 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'T' and resid 19 through 21 removed outlier: 5.083A pdb=" N ASP T 118 " --> pdb=" O SER T 109 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N SER T 109 " --> pdb=" O ASP T 118 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N TRP T 120 " --> pdb=" O ILE T 107 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE T 107 " --> pdb=" O TRP T 120 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN T 122 " --> pdb=" O CYS T 105 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N MET T 43 " --> pdb=" O VAL T 59 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N VAL T 59 " --> pdb=" O MET T 43 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TRP T 45 " --> pdb=" O VAL T 57 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE T 68 " --> pdb=" O VAL T 59 " (cutoff:3.500A) 1416 hydrogen bonds defined for protein. 3756 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: 22.19 Time building geometry restraints manager: 16.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 6036 1.32 - 1.45: 10521 1.45 - 1.58: 20249 1.58 - 1.70: 0 1.70 - 1.83: 191 Bond restraints: 36997 Sorted by residual: bond pdb=" CA SER A 359 " pdb=" CB SER A 359 " ideal model delta sigma weight residual 1.535 1.483 0.051 1.32e-02 5.74e+03 1.52e+01 bond pdb=" C GLU R 158 " pdb=" N PRO R 159 " ideal model delta sigma weight residual 1.328 1.373 -0.044 1.26e-02 6.30e+03 1.24e+01 bond pdb=" N VAL R 160 " pdb=" CA VAL R 160 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.22e-02 6.72e+03 1.18e+01 bond pdb=" N LEU R 151 " pdb=" CA LEU R 151 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.25e-02 6.40e+03 9.28e+00 bond pdb=" N TYR U 155 " pdb=" CA TYR U 155 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.23e-02 6.61e+03 9.16e+00 ... (remaining 36992 not shown) Histogram of bond angle deviations from ideal: 99.83 - 106.66: 1096 106.66 - 113.50: 20217 113.50 - 120.33: 12622 120.33 - 127.16: 16132 127.16 - 134.00: 388 Bond angle restraints: 50455 Sorted by residual: angle pdb=" C PRO C 209 " pdb=" CA PRO C 209 " pdb=" CB PRO C 209 " ideal model delta sigma weight residual 111.40 103.63 7.77 1.54e+00 4.22e-01 2.54e+01 angle pdb=" CA GLU R 158 " pdb=" C GLU R 158 " pdb=" N PRO R 159 " ideal model delta sigma weight residual 116.90 124.12 -7.22 1.50e+00 4.44e-01 2.32e+01 angle pdb=" N CYS A 361 " pdb=" CA CYS A 361 " pdb=" C CYS A 361 " ideal model delta sigma weight residual 108.52 115.76 -7.24 1.52e+00 4.33e-01 2.27e+01 angle pdb=" O LEU A 335 " pdb=" C LEU A 335 " pdb=" N CYS A 336 " ideal model delta sigma weight residual 123.19 128.62 -5.43 1.17e+00 7.31e-01 2.16e+01 angle pdb=" CA CYS V 134 " pdb=" C CYS V 134 " pdb=" O CYS V 134 " ideal model delta sigma weight residual 121.66 116.06 5.60 1.22e+00 6.72e-01 2.10e+01 ... (remaining 50450 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 20381 17.95 - 35.90: 1568 35.90 - 53.84: 335 53.84 - 71.79: 81 71.79 - 89.74: 34 Dihedral angle restraints: 22399 sinusoidal: 8678 harmonic: 13721 Sorted by residual: dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -151.79 65.79 1 1.00e+01 1.00e-02 5.66e+01 dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual 93.00 27.29 65.71 1 1.00e+01 1.00e-02 5.65e+01 dihedral pdb=" CB CYS V 134 " pdb=" SG CYS V 134 " pdb=" SG CYS V 194 " pdb=" CB CYS V 194 " ideal model delta sinusoidal sigma weight residual 93.00 153.38 -60.38 1 1.00e+01 1.00e-02 4.86e+01 ... (remaining 22396 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 5389 0.093 - 0.186: 481 0.186 - 0.279: 14 0.279 - 0.372: 1 0.372 - 0.465: 1 Chirality restraints: 5886 Sorted by residual: chirality pdb=" CB VAL C 70 " pdb=" CA VAL C 70 " pdb=" CG1 VAL C 70 " pdb=" CG2 VAL C 70 " both_signs ideal model delta sigma weight residual False -2.63 -2.16 -0.46 2.00e-01 2.50e+01 5.40e+00 chirality pdb=" CA VAL R 152 " pdb=" N VAL R 152 " pdb=" C VAL R 152 " pdb=" CB VAL R 152 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA ILE A 210 " pdb=" N ILE A 210 " pdb=" C ILE A 210 " pdb=" CB ILE A 210 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 5883 not shown) Planarity restraints: 6517 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1312 " 0.193 2.00e-02 2.50e+03 1.59e-01 3.17e+02 pdb=" C7 NAG B1312 " -0.055 2.00e-02 2.50e+03 pdb=" C8 NAG B1312 " 0.141 2.00e-02 2.50e+03 pdb=" N2 NAG B1312 " -0.257 2.00e-02 2.50e+03 pdb=" O7 NAG B1312 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 357 " -0.025 2.00e-02 2.50e+03 5.16e-02 2.66e+01 pdb=" C ARG A 357 " 0.089 2.00e-02 2.50e+03 pdb=" O ARG A 357 " -0.034 2.00e-02 2.50e+03 pdb=" N ILE A 358 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B1133 " -0.022 2.00e-02 2.50e+03 4.50e-02 2.02e+01 pdb=" C VAL B1133 " 0.078 2.00e-02 2.50e+03 pdb=" O VAL B1133 " -0.030 2.00e-02 2.50e+03 pdb=" N ASN B1134 " -0.026 2.00e-02 2.50e+03 ... (remaining 6514 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.35: 25 2.35 - 2.99: 19708 2.99 - 3.63: 51161 3.63 - 4.26: 79414 4.26 - 4.90: 134024 Nonbonded interactions: 284332 Sorted by model distance: nonbonded pdb=" OD1 ASP T 108 " pdb=" OD1 ASP T 118 " model vdw 1.716 3.040 nonbonded pdb=" OE1 GLN S 6 " pdb=" O THR S 22 " model vdw 1.977 3.040 nonbonded pdb=" CG ASP T 108 " pdb=" OD1 ASP T 118 " model vdw 2.005 3.270 nonbonded pdb=" NE2 GLN S 6 " pdb=" CB CYS S 23 " model vdw 2.148 3.520 nonbonded pdb=" O GLY A1099 " pdb=" OG1 THR A1100 " model vdw 2.175 2.440 ... (remaining 284327 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 through 41 and (name N or name \ CA or name C or name O or name CB )) or resid 42 through 45 or (resid 46 and (na \ me N or name CA or name C or name O or name CB )) or resid 47 through 51 or (res \ id 52 through 53 and (name N or name CA or name C or name O or name CB )) or res \ id 54 through 70 or resid 81 through 86 or (resid 87 and (name N or name CA or n \ ame C or name O or name CB )) or resid 88 through 96 or (resid 97 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 11 \ 6 through 133 or (resid 134 and (name N or name CA or name C or name O or name C \ B )) or resid 135 through 136 or (resid 137 and (name N or name CA or name C or \ name O or name CB )) or resid 138 through 160 or (resid 161 through 164 and (nam \ e N or name CA or name C or name O or name CB )) or resid 165 through 253 or (re \ sid 254 and (name N or name CA or name C or name O or name CB )) or resid 255 th \ rough 318 or (resid 319 and (name N or name CA or name C or name O or name CB )) \ or resid 320 through 355 or (resid 356 through 357 and (name N or name CA or na \ me C or name O or name CB )) or resid 358 through 387 or (resid 388 and (name N \ or name CA or name C or name O or name CB )) or resid 389 through 453 or (resid \ 454 and (name N or name CA or name C or name O or name CB )) or resid 455 throug \ h 458 or (resid 459 and (name N or name CA or name C or name O or name CB )) or \ resid 460 through 553 or (resid 554 and (name N or name CA or name C or name O o \ r name CB )) or resid 555 or (resid 556 through 558 and (name N or name CA or na \ me C or name O or name CB )) or resid 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 name CA or name C or name O or name CB )) or resi \ d 573 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 747 or (resid 748 and (na \ me N or name CA or name C or name O or name CB )) or resid 749 through 827 or (r \ esid 828 and (name N or name CA or name C or name O or name CB )) or resid 855 t \ hrough 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 989 and (name N or name CA or n \ ame C or name O or name CB )) or resid 990 through 993 or (resid 994 and (name N \ or name CA or name C or name O or name CB )) or resid 995 through 1037 or (resi \ d 1038 and (name N or name CA or name C or name O or name CB )) or resid 1039 th \ rough 1050 or (resid 1051 and (name N or name CA or name C or name O or name CB \ )) or resid 1052 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 1311 \ )) selection = (chain 'B' and (resid 27 through 39 or (resid 40 through 41 and (name N or name \ CA or name C or name O or name CB )) or resid 42 through 45 or (resid 46 and (na \ me N or name CA or name C or name O or name CB )) or resid 47 through 51 or (res \ id 52 through 53 and (name N or name CA or name C or name O or name CB )) or res \ id 54 through 86 or (resid 87 and (name N or name CA or name C or name O or name \ CB )) or resid 88 through 96 or (resid 97 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 133 or (resid \ 134 and (name N or name CA or name C or name O or name CB )) or resid 135 throu \ gh 136 or (resid 137 and (name N or name CA or name C or name O or name CB )) or \ resid 138 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 253 or (resid 254 and (name N or \ name CA or name C or name O or name CB )) or resid 255 through 318 or (resid 319 \ and (name N or name CA or name C or name O or name CB )) or resid 320 through 3 \ 31 or (resid 332 and (name N or name CA or name C or name O or name CB )) or res \ id 333 through 355 or (resid 356 through 357 and (name N or name CA or name C or \ name O or name CB )) or resid 358 through 387 or (resid 388 and (name N or name \ CA or name C or name O or name CB )) or resid 389 through 453 or (resid 454 and \ (name N or name CA or name C or name O or name CB )) or resid 455 through 458 o \ r (resid 459 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 60 through 553 or (resid 554 and (name N or name CA or name C or name O or name \ CB )) or resid 555 or (resid 556 through 558 and (name N or name CA or name C or \ name O or name CB )) or resid 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 thr \ ough 572 and (name N or name CA or name C or name O or name CB )) or resid 573 t \ hrough 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 747 or (resid 748 and (name N or \ name CA or name C or name O or name CB )) or resid 749 through 827 or (resid 82 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 855 through \ 984 or (resid 985 and (name N or name CA or name C or name O or name CB )) or re \ sid 986 through 987 or (resid 988 through 989 and (name N or name CA or name C o \ r name O or name CB )) or resid 990 through 1037 or (resid 1038 and (name N or n \ ame CA or name C or name O or name CB )) or resid 1039 through 1050 or (resid 10 \ 51 and (name N or name CA or name C or name O or name CB )) or resid 1052 throug \ h 1110 or (resid 1111 and (name N or name CA or name C or name O or name CB )) o \ r 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 1311)) selection = (chain 'C' and (resid 27 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 67 or (resid 68 and (name N or nam \ e CA or name C or name O or name CB )) or resid 69 through 70 or resid 81 throug \ h 107 or (resid 108 through 113 and (name N or name CA or name C or name O or na \ me CB )) or resid 114 through 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 name C or name O or name CB )) or resid 201 through 217 or \ (resid 218 and (name N or name CA or name C or name O or name CB )) or resid 21 \ 9 through 223 or (resid 224 and (name N or name CA or name C or name O or name C \ B )) or resid 225 through 248 or (resid 249 through 250 and (name N or name CA o \ r name C or name O or name CB )) or resid 251 through 303 or (resid 304 and (nam \ e N or name CA or name C or name O or name CB )) or resid 305 through 320 or (re \ sid 321 and (name N or name CA or name C or name O or name CB )) or resid 322 th \ rough 368 or (resid 369 and (name N or name CA or name C or name O or name CB )) \ or resid 370 through 402 or (resid 403 and (name N or name CA or name C or name \ O or name CB )) or resid 404 through 405 or (resid 406 and (name N or name CA o \ r name C or name O or name CB )) or resid 407 through 423 or (resid 424 and (nam \ e N or name CA or name C or name O or name CB )) or resid 425 through 427 or (re \ sid 428 and (name N or name CA or name C or name O or name CB )) or resid 429 th \ rough 438 or (resid 439 and (name N or name CA or name C or name O or name CB )) \ or resid 440 through 441 or (resid 442 and (name N or name CA or name C or name \ O or name CB )) or resid 443 or (resid 444 through 445 and (name N or name CA o \ r name C or name O or name CB )) or resid 446 through 461 or (resid 462 and (nam \ e N or name CA or name C or name O or name CB )) or resid 463 through 508 or (re \ sid 509 and (name N or name CA or name C or name O or name CB )) or resid 510 th \ rough 556 or (resid 557 through 558 and (name N or name CA or name C or name O o \ r name CB )) or resid 559 through 568 or (resid 569 through 572 and (name N or n \ ame CA or name C or name O or name CB )) or resid 573 through 662 or (resid 663 \ and (name N or name CA or name C or name O or name CB )) or resid 664 through 70 \ 1 or (resid 702 and (name N or name CA or name C or name O or name CB )) or resi \ d 703 through 739 or (resid 740 and (name N or name CA or name C or name O or na \ me CB )) or resid 741 through 794 or (resid 795 and (name N or name CA or name C \ or name O or name CB )) or resid 796 through 807 or (resid 808 and (name N or n \ ame CA or name C or name O or name CB )) or resid 809 through 818 or (resid 819 \ and (name N or name CA or name C or name O or name CB )) or resid 820 through 82 \ 4 or (resid 825 and (name N or name CA or name C or name O or name CB )) or resi \ d 826 through 917 or (resid 918 and (name N or name CA or name C or name O or na \ me CB )) or resid 919 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 993 or (resid 994 \ and (name N or name CA or name C or name O or name CB )) or resid 995 through 10 \ 72 or (resid 1073 and (name N or name CA or name C or name O or name CB )) or re \ sid 1074 through 1137 or (resid 1138 and (name N or name CA or name C or name O \ or name CB )) or resid 1139 through 1140 or (resid 1141 through 1142 and (name N \ or name CA or name C or name O or name CB )) or resid 1143 through 1145 or (res \ id 1146 and (name N or name CA or name C or name O or name CB )) or resid 1301 t \ hrough 1311)) } ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = (chain 'R' and (resid 1 through 33 or (resid 34 and (name N or name CA or name C \ or name O or name CB )) or resid 35 through 49 or (resid 50 and (name N or name \ CA or name C or name O or name CB )) or resid 51 through 72 or (resid 73 and (n \ ame N or name CA or name C or name O or name CB )) or resid 74 through 133 or (r \ esid 134 through 135 and (name N or name CA or name C or name O or name CB )) or \ resid 136 through 156 or resid 160 through 173 or (resid 174 and (name N or nam \ e CA or name C or name O or name CB )) or resid 175 through 225)) selection = (chain 'U' and (resid 1 through 37 or (resid 38 and (name N or name CA or name C \ or name O or name CB )) or resid 39 through 72 or (resid 73 and (name N or name \ CA or name C or name O or name CB )) or resid 74 through 156 or resid 160 throu \ gh 225)) selection = (chain 'X' and (resid 1 through 33 or (resid 34 and (name N or name CA or name C \ or name O or name CB )) or resid 35 through 49 or (resid 50 and (name N or name \ CA or name C or name O or name CB )) or resid 51 through 133 or (resid 134 thro \ ugh 135 and (name N or name CA or name C or name O or name CB )) or resid 136 th \ rough 173 or (resid 174 and (name N or name CA or name C or name O or name CB )) \ or resid 175 through 225)) } ncs_group { reference = (chain 'S' and (resid 1 through 7 or resid 9 through 32 or (resid 33 through 34 \ and (name N or name CA or name C or name O or name CB )) or resid 35 through 104 \ or (resid 105 and (name N or name CA or name C or name O or name CB )) or resid \ 106 through 107 or (resid 108 and (name N or name CA or name C or name O or nam \ e CB )) or resid 109 through 130 or (resid 131 and (name N or name CA or name C \ or name O or name CB )) or resid 132 through 139 or resid 141 through 213)) selection = (chain 'V' and (resid 1 through 48 or (resid 49 and (name N or name CA or name C \ or name O or name CB )) or resid 50 through 104 or (resid 105 and (name N or na \ me CA or name C or name O or name CB )) or resid 106 through 107 or (resid 108 a \ nd (name N or name CA or name C or name O or name CB )) or resid 109 through 130 \ or (resid 131 and (name N or name CA or name C or name O or name CB )) or resid \ 132 through 144 or (resid 145 and (name N or name CA or name C or name O or nam \ e CB )) or resid 146 through 213)) selection = (chain 'Y' and (resid 1 through 7 or resid 9 through 32 or (resid 33 through 34 \ and (name N or name CA or name C or name O or name CB )) or resid 35 through 48 \ or (resid 49 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 0 through 139 or resid 141 through 144 or (resid 145 and (name N or name CA or n \ ame C or name O or name CB )) or resid 146 through 213)) } ncs_group { reference = (chain 'T' and (resid 10 through 121 or (resid 122 and (name N or name CA or nam \ e C or name O or name CB )) or resid 123 through 129)) selection = (chain 'W' and (resid 10 through 121 or (resid 122 and (name N or name CA or nam \ e C or name O or name CB )) or resid 123 through 129)) selection = chain 'Z' } 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: 10.340 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: 0.010 Extract box with map and model: 1.700 Check model and map are aligned: 0.440 Set scattering table: 0.370 Process input model: 109.730 Find NCS groups from input model: 3.820 Set up NCS constraints: 0.240 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: 0.020 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6539 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 0.051 36997 Z= 0.205 Angle : 0.603 7.767 50455 Z= 0.351 Chirality : 0.046 0.465 5886 Planarity : 0.004 0.159 6480 Dihedral : 13.941 89.739 13425 Min Nonbonded Distance : 1.716 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.16 % Allowed : 9.20 % Favored : 90.64 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % 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: -2.45 (0.11), residues: 4666 helix: 0.30 (0.19), residues: 682 sheet: -1.44 (0.12), residues: 1341 loop : -2.32 (0.10), residues: 2643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 353 HIS 0.003 0.000 HIS C 69 PHE 0.014 0.001 PHE A 347 TYR 0.018 0.001 TYR U 155 ARG 0.015 0.001 ARG Z 54 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 4091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 698 time to evaluate : 3.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.7484 (mt) cc_final: 0.7191 (mp) REVERT: A 308 VAL cc_start: 0.8149 (t) cc_final: 0.7841 (m) REVERT: A 564 GLN cc_start: 0.7562 (mm-40) cc_final: 0.7309 (mm-40) REVERT: A 576 VAL cc_start: 0.8548 (m) cc_final: 0.8337 (t) REVERT: A 975 SER cc_start: 0.8194 (p) cc_final: 0.7757 (t) REVERT: A 1084 ASP cc_start: 0.7476 (t0) cc_final: 0.6840 (t0) REVERT: A 1105 THR cc_start: 0.8144 (t) cc_final: 0.7901 (p) REVERT: B 51 THR cc_start: 0.8434 (t) cc_final: 0.8051 (p) REVERT: B 169 GLU cc_start: 0.6350 (mp0) cc_final: 0.5955 (mp0) REVERT: B 281 GLU cc_start: 0.6664 (tm-30) cc_final: 0.6019 (tm-30) REVERT: B 282 ASN cc_start: 0.7343 (m-40) cc_final: 0.7128 (m-40) REVERT: B 605 SER cc_start: 0.7770 (p) cc_final: 0.7485 (p) REVERT: B 698 SER cc_start: 0.8548 (t) cc_final: 0.8236 (p) REVERT: B 773 GLU cc_start: 0.6039 (tt0) cc_final: 0.5812 (tt0) REVERT: B 970 PHE cc_start: 0.8351 (m-80) cc_final: 0.8112 (m-80) REVERT: B 973 ILE cc_start: 0.8717 (tt) cc_final: 0.8468 (tt) REVERT: B 983 ARG cc_start: 0.7309 (mtm110) cc_final: 0.7094 (ttp80) REVERT: B 990 GLU cc_start: 0.7548 (tp30) cc_final: 0.7113 (tp30) REVERT: B 1084 ASP cc_start: 0.7458 (t0) cc_final: 0.7098 (t0) REVERT: B 1091 ARG cc_start: 0.7451 (mtt180) cc_final: 0.6304 (mtt180) REVERT: C 54 LEU cc_start: 0.7960 (mt) cc_final: 0.7749 (mp) REVERT: C 290 ASP cc_start: 0.7307 (t0) cc_final: 0.7000 (t0) REVERT: C 317 ASN cc_start: 0.7251 (m-40) cc_final: 0.6985 (m-40) REVERT: C 383 SER cc_start: 0.7906 (t) cc_final: 0.7543 (m) REVERT: C 398 ASP cc_start: 0.7497 (m-30) cc_final: 0.6693 (m-30) REVERT: C 406 GLU cc_start: 0.6792 (tt0) cc_final: 0.6515 (tt0) REVERT: C 440 LYS cc_start: 0.8152 (mmtm) cc_final: 0.7783 (mmtm) REVERT: C 498 ARG cc_start: 0.7216 (mtt90) cc_final: 0.6844 (mtt90) REVERT: C 574 ASP cc_start: 0.7520 (t70) cc_final: 0.7132 (t0) REVERT: C 670 ILE cc_start: 0.8229 (mm) cc_final: 0.7947 (mt) REVERT: C 945 LEU cc_start: 0.7716 (mm) cc_final: 0.7503 (mp) REVERT: C 964 LYS cc_start: 0.8315 (tttt) cc_final: 0.8031 (tttm) REVERT: C 1105 THR cc_start: 0.8214 (t) cc_final: 0.7926 (t) REVERT: X 81 MET cc_start: 0.4886 (tmm) cc_final: 0.4407 (tmm) REVERT: X 122 SER cc_start: 0.5429 (t) cc_final: 0.5180 (p) REVERT: U 70 ILE cc_start: 0.5986 (tp) cc_final: 0.5783 (tp) REVERT: U 81 MET cc_start: 0.6720 (tpp) cc_final: 0.5978 (tpt) REVERT: V 31 SER cc_start: 0.8102 (m) cc_final: 0.7862 (p) REVERT: V 53 ASN cc_start: 0.5434 (t0) cc_final: 0.5197 (t0) REVERT: V 97 THR cc_start: 0.6490 (p) cc_final: 0.6273 (m) REVERT: R 118 MET cc_start: 0.1037 (tpt) cc_final: -0.0377 (tpt) outliers start: 6 outliers final: 3 residues processed: 702 average time/residue: 0.4884 time to fit residues: 574.1342 Evaluate side-chains 582 residues out of total 4091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 579 time to evaluate : 3.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 69 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 397 optimal weight: 5.9990 chunk 356 optimal weight: 30.0000 chunk 198 optimal weight: 0.8980 chunk 121 optimal weight: 7.9990 chunk 240 optimal weight: 1.9990 chunk 190 optimal weight: 0.9990 chunk 369 optimal weight: 8.9990 chunk 142 optimal weight: 30.0000 chunk 224 optimal weight: 0.8980 chunk 274 optimal weight: 0.9980 chunk 427 optimal weight: 30.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 164 ASN A 239 GLN ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN A 762 GLN A 784 GLN A 901 GLN A 955 ASN A 957 GLN B 207 HIS B 317 ASN B 481 ASN B 506 GLN B 710 ASN B 856 ASN B 907 ASN B 949 GLN B 955 ASN B1005 GLN B1010 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 ASN C 784 GLN C 804 GLN C 856 ASN C 913 GLN C1054 GLN X 59 ASN X 214 ASN Y 53 ASN Z 86 ASN U 6 GLN U 181 GLN U 202 GLN V 189 HIS R 43 GLN ** R 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 210 HIS S 6 GLN S 124 GLN S 147 GLN ** S 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 199 GLN T 122 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 36997 Z= 0.352 Angle : 0.665 12.582 50455 Z= 0.346 Chirality : 0.049 0.269 5886 Planarity : 0.005 0.047 6480 Dihedral : 5.815 57.579 5870 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.97 % Favored : 95.01 % Rotamer: Outliers : 2.42 % Allowed : 14.91 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.11), residues: 4666 helix: 1.19 (0.20), residues: 694 sheet: -0.80 (0.13), residues: 1400 loop : -1.79 (0.11), residues: 2572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP V 35 HIS 0.010 0.001 HIS A1064 PHE 0.023 0.002 PHE B1103 TYR 0.039 0.002 TYR B 265 ARG 0.007 0.001 ARG C 765 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 4091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 598 time to evaluate : 4.031 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: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8396 (mt) cc_final: 0.8115 (mp) REVERT: A 242 LEU cc_start: 0.7601 (mt) cc_final: 0.7334 (mp) REVERT: A 452 LEU cc_start: 0.1630 (OUTLIER) cc_final: 0.1394 (pp) REVERT: A 533 LEU cc_start: 0.5426 (tt) cc_final: 0.5157 (tp) REVERT: A 564 GLN cc_start: 0.7779 (mm-40) cc_final: 0.7564 (mm-40) REVERT: A 602 THR cc_start: 0.7827 (p) cc_final: 0.7417 (m) REVERT: A 745 ASP cc_start: 0.7419 (t0) cc_final: 0.7168 (t0) REVERT: A 974 SER cc_start: 0.8545 (p) cc_final: 0.8317 (m) REVERT: A 975 SER cc_start: 0.8450 (p) cc_final: 0.8130 (t) REVERT: A 1072 GLU cc_start: 0.7806 (pm20) cc_final: 0.7540 (pm20) REVERT: A 1084 ASP cc_start: 0.7367 (t0) cc_final: 0.6725 (t0) REVERT: B 51 THR cc_start: 0.8338 (OUTLIER) cc_final: 0.8019 (p) REVERT: B 196 ASN cc_start: 0.7111 (t0) cc_final: 0.6634 (t0) REVERT: B 276 LEU cc_start: 0.8311 (tp) cc_final: 0.8033 (tt) REVERT: B 281 GLU cc_start: 0.6749 (tm-30) cc_final: 0.6230 (tm-30) REVERT: B 524 VAL cc_start: 0.4884 (OUTLIER) cc_final: 0.4646 (m) REVERT: B 659 SER cc_start: 0.8501 (m) cc_final: 0.8219 (p) REVERT: B 698 SER cc_start: 0.8676 (t) cc_final: 0.8415 (p) REVERT: B 710 ASN cc_start: 0.7572 (p0) cc_final: 0.7255 (p0) REVERT: B 720 ILE cc_start: 0.8406 (mm) cc_final: 0.8163 (mm) REVERT: B 856 ASN cc_start: 0.8128 (OUTLIER) cc_final: 0.7722 (p0) REVERT: B 900 MET cc_start: 0.7520 (mtt) cc_final: 0.7282 (mtp) REVERT: B 948 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8246 (mp) REVERT: B 967 SER cc_start: 0.8297 (t) cc_final: 0.8007 (t) REVERT: B 973 ILE cc_start: 0.8713 (tt) cc_final: 0.8417 (tt) REVERT: B 983 ARG cc_start: 0.7584 (mtm110) cc_final: 0.7318 (mtm110) REVERT: B 998 THR cc_start: 0.8391 (OUTLIER) cc_final: 0.7975 (p) REVERT: C 317 ASN cc_start: 0.7383 (m-40) cc_final: 0.7028 (m-40) REVERT: C 349 SER cc_start: 0.7406 (p) cc_final: 0.7033 (p) REVERT: C 364 ASP cc_start: 0.6861 (p0) cc_final: 0.6629 (p0) REVERT: C 378 LYS cc_start: 0.7810 (mtmt) cc_final: 0.7471 (mtpp) REVERT: C 383 SER cc_start: 0.7840 (t) cc_final: 0.7542 (m) REVERT: C 406 GLU cc_start: 0.6733 (tt0) cc_final: 0.6458 (tt0) REVERT: C 428 ASP cc_start: 0.7384 (p0) cc_final: 0.7094 (p0) REVERT: C 440 LYS cc_start: 0.8308 (mmtm) cc_final: 0.7899 (mmtm) REVERT: C 466 ARG cc_start: 0.7816 (ttt-90) cc_final: 0.7096 (ttt-90) REVERT: C 539 VAL cc_start: 0.8429 (p) cc_final: 0.8208 (m) REVERT: C 574 ASP cc_start: 0.7602 (t70) cc_final: 0.7177 (t0) REVERT: C 605 SER cc_start: 0.8060 (p) cc_final: 0.7797 (t) REVERT: C 617 CYS cc_start: 0.6228 (m) cc_final: 0.5966 (m) REVERT: C 670 ILE cc_start: 0.8287 (mm) cc_final: 0.8029 (mt) REVERT: C 719 THR cc_start: 0.8357 (t) cc_final: 0.8041 (p) REVERT: C 931 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8281 (tp) REVERT: C 960 ASN cc_start: 0.7889 (t0) cc_final: 0.7687 (t0) REVERT: C 964 LYS cc_start: 0.8321 (tttt) cc_final: 0.8117 (tttm) REVERT: C 967 SER cc_start: 0.8451 (t) cc_final: 0.8220 (p) REVERT: C 1105 THR cc_start: 0.8378 (t) cc_final: 0.8155 (p) REVERT: X 81 MET cc_start: 0.5060 (tmm) cc_final: 0.4377 (tmm) REVERT: Y 4 MET cc_start: 0.5967 (pmm) cc_final: 0.5738 (pmm) REVERT: Y 146 VAL cc_start: -0.1270 (OUTLIER) cc_final: -0.1518 (p) REVERT: U 81 MET cc_start: 0.6927 (tpp) cc_final: 0.6375 (tpt) REVERT: V 31 SER cc_start: 0.8094 (m) cc_final: 0.7809 (p) REVERT: R 118 MET cc_start: 0.0849 (tpt) cc_final: -0.0209 (tpt) REVERT: T 43 MET cc_start: -0.4129 (mmm) cc_final: -0.5193 (tmm) outliers start: 92 outliers final: 56 residues processed: 665 average time/residue: 0.4449 time to fit residues: 497.7201 Evaluate side-chains 596 residues out of total 4091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 532 time to evaluate : 3.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain X residue 152 VAL Chi-restraints excluded: chain Y residue 146 VAL Chi-restraints excluded: chain Z residue 46 PHE Chi-restraints excluded: chain U residue 52 ILE Chi-restraints excluded: chain V residue 21 ILE Chi-restraints excluded: chain V residue 104 VAL Chi-restraints excluded: chain W residue 27 LEU Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain S residue 109 THR Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 191 VAL Chi-restraints excluded: chain S residue 199 GLN Chi-restraints excluded: chain S residue 205 VAL Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain T residue 93 ASN Chi-restraints excluded: chain T residue 122 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 237 optimal weight: 0.7980 chunk 132 optimal weight: 30.0000 chunk 355 optimal weight: 10.0000 chunk 291 optimal weight: 0.9980 chunk 117 optimal weight: 9.9990 chunk 428 optimal weight: 1.9990 chunk 462 optimal weight: 9.9990 chunk 381 optimal weight: 30.0000 chunk 424 optimal weight: 5.9990 chunk 146 optimal weight: 7.9990 chunk 343 optimal weight: 50.0000 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 69 HIS A 81 ASN ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A 925 ASN B 49 HIS B 207 HIS B 505 HIS ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B1135 ASN C 69 HIS ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN C 774 GLN C 777 ASN C 856 ASN C 913 GLN C 955 ASN C1101 HIS W 48 GLN ** R 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.143 36997 Z= 0.968 Angle : 0.887 16.603 50455 Z= 0.466 Chirality : 0.062 0.361 5886 Planarity : 0.007 0.071 6480 Dihedral : 6.780 59.650 5866 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.47 % Favored : 93.44 % Rotamer: Outliers : 4.39 % Allowed : 17.04 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.11), residues: 4666 helix: 0.34 (0.19), residues: 699 sheet: -0.73 (0.13), residues: 1433 loop : -1.94 (0.11), residues: 2534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP V 32 HIS 0.015 0.002 HIS A1064 PHE 0.057 0.004 PHE B1103 TYR 0.055 0.003 TYR A 265 ARG 0.011 0.001 ARG C 509 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 4091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 593 time to evaluate : 4.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 ASP cc_start: 0.5623 (OUTLIER) cc_final: 0.5296 (p0) REVERT: A 170 TYR cc_start: 0.7809 (OUTLIER) cc_final: 0.7363 (t80) REVERT: A 281 GLU cc_start: 0.6865 (pt0) cc_final: 0.6577 (pt0) REVERT: A 338 PHE cc_start: 0.7951 (m-80) cc_final: 0.7579 (m-80) REVERT: A 737 ASP cc_start: 0.7704 (t0) cc_final: 0.7378 (t0) REVERT: A 751 ASN cc_start: 0.8478 (OUTLIER) cc_final: 0.8189 (m-40) REVERT: A 796 TYR cc_start: 0.8228 (t80) cc_final: 0.7870 (t80) REVERT: A 884 SER cc_start: 0.8490 (m) cc_final: 0.8030 (p) REVERT: A 969 LYS cc_start: 0.8602 (mtpp) cc_final: 0.8314 (mtmt) REVERT: A 975 SER cc_start: 0.8524 (p) cc_final: 0.8201 (t) REVERT: A 995 ARG cc_start: 0.7971 (ttm170) cc_final: 0.7659 (mtt180) REVERT: A 1002 GLN cc_start: 0.7846 (tt0) cc_final: 0.7637 (tt0) REVERT: A 1072 GLU cc_start: 0.7778 (pm20) cc_final: 0.7416 (pm20) REVERT: A 1084 ASP cc_start: 0.7402 (t0) cc_final: 0.6749 (t0) REVERT: B 34 ARG cc_start: 0.6995 (mtp85) cc_final: 0.6659 (mmt-90) REVERT: B 106 PHE cc_start: 0.7538 (OUTLIER) cc_final: 0.7092 (m-80) REVERT: B 196 ASN cc_start: 0.7825 (t0) cc_final: 0.7395 (t0) REVERT: B 201 PHE cc_start: 0.8298 (t80) cc_final: 0.7821 (t80) REVERT: B 281 GLU cc_start: 0.6827 (tm-30) cc_final: 0.6623 (tm-30) REVERT: B 524 VAL cc_start: 0.4679 (OUTLIER) cc_final: 0.4411 (m) REVERT: B 552 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7698 (mt) REVERT: B 708 SER cc_start: 0.8096 (OUTLIER) cc_final: 0.7820 (p) REVERT: B 720 ILE cc_start: 0.8465 (mm) cc_final: 0.8179 (mm) REVERT: B 855 PHE cc_start: 0.7603 (OUTLIER) cc_final: 0.7209 (t80) REVERT: B 895 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7437 (pt0) REVERT: B 900 MET cc_start: 0.7743 (mtt) cc_final: 0.7515 (mtp) REVERT: B 969 LYS cc_start: 0.8869 (mtpt) cc_final: 0.8656 (mtpp) REVERT: B 973 ILE cc_start: 0.8695 (tt) cc_final: 0.8337 (tt) REVERT: B 983 ARG cc_start: 0.7645 (mtm110) cc_final: 0.7310 (mtm110) REVERT: B 1005 GLN cc_start: 0.7753 (tp40) cc_final: 0.7514 (tp40) REVERT: B 1040 VAL cc_start: 0.8257 (OUTLIER) cc_final: 0.7970 (t) REVERT: B 1041 ASP cc_start: 0.7800 (t0) cc_final: 0.7590 (t0) REVERT: B 1084 ASP cc_start: 0.7400 (t0) cc_final: 0.7073 (t0) REVERT: C 205 SER cc_start: 0.8142 (m) cc_final: 0.7893 (t) REVERT: C 266 TYR cc_start: 0.7454 (OUTLIER) cc_final: 0.7012 (m-80) REVERT: C 317 ASN cc_start: 0.7632 (m-40) cc_final: 0.7221 (m-40) REVERT: C 349 SER cc_start: 0.7562 (p) cc_final: 0.7255 (p) REVERT: C 364 ASP cc_start: 0.7259 (p0) cc_final: 0.7022 (p0) REVERT: C 378 LYS cc_start: 0.7946 (mtmt) cc_final: 0.7675 (mtmt) REVERT: C 380 TYR cc_start: 0.8313 (m-80) cc_final: 0.8026 (m-10) REVERT: C 420 ASP cc_start: 0.7065 (OUTLIER) cc_final: 0.6633 (t0) REVERT: C 440 LYS cc_start: 0.8501 (mmtm) cc_final: 0.8172 (mmtm) REVERT: C 453 TYR cc_start: 0.7116 (p90) cc_final: 0.6724 (p90) REVERT: C 466 ARG cc_start: 0.7901 (ttt-90) cc_final: 0.6944 (ttt-90) REVERT: C 539 VAL cc_start: 0.8472 (p) cc_final: 0.8209 (m) REVERT: C 574 ASP cc_start: 0.7813 (t70) cc_final: 0.7534 (t0) REVERT: C 719 THR cc_start: 0.8345 (OUTLIER) cc_final: 0.8076 (p) REVERT: C 720 ILE cc_start: 0.8232 (pt) cc_final: 0.7993 (mt) REVERT: C 825 LYS cc_start: 0.8252 (mmmt) cc_final: 0.8040 (mmtm) REVERT: C 964 LYS cc_start: 0.8391 (tttt) cc_final: 0.8121 (mtpt) REVERT: C 976 VAL cc_start: 0.8604 (p) cc_final: 0.8312 (m) REVERT: C 984 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8395 (mp) REVERT: C 990 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7525 (tp30) REVERT: C 1019 ARG cc_start: 0.7400 (ttp80) cc_final: 0.7183 (ttp-110) REVERT: X 81 MET cc_start: 0.4837 (tmm) cc_final: 0.4132 (tmm) REVERT: U 81 MET cc_start: 0.6983 (tpp) cc_final: 0.6534 (tpt) REVERT: U 89 GLU cc_start: 0.8012 (tp30) cc_final: 0.7305 (tp30) REVERT: U 110 PHE cc_start: 0.7928 (m-80) cc_final: 0.7676 (m-80) REVERT: V 35 TRP cc_start: 0.5443 (m100) cc_final: 0.5230 (m100) REVERT: R 118 MET cc_start: 0.0767 (tpt) cc_final: -0.0296 (tpt) REVERT: T 43 MET cc_start: -0.3974 (mmm) cc_final: -0.5243 (tmm) outliers start: 167 outliers final: 110 residues processed: 716 average time/residue: 0.4392 time to fit residues: 534.5123 Evaluate side-chains 677 residues out of total 4091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 553 time to evaluate : 3.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 170 TYR Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 439 ASN Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 5 VAL Chi-restraints excluded: chain X residue 152 VAL Chi-restraints excluded: chain Y residue 19 VAL Chi-restraints excluded: chain Y residue 79 GLN Chi-restraints excluded: chain Z residue 46 PHE Chi-restraints excluded: chain U residue 37 VAL Chi-restraints excluded: chain U residue 51 ILE Chi-restraints excluded: chain U residue 54 ILE Chi-restraints excluded: chain U residue 117 THR Chi-restraints excluded: chain U residue 120 THR Chi-restraints excluded: chain V residue 22 THR Chi-restraints excluded: chain V residue 75 ILE Chi-restraints excluded: chain V residue 104 VAL Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain W residue 27 LEU Chi-restraints excluded: chain W residue 78 THR Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 150 VAL Chi-restraints excluded: chain S residue 178 THR Chi-restraints excluded: chain S residue 191 VAL Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain T residue 93 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 423 optimal weight: 3.9990 chunk 322 optimal weight: 30.0000 chunk 222 optimal weight: 0.0270 chunk 47 optimal weight: 0.8980 chunk 204 optimal weight: 0.5980 chunk 287 optimal weight: 0.6980 chunk 430 optimal weight: 20.0000 chunk 455 optimal weight: 30.0000 chunk 224 optimal weight: 0.6980 chunk 407 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 762 GLN A 935 GLN A1005 GLN A1058 HIS B 317 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 81 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN C 784 GLN C 856 ASN C 913 GLN C 955 ASN Y 166 GLN ** R 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 199 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 36997 Z= 0.223 Angle : 0.611 12.608 50455 Z= 0.317 Chirality : 0.047 0.295 5886 Planarity : 0.005 0.061 6480 Dihedral : 5.842 58.972 5864 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.55 % Allowed : 19.30 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.12), residues: 4666 helix: 1.25 (0.20), residues: 687 sheet: -0.46 (0.13), residues: 1458 loop : -1.63 (0.12), residues: 2521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 258 HIS 0.010 0.001 HIS C 69 PHE 0.024 0.002 PHE A 168 TYR 0.024 0.001 TYR U 32 ARG 0.007 0.000 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 4091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 542 time to evaluate : 3.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8416 (mt) cc_final: 0.8113 (mp) REVERT: A 338 PHE cc_start: 0.7778 (m-80) cc_final: 0.7394 (m-80) REVERT: A 751 ASN cc_start: 0.8287 (t0) cc_final: 0.7962 (m-40) REVERT: A 821 LEU cc_start: 0.8074 (mt) cc_final: 0.7765 (mp) REVERT: A 969 LYS cc_start: 0.8601 (mtpp) cc_final: 0.8363 (mtmt) REVERT: A 975 SER cc_start: 0.8609 (p) cc_final: 0.8216 (t) REVERT: A 995 ARG cc_start: 0.7808 (ttm170) cc_final: 0.7566 (mtt90) REVERT: A 1002 GLN cc_start: 0.7644 (tt0) cc_final: 0.7401 (tt0) REVERT: A 1072 GLU cc_start: 0.7712 (pm20) cc_final: 0.7355 (pm20) REVERT: A 1084 ASP cc_start: 0.7295 (t0) cc_final: 0.6627 (t0) REVERT: B 34 ARG cc_start: 0.6789 (mtp85) cc_final: 0.6328 (mmt-90) REVERT: B 196 ASN cc_start: 0.7336 (t0) cc_final: 0.6905 (t0) REVERT: B 201 PHE cc_start: 0.8097 (t80) cc_final: 0.7853 (t80) REVERT: B 239 GLN cc_start: 0.6650 (mt0) cc_final: 0.6357 (tt0) REVERT: B 524 VAL cc_start: 0.4566 (OUTLIER) cc_final: 0.4318 (m) REVERT: B 552 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7613 (mt) REVERT: B 864 LEU cc_start: 0.7862 (tp) cc_final: 0.7650 (tt) REVERT: B 882 ILE cc_start: 0.8355 (pt) cc_final: 0.8095 (mt) REVERT: B 900 MET cc_start: 0.7515 (mtt) cc_final: 0.7310 (mtp) REVERT: B 973 ILE cc_start: 0.8642 (tt) cc_final: 0.8273 (tt) REVERT: B 983 ARG cc_start: 0.7603 (mtm110) cc_final: 0.7269 (mtm110) REVERT: B 990 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7273 (tp30) REVERT: B 1108 ASN cc_start: 0.8453 (m110) cc_final: 0.8180 (m110) REVERT: B 1137 VAL cc_start: 0.8640 (t) cc_final: 0.8359 (m) REVERT: C 81 ASN cc_start: 0.5658 (OUTLIER) cc_final: 0.5401 (t0) REVERT: C 118 LEU cc_start: 0.6955 (OUTLIER) cc_final: 0.6660 (mt) REVERT: C 317 ASN cc_start: 0.7438 (m-40) cc_final: 0.7077 (m-40) REVERT: C 351 TYR cc_start: 0.6557 (OUTLIER) cc_final: 0.6356 (p90) REVERT: C 364 ASP cc_start: 0.7118 (p0) cc_final: 0.6913 (p0) REVERT: C 378 LYS cc_start: 0.7811 (mtmt) cc_final: 0.7491 (mtmt) REVERT: C 385 THR cc_start: 0.8158 (OUTLIER) cc_final: 0.7946 (p) REVERT: C 406 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6736 (mt-10) REVERT: C 423 TYR cc_start: 0.7795 (t80) cc_final: 0.7329 (t80) REVERT: C 440 LYS cc_start: 0.8413 (mmtm) cc_final: 0.8044 (mmtm) REVERT: C 466 ARG cc_start: 0.7929 (ttt-90) cc_final: 0.7157 (ttt-90) REVERT: C 539 VAL cc_start: 0.8332 (p) cc_final: 0.8098 (m) REVERT: C 574 ASP cc_start: 0.7789 (t70) cc_final: 0.7479 (t0) REVERT: C 719 THR cc_start: 0.8242 (t) cc_final: 0.8026 (p) REVERT: C 720 ILE cc_start: 0.8234 (pt) cc_final: 0.7979 (mt) REVERT: C 934 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8559 (tt) REVERT: C 964 LYS cc_start: 0.8418 (tttt) cc_final: 0.8079 (mtpt) REVERT: C 976 VAL cc_start: 0.8592 (p) cc_final: 0.8325 (m) REVERT: C 1105 THR cc_start: 0.8650 (OUTLIER) cc_final: 0.8395 (p) REVERT: X 81 MET cc_start: 0.5068 (tmm) cc_final: 0.4407 (tmm) REVERT: Y 4 MET cc_start: 0.6014 (pmm) cc_final: 0.3346 (tpp) REVERT: Y 146 VAL cc_start: -0.1044 (OUTLIER) cc_final: -0.1279 (p) REVERT: U 81 MET cc_start: 0.7002 (tpp) cc_final: 0.6712 (tpt) REVERT: V 147 GLN cc_start: 0.2528 (OUTLIER) cc_final: 0.1661 (tm-30) REVERT: R 118 MET cc_start: 0.0690 (tpt) cc_final: -0.0305 (tpt) REVERT: T 43 MET cc_start: -0.3873 (mmm) cc_final: -0.5189 (tmm) outliers start: 135 outliers final: 88 residues processed: 639 average time/residue: 0.4160 time to fit residues: 450.9912 Evaluate side-chains 627 residues out of total 4091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 527 time to evaluate : 3.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 5 VAL Chi-restraints excluded: chain X residue 45 LEU Chi-restraints excluded: chain X residue 152 VAL Chi-restraints excluded: chain Y residue 19 VAL Chi-restraints excluded: chain Y residue 79 GLN Chi-restraints excluded: chain Y residue 146 VAL Chi-restraints excluded: chain Z residue 46 PHE Chi-restraints excluded: chain Z residue 92 MET Chi-restraints excluded: chain U residue 37 VAL Chi-restraints excluded: chain U residue 120 THR Chi-restraints excluded: chain U residue 126 THR Chi-restraints excluded: chain V residue 21 ILE Chi-restraints excluded: chain V residue 75 ILE Chi-restraints excluded: chain V residue 88 CYS Chi-restraints excluded: chain V residue 147 GLN Chi-restraints excluded: chain W residue 27 LEU Chi-restraints excluded: chain W residue 78 THR Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain S residue 109 THR Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 191 VAL Chi-restraints excluded: chain S residue 199 GLN Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain T residue 93 ASN Chi-restraints excluded: chain T residue 100 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 379 optimal weight: 10.0000 chunk 258 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 338 optimal weight: 0.0170 chunk 187 optimal weight: 0.9990 chunk 388 optimal weight: 7.9990 chunk 314 optimal weight: 10.0000 chunk 0 optimal weight: 2.9990 chunk 232 optimal weight: 1.9990 chunk 408 optimal weight: 8.9990 chunk 114 optimal weight: 1.9990 overall best weight: 1.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN A1058 HIS B 317 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 856 ASN B1010 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN C 784 GLN C 856 ASN C 913 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 59 ASN ** R 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 199 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 36997 Z= 0.355 Angle : 0.619 12.663 50455 Z= 0.321 Chirality : 0.047 0.233 5886 Planarity : 0.005 0.067 6480 Dihedral : 5.738 59.339 5864 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 4.50 % Allowed : 19.38 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.12), residues: 4666 helix: 1.28 (0.20), residues: 697 sheet: -0.39 (0.13), residues: 1442 loop : -1.56 (0.12), residues: 2527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP V 35 HIS 0.006 0.001 HIS C1064 PHE 0.025 0.002 PHE C 43 TYR 0.033 0.002 TYR B 265 ARG 0.007 0.000 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 4091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 548 time to evaluate : 3.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8407 (mt) cc_final: 0.8129 (mp) REVERT: A 138 ASP cc_start: 0.7798 (m-30) cc_final: 0.7507 (m-30) REVERT: A 142 ASP cc_start: 0.5191 (OUTLIER) cc_final: 0.4579 (p0) REVERT: A 338 PHE cc_start: 0.7767 (m-80) cc_final: 0.7336 (m-80) REVERT: A 468 ILE cc_start: 0.2631 (OUTLIER) cc_final: 0.2327 (mm) REVERT: A 751 ASN cc_start: 0.8316 (t0) cc_final: 0.8008 (m-40) REVERT: A 884 SER cc_start: 0.8562 (m) cc_final: 0.8044 (p) REVERT: A 969 LYS cc_start: 0.8587 (mtpp) cc_final: 0.8332 (mtmt) REVERT: A 975 SER cc_start: 0.8566 (p) cc_final: 0.8215 (t) REVERT: A 995 ARG cc_start: 0.7827 (ttm170) cc_final: 0.7619 (mtt90) REVERT: A 1002 GLN cc_start: 0.7679 (tt0) cc_final: 0.7471 (tt0) REVERT: A 1040 VAL cc_start: 0.7725 (OUTLIER) cc_final: 0.7508 (t) REVERT: A 1072 GLU cc_start: 0.7703 (pm20) cc_final: 0.7423 (pm20) REVERT: A 1084 ASP cc_start: 0.7350 (t0) cc_final: 0.6693 (t0) REVERT: B 142 ASP cc_start: 0.3832 (OUTLIER) cc_final: 0.2092 (p0) REVERT: B 196 ASN cc_start: 0.7391 (t0) cc_final: 0.6955 (t0) REVERT: B 239 GLN cc_start: 0.6684 (mt0) cc_final: 0.6421 (tt0) REVERT: B 307 THR cc_start: 0.8673 (m) cc_final: 0.8279 (p) REVERT: B 552 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7649 (mt) REVERT: B 720 ILE cc_start: 0.8404 (mm) cc_final: 0.8074 (mm) REVERT: B 726 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.8223 (mm) REVERT: B 882 ILE cc_start: 0.8352 (pt) cc_final: 0.8104 (mt) REVERT: B 900 MET cc_start: 0.7542 (mtt) cc_final: 0.7323 (mtp) REVERT: B 973 ILE cc_start: 0.8646 (tt) cc_final: 0.8263 (tt) REVERT: B 983 ARG cc_start: 0.7627 (mtm110) cc_final: 0.7276 (mtm110) REVERT: B 990 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7285 (tp30) REVERT: B 1108 ASN cc_start: 0.8485 (m110) cc_final: 0.8215 (m110) REVERT: B 1111 GLU cc_start: 0.7191 (tt0) cc_final: 0.6988 (tt0) REVERT: C 43 PHE cc_start: 0.8188 (t80) cc_final: 0.7926 (t80) REVERT: C 54 LEU cc_start: 0.8399 (mt) cc_final: 0.8112 (mp) REVERT: C 81 ASN cc_start: 0.5765 (OUTLIER) cc_final: 0.5498 (t0) REVERT: C 118 LEU cc_start: 0.7008 (OUTLIER) cc_final: 0.6691 (mt) REVERT: C 270 LEU cc_start: 0.8403 (mp) cc_final: 0.8199 (mt) REVERT: C 317 ASN cc_start: 0.7457 (m-40) cc_final: 0.7060 (m-40) REVERT: C 347 PHE cc_start: 0.7611 (m-10) cc_final: 0.7371 (m-10) REVERT: C 349 SER cc_start: 0.7608 (p) cc_final: 0.7149 (p) REVERT: C 351 TYR cc_start: 0.6589 (OUTLIER) cc_final: 0.6063 (p90) REVERT: C 364 ASP cc_start: 0.7180 (p0) cc_final: 0.6977 (p0) REVERT: C 378 LYS cc_start: 0.7905 (mtmt) cc_final: 0.7560 (mtmt) REVERT: C 385 THR cc_start: 0.8188 (OUTLIER) cc_final: 0.7971 (p) REVERT: C 420 ASP cc_start: 0.7138 (OUTLIER) cc_final: 0.6611 (t0) REVERT: C 440 LYS cc_start: 0.8460 (mmtm) cc_final: 0.8104 (mmtm) REVERT: C 466 ARG cc_start: 0.7898 (ttt-90) cc_final: 0.7151 (ttt-90) REVERT: C 539 VAL cc_start: 0.8383 (p) cc_final: 0.8108 (m) REVERT: C 574 ASP cc_start: 0.7794 (t70) cc_final: 0.7492 (t0) REVERT: C 670 ILE cc_start: 0.8211 (mm) cc_final: 0.8008 (mt) REVERT: C 719 THR cc_start: 0.8284 (t) cc_final: 0.8073 (p) REVERT: C 753 LEU cc_start: 0.8515 (tp) cc_final: 0.8294 (tt) REVERT: C 773 GLU cc_start: 0.6753 (tt0) cc_final: 0.6534 (tt0) REVERT: C 934 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8572 (tt) REVERT: C 964 LYS cc_start: 0.8381 (tttt) cc_final: 0.8089 (mtpt) REVERT: C 976 VAL cc_start: 0.8576 (p) cc_final: 0.8308 (m) REVERT: C 990 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7450 (tp30) REVERT: C 1105 THR cc_start: 0.8592 (OUTLIER) cc_final: 0.8363 (p) REVERT: X 81 MET cc_start: 0.5114 (tmm) cc_final: 0.4459 (tmm) REVERT: X 118 MET cc_start: 0.2910 (tpt) cc_final: 0.2644 (tpt) REVERT: Z 15 GLU cc_start: 0.4040 (OUTLIER) cc_final: 0.3750 (mm-30) REVERT: U 81 MET cc_start: 0.6993 (tpp) cc_final: 0.6550 (tpt) REVERT: V 147 GLN cc_start: 0.2526 (OUTLIER) cc_final: 0.1645 (tm-30) REVERT: R 118 MET cc_start: 0.0642 (tpt) cc_final: -0.0319 (tpt) REVERT: T 43 MET cc_start: -0.3856 (mmm) cc_final: -0.5267 (tmm) outliers start: 171 outliers final: 116 residues processed: 668 average time/residue: 0.4371 time to fit residues: 493.6886 Evaluate side-chains 658 residues out of total 4091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 526 time to evaluate : 3.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 5 VAL Chi-restraints excluded: chain X residue 45 LEU Chi-restraints excluded: chain X residue 152 VAL Chi-restraints excluded: chain Y residue 19 VAL Chi-restraints excluded: chain Y residue 79 GLN Chi-restraints excluded: chain Y residue 115 VAL Chi-restraints excluded: chain Z residue 15 GLU Chi-restraints excluded: chain Z residue 46 PHE Chi-restraints excluded: chain Z residue 92 MET Chi-restraints excluded: chain U residue 37 VAL Chi-restraints excluded: chain U residue 51 ILE Chi-restraints excluded: chain U residue 117 THR Chi-restraints excluded: chain U residue 120 THR Chi-restraints excluded: chain U residue 126 THR Chi-restraints excluded: chain U residue 187 SER Chi-restraints excluded: chain V residue 21 ILE Chi-restraints excluded: chain V residue 67 SER Chi-restraints excluded: chain V residue 75 ILE Chi-restraints excluded: chain V residue 88 CYS Chi-restraints excluded: chain V residue 104 VAL Chi-restraints excluded: chain V residue 147 GLN Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain W residue 27 LEU Chi-restraints excluded: chain W residue 78 THR Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain S residue 42 LYS Chi-restraints excluded: chain S residue 109 THR Chi-restraints excluded: chain S residue 135 LEU Chi-restraints excluded: chain S residue 191 VAL Chi-restraints excluded: chain S residue 199 GLN Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain T residue 93 ASN Chi-restraints excluded: chain T residue 100 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 153 optimal weight: 0.8980 chunk 409 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 267 optimal weight: 0.8980 chunk 112 optimal weight: 0.4980 chunk 455 optimal weight: 30.0000 chunk 378 optimal weight: 10.0000 chunk 210 optimal weight: 3.9990 chunk 37 optimal weight: 0.0980 chunk 150 optimal weight: 2.9990 chunk 239 optimal weight: 0.0970 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 762 GLN A1058 HIS B 81 ASN B 317 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B1010 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 460 ASN C 613 GLN C 658 ASN C 856 ASN C 913 GLN ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN U 59 ASN ** R 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 199 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 36997 Z= 0.190 Angle : 0.565 10.301 50455 Z= 0.292 Chirality : 0.045 0.224 5886 Planarity : 0.004 0.067 6480 Dihedral : 5.352 57.880 5864 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.84 % Allowed : 20.72 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.87 (0.12), residues: 4666 helix: 1.66 (0.20), residues: 689 sheet: -0.27 (0.13), residues: 1452 loop : -1.43 (0.12), residues: 2525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP V 35 HIS 0.003 0.001 HIS S 198 PHE 0.021 0.001 PHE C 43 TYR 0.024 0.001 TYR U 32 ARG 0.006 0.000 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 4091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 541 time to evaluate : 3.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8416 (mt) cc_final: 0.8108 (mp) REVERT: A 338 PHE cc_start: 0.7720 (m-80) cc_final: 0.7306 (m-80) REVERT: A 452 LEU cc_start: 0.1120 (OUTLIER) cc_final: 0.0910 (pp) REVERT: A 751 ASN cc_start: 0.8248 (t0) cc_final: 0.7957 (m-40) REVERT: A 821 LEU cc_start: 0.8046 (mt) cc_final: 0.7735 (mp) REVERT: A 969 LYS cc_start: 0.8576 (mtpp) cc_final: 0.8326 (mtmt) REVERT: A 975 SER cc_start: 0.8549 (p) cc_final: 0.8218 (t) REVERT: A 976 VAL cc_start: 0.8556 (OUTLIER) cc_final: 0.8268 (m) REVERT: A 995 ARG cc_start: 0.7705 (ttm170) cc_final: 0.7490 (mtt90) REVERT: A 1002 GLN cc_start: 0.7627 (tt0) cc_final: 0.7387 (tp40) REVERT: A 1084 ASP cc_start: 0.7322 (t0) cc_final: 0.6652 (t0) REVERT: B 142 ASP cc_start: 0.3557 (OUTLIER) cc_final: 0.1854 (p0) REVERT: B 196 ASN cc_start: 0.7141 (t0) cc_final: 0.6723 (t0) REVERT: B 239 GLN cc_start: 0.6627 (mt0) cc_final: 0.6344 (tt0) REVERT: B 307 THR cc_start: 0.8648 (m) cc_final: 0.8225 (p) REVERT: B 973 ILE cc_start: 0.8618 (tt) cc_final: 0.8237 (tt) REVERT: B 983 ARG cc_start: 0.7618 (mtm110) cc_final: 0.7259 (mtm110) REVERT: B 990 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7236 (tp30) REVERT: B 1084 ASP cc_start: 0.7342 (t0) cc_final: 0.6999 (t0) REVERT: B 1108 ASN cc_start: 0.8462 (m110) cc_final: 0.8181 (m110) REVERT: C 43 PHE cc_start: 0.8129 (t80) cc_final: 0.7856 (t80) REVERT: C 118 LEU cc_start: 0.6935 (OUTLIER) cc_final: 0.6620 (mt) REVERT: C 270 LEU cc_start: 0.8394 (mp) cc_final: 0.8176 (mt) REVERT: C 347 PHE cc_start: 0.7462 (m-10) cc_final: 0.7130 (m-10) REVERT: C 349 SER cc_start: 0.7622 (p) cc_final: 0.7168 (p) REVERT: C 351 TYR cc_start: 0.6642 (OUTLIER) cc_final: 0.6186 (p90) REVERT: C 364 ASP cc_start: 0.7158 (p0) cc_final: 0.6930 (p0) REVERT: C 378 LYS cc_start: 0.7827 (mtmt) cc_final: 0.7470 (mtmt) REVERT: C 440 LYS cc_start: 0.8440 (mmtm) cc_final: 0.8082 (mmtm) REVERT: C 466 ARG cc_start: 0.7880 (ttt-90) cc_final: 0.7096 (ttt-90) REVERT: C 501 TYR cc_start: 0.6673 (m-80) cc_final: 0.6358 (m-80) REVERT: C 539 VAL cc_start: 0.8340 (p) cc_final: 0.8071 (m) REVERT: C 574 ASP cc_start: 0.7771 (t70) cc_final: 0.7466 (t0) REVERT: C 670 ILE cc_start: 0.8176 (mm) cc_final: 0.7965 (mt) REVERT: C 719 THR cc_start: 0.8264 (t) cc_final: 0.8047 (p) REVERT: C 724 THR cc_start: 0.8606 (OUTLIER) cc_final: 0.8386 (p) REVERT: C 934 ILE cc_start: 0.8824 (tt) cc_final: 0.8515 (tt) REVERT: C 964 LYS cc_start: 0.8384 (tttt) cc_final: 0.8082 (mtpt) REVERT: C 976 VAL cc_start: 0.8571 (p) cc_final: 0.8315 (m) REVERT: C 1105 THR cc_start: 0.8614 (OUTLIER) cc_final: 0.8380 (p) REVERT: X 81 MET cc_start: 0.5205 (tmm) cc_final: 0.4584 (tmm) REVERT: Z 15 GLU cc_start: 0.4056 (OUTLIER) cc_final: 0.3827 (mm-30) REVERT: U 81 MET cc_start: 0.6990 (tpp) cc_final: 0.6487 (tpt) REVERT: V 147 GLN cc_start: 0.2362 (OUTLIER) cc_final: 0.1573 (tm-30) REVERT: R 118 MET cc_start: 0.0797 (tpt) cc_final: -0.0159 (tpt) REVERT: T 43 MET cc_start: -0.3951 (mmm) cc_final: -0.5117 (tmm) outliers start: 146 outliers final: 111 residues processed: 644 average time/residue: 0.4288 time to fit residues: 467.7635 Evaluate side-chains 638 residues out of total 4091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 517 time to evaluate : 4.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 5 VAL Chi-restraints excluded: chain X residue 93 VAL Chi-restraints excluded: chain X residue 152 VAL Chi-restraints excluded: chain Y residue 19 VAL Chi-restraints excluded: chain Y residue 79 GLN Chi-restraints excluded: chain Y residue 115 VAL Chi-restraints excluded: chain Z residue 15 GLU Chi-restraints excluded: chain Z residue 46 PHE Chi-restraints excluded: chain Z residue 92 MET Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 37 VAL Chi-restraints excluded: chain U residue 120 THR Chi-restraints excluded: chain U residue 126 THR Chi-restraints excluded: chain U residue 187 SER Chi-restraints excluded: chain V residue 21 ILE Chi-restraints excluded: chain V residue 75 ILE Chi-restraints excluded: chain V residue 88 CYS Chi-restraints excluded: chain V residue 147 GLN Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain W residue 27 LEU Chi-restraints excluded: chain W residue 78 THR Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain S residue 42 LYS Chi-restraints excluded: chain S residue 109 THR Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 135 LEU Chi-restraints excluded: chain S residue 150 VAL Chi-restraints excluded: chain S residue 191 VAL Chi-restraints excluded: chain S residue 194 CYS Chi-restraints excluded: chain S residue 199 GLN Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 73 VAL Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain T residue 93 ASN Chi-restraints excluded: chain T residue 100 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 439 optimal weight: 0.0000 chunk 51 optimal weight: 0.6980 chunk 259 optimal weight: 0.9990 chunk 332 optimal weight: 10.0000 chunk 257 optimal weight: 1.9990 chunk 383 optimal weight: 6.9990 chunk 254 optimal weight: 0.8980 chunk 453 optimal weight: 2.9990 chunk 284 optimal weight: 0.5980 chunk 276 optimal weight: 0.8980 chunk 209 optimal weight: 2.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 317 ASN A 762 GLN A 784 GLN B 317 ASN B 755 GLN B1010 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN C 913 GLN ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN U 59 ASN ** R 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 199 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 36997 Z= 0.219 Angle : 0.562 11.137 50455 Z= 0.290 Chirality : 0.045 0.198 5886 Planarity : 0.004 0.067 6480 Dihedral : 5.203 56.695 5864 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 4.34 % Allowed : 20.35 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.76 (0.12), residues: 4666 helix: 1.61 (0.20), residues: 702 sheet: -0.16 (0.13), residues: 1455 loop : -1.36 (0.12), residues: 2509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP V 35 HIS 0.003 0.001 HIS B1064 PHE 0.021 0.001 PHE A 592 TYR 0.024 0.001 TYR B 265 ARG 0.007 0.000 ARG C 498 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 4091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 528 time to evaluate : 3.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8396 (mt) cc_final: 0.8097 (mp) REVERT: A 138 ASP cc_start: 0.7774 (m-30) cc_final: 0.7565 (t0) REVERT: A 142 ASP cc_start: 0.5003 (OUTLIER) cc_final: 0.4488 (p0) REVERT: A 338 PHE cc_start: 0.7657 (m-80) cc_final: 0.7243 (m-80) REVERT: A 468 ILE cc_start: 0.2634 (OUTLIER) cc_final: 0.2330 (mm) REVERT: A 602 THR cc_start: 0.7863 (p) cc_final: 0.7481 (m) REVERT: A 751 ASN cc_start: 0.8265 (t0) cc_final: 0.7973 (m-40) REVERT: A 821 LEU cc_start: 0.8051 (mt) cc_final: 0.7786 (mp) REVERT: A 969 LYS cc_start: 0.8567 (mtpp) cc_final: 0.8323 (mtmt) REVERT: A 975 SER cc_start: 0.8595 (p) cc_final: 0.8266 (t) REVERT: A 976 VAL cc_start: 0.8512 (OUTLIER) cc_final: 0.8245 (m) REVERT: A 995 ARG cc_start: 0.7708 (ttm170) cc_final: 0.7506 (mtt90) REVERT: A 1002 GLN cc_start: 0.7638 (tt0) cc_final: 0.7393 (tp40) REVERT: A 1084 ASP cc_start: 0.7332 (t0) cc_final: 0.6672 (t0) REVERT: A 1139 ASP cc_start: 0.7529 (t0) cc_final: 0.7232 (t0) REVERT: B 52 GLN cc_start: 0.7504 (tm-30) cc_final: 0.6975 (tm-30) REVERT: B 81 ASN cc_start: 0.5899 (OUTLIER) cc_final: 0.5662 (p0) REVERT: B 142 ASP cc_start: 0.3544 (OUTLIER) cc_final: 0.1864 (p0) REVERT: B 196 ASN cc_start: 0.7161 (t0) cc_final: 0.6726 (t0) REVERT: B 239 GLN cc_start: 0.6639 (mt0) cc_final: 0.6332 (tt0) REVERT: B 307 THR cc_start: 0.8644 (m) cc_final: 0.8265 (p) REVERT: B 720 ILE cc_start: 0.8397 (mm) cc_final: 0.8045 (mm) REVERT: B 900 MET cc_start: 0.7472 (mtt) cc_final: 0.7272 (mtp) REVERT: B 973 ILE cc_start: 0.8603 (tt) cc_final: 0.8318 (tt) REVERT: B 983 ARG cc_start: 0.7626 (mtm110) cc_final: 0.7315 (mtm110) REVERT: B 990 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.7241 (tp30) REVERT: B 1084 ASP cc_start: 0.7359 (t0) cc_final: 0.7018 (t0) REVERT: B 1108 ASN cc_start: 0.8478 (m110) cc_final: 0.8216 (m110) REVERT: C 118 LEU cc_start: 0.6948 (OUTLIER) cc_final: 0.6640 (mt) REVERT: C 270 LEU cc_start: 0.8410 (mp) cc_final: 0.8191 (mt) REVERT: C 347 PHE cc_start: 0.7485 (m-10) cc_final: 0.7225 (m-10) REVERT: C 349 SER cc_start: 0.7761 (p) cc_final: 0.7332 (p) REVERT: C 351 TYR cc_start: 0.6672 (OUTLIER) cc_final: 0.6214 (p90) REVERT: C 364 ASP cc_start: 0.7177 (p0) cc_final: 0.6956 (p0) REVERT: C 378 LYS cc_start: 0.7851 (mtmt) cc_final: 0.7478 (mtmt) REVERT: C 420 ASP cc_start: 0.7208 (OUTLIER) cc_final: 0.6646 (t0) REVERT: C 440 LYS cc_start: 0.8430 (mmtm) cc_final: 0.8068 (mmtm) REVERT: C 466 ARG cc_start: 0.7840 (ttt-90) cc_final: 0.7065 (ttt-90) REVERT: C 501 TYR cc_start: 0.6658 (m-80) cc_final: 0.6265 (m-80) REVERT: C 539 VAL cc_start: 0.8355 (p) cc_final: 0.8089 (m) REVERT: C 574 ASP cc_start: 0.7771 (t70) cc_final: 0.7452 (t0) REVERT: C 670 ILE cc_start: 0.8187 (mm) cc_final: 0.7985 (mt) REVERT: C 724 THR cc_start: 0.8706 (OUTLIER) cc_final: 0.8484 (p) REVERT: C 764 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7685 (ttpp) REVERT: C 934 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8504 (tt) REVERT: C 964 LYS cc_start: 0.8374 (tttt) cc_final: 0.8084 (mtpt) REVERT: C 976 VAL cc_start: 0.8566 (p) cc_final: 0.8306 (m) REVERT: C 990 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7431 (tp30) REVERT: C 1105 THR cc_start: 0.8601 (OUTLIER) cc_final: 0.8385 (p) REVERT: X 81 MET cc_start: 0.5196 (tmm) cc_final: 0.4580 (tmm) REVERT: Z 15 GLU cc_start: 0.4064 (OUTLIER) cc_final: 0.3854 (mm-30) REVERT: U 81 MET cc_start: 0.7042 (tpp) cc_final: 0.6466 (tpt) REVERT: V 147 GLN cc_start: 0.2559 (OUTLIER) cc_final: 0.1712 (tm-30) REVERT: R 118 MET cc_start: 0.0782 (tpt) cc_final: -0.0164 (tpt) REVERT: T 43 MET cc_start: -0.3872 (mmm) cc_final: -0.5113 (tmm) outliers start: 165 outliers final: 133 residues processed: 643 average time/residue: 0.4302 time to fit residues: 467.9799 Evaluate side-chains 659 residues out of total 4091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 511 time to evaluate : 3.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 5 VAL Chi-restraints excluded: chain X residue 93 VAL Chi-restraints excluded: chain X residue 152 VAL Chi-restraints excluded: chain Y residue 19 VAL Chi-restraints excluded: chain Y residue 79 GLN Chi-restraints excluded: chain Y residue 115 VAL Chi-restraints excluded: chain Z residue 15 GLU Chi-restraints excluded: chain Z residue 31 CYS Chi-restraints excluded: chain Z residue 46 PHE Chi-restraints excluded: chain Z residue 92 MET Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 37 VAL Chi-restraints excluded: chain U residue 51 ILE Chi-restraints excluded: chain U residue 120 THR Chi-restraints excluded: chain U residue 126 THR Chi-restraints excluded: chain U residue 187 SER Chi-restraints excluded: chain V residue 21 ILE Chi-restraints excluded: chain V residue 75 ILE Chi-restraints excluded: chain V residue 88 CYS Chi-restraints excluded: chain V residue 147 GLN Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain W residue 27 LEU Chi-restraints excluded: chain W residue 78 THR Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain S residue 42 LYS Chi-restraints excluded: chain S residue 83 ILE Chi-restraints excluded: chain S residue 109 THR Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 135 LEU Chi-restraints excluded: chain S residue 150 VAL Chi-restraints excluded: chain S residue 191 VAL Chi-restraints excluded: chain S residue 194 CYS Chi-restraints excluded: chain S residue 199 GLN Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 73 VAL Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain T residue 93 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 280 optimal weight: 1.9990 chunk 181 optimal weight: 0.6980 chunk 271 optimal weight: 1.9990 chunk 136 optimal weight: 0.5980 chunk 89 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 chunk 288 optimal weight: 0.9980 chunk 309 optimal weight: 6.9990 chunk 224 optimal weight: 0.9990 chunk 42 optimal weight: 0.0010 chunk 356 optimal weight: 30.0000 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A 935 GLN B 317 ASN B 755 GLN B1010 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN C 913 GLN ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN U 59 ASN ** R 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 198 HIS S 199 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 36997 Z= 0.211 Angle : 0.559 11.118 50455 Z= 0.288 Chirality : 0.045 0.198 5886 Planarity : 0.004 0.067 6480 Dihedral : 5.085 55.770 5864 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 4.13 % Allowed : 20.96 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.68 (0.12), residues: 4666 helix: 1.76 (0.20), residues: 685 sheet: -0.12 (0.13), residues: 1465 loop : -1.31 (0.12), residues: 2516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP V 35 HIS 0.005 0.001 HIS S 198 PHE 0.025 0.001 PHE B 201 TYR 0.024 0.001 TYR B 265 ARG 0.007 0.000 ARG C 498 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 4091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 522 time to evaluate : 3.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8391 (mt) cc_final: 0.8108 (mp) REVERT: A 138 ASP cc_start: 0.7736 (m-30) cc_final: 0.7528 (t0) REVERT: A 142 ASP cc_start: 0.4949 (OUTLIER) cc_final: 0.4444 (p0) REVERT: A 338 PHE cc_start: 0.7701 (m-80) cc_final: 0.7277 (m-80) REVERT: A 468 ILE cc_start: 0.2610 (OUTLIER) cc_final: 0.2307 (mm) REVERT: A 533 LEU cc_start: 0.5725 (OUTLIER) cc_final: 0.5469 (tt) REVERT: A 602 THR cc_start: 0.7856 (p) cc_final: 0.7561 (m) REVERT: A 751 ASN cc_start: 0.8258 (t0) cc_final: 0.7970 (m-40) REVERT: A 821 LEU cc_start: 0.8048 (mt) cc_final: 0.7785 (mp) REVERT: A 969 LYS cc_start: 0.8568 (mtpp) cc_final: 0.8305 (mtmt) REVERT: A 975 SER cc_start: 0.8554 (p) cc_final: 0.8251 (t) REVERT: A 1002 GLN cc_start: 0.7629 (tt0) cc_final: 0.7388 (tp40) REVERT: A 1084 ASP cc_start: 0.7331 (t0) cc_final: 0.6682 (t0) REVERT: A 1139 ASP cc_start: 0.7517 (t0) cc_final: 0.7225 (t0) REVERT: B 52 GLN cc_start: 0.7505 (tm-30) cc_final: 0.6984 (tm-30) REVERT: B 196 ASN cc_start: 0.7137 (t0) cc_final: 0.6703 (t0) REVERT: B 239 GLN cc_start: 0.6666 (mt0) cc_final: 0.6381 (tt0) REVERT: B 307 THR cc_start: 0.8645 (m) cc_final: 0.8265 (p) REVERT: B 708 SER cc_start: 0.8011 (t) cc_final: 0.7788 (p) REVERT: B 720 ILE cc_start: 0.8363 (mm) cc_final: 0.8004 (mm) REVERT: B 900 MET cc_start: 0.7469 (mtt) cc_final: 0.7264 (mtp) REVERT: B 973 ILE cc_start: 0.8691 (tt) cc_final: 0.8276 (tt) REVERT: B 983 ARG cc_start: 0.7623 (mtm110) cc_final: 0.7288 (mtm110) REVERT: B 990 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7063 (tp30) REVERT: B 1060 VAL cc_start: 0.8586 (p) cc_final: 0.8279 (t) REVERT: B 1084 ASP cc_start: 0.7367 (t0) cc_final: 0.7028 (t0) REVERT: B 1108 ASN cc_start: 0.8481 (m110) cc_final: 0.8208 (m110) REVERT: C 118 LEU cc_start: 0.6913 (OUTLIER) cc_final: 0.6608 (mt) REVERT: C 270 LEU cc_start: 0.8401 (mp) cc_final: 0.8189 (mt) REVERT: C 347 PHE cc_start: 0.7467 (m-10) cc_final: 0.7231 (m-10) REVERT: C 349 SER cc_start: 0.7775 (p) cc_final: 0.7339 (p) REVERT: C 351 TYR cc_start: 0.6679 (OUTLIER) cc_final: 0.6202 (p90) REVERT: C 364 ASP cc_start: 0.7188 (p0) cc_final: 0.6961 (p0) REVERT: C 378 LYS cc_start: 0.7847 (mtmt) cc_final: 0.7474 (mtmt) REVERT: C 420 ASP cc_start: 0.7212 (OUTLIER) cc_final: 0.6662 (t0) REVERT: C 440 LYS cc_start: 0.8439 (mmtm) cc_final: 0.8077 (mmtm) REVERT: C 466 ARG cc_start: 0.7846 (ttt-90) cc_final: 0.7189 (ttt-90) REVERT: C 501 TYR cc_start: 0.6671 (m-80) cc_final: 0.6244 (m-80) REVERT: C 539 VAL cc_start: 0.8356 (p) cc_final: 0.8081 (m) REVERT: C 574 ASP cc_start: 0.7772 (t70) cc_final: 0.7448 (t0) REVERT: C 670 ILE cc_start: 0.8196 (mm) cc_final: 0.7985 (mt) REVERT: C 934 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8383 (tt) REVERT: C 964 LYS cc_start: 0.8367 (tttt) cc_final: 0.8077 (mtpt) REVERT: C 976 VAL cc_start: 0.8553 (p) cc_final: 0.8299 (m) REVERT: C 990 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7403 (tp30) REVERT: C 1105 THR cc_start: 0.8598 (OUTLIER) cc_final: 0.8383 (p) REVERT: X 81 MET cc_start: 0.5207 (tmm) cc_final: 0.4592 (tmm) REVERT: U 81 MET cc_start: 0.6968 (tpp) cc_final: 0.6500 (tpt) REVERT: V 147 GLN cc_start: 0.2512 (OUTLIER) cc_final: 0.1687 (tm-30) REVERT: W 54 ARG cc_start: 0.1821 (OUTLIER) cc_final: 0.0201 (ptt180) REVERT: R 118 MET cc_start: 0.0779 (tpt) cc_final: -0.0129 (tpt) REVERT: T 43 MET cc_start: -0.3813 (mmm) cc_final: -0.5098 (tmm) outliers start: 157 outliers final: 127 residues processed: 633 average time/residue: 0.4298 time to fit residues: 460.5545 Evaluate side-chains 655 residues out of total 4091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 517 time to evaluate : 3.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain X residue 5 VAL Chi-restraints excluded: chain X residue 45 LEU Chi-restraints excluded: chain X residue 93 VAL Chi-restraints excluded: chain X residue 152 VAL Chi-restraints excluded: chain Y residue 19 VAL Chi-restraints excluded: chain Y residue 79 GLN Chi-restraints excluded: chain Y residue 115 VAL Chi-restraints excluded: chain Z residue 31 CYS Chi-restraints excluded: chain Z residue 46 PHE Chi-restraints excluded: chain Z residue 92 MET Chi-restraints excluded: chain Z residue 102 VAL Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 37 VAL Chi-restraints excluded: chain U residue 51 ILE Chi-restraints excluded: chain U residue 120 THR Chi-restraints excluded: chain U residue 126 THR Chi-restraints excluded: chain U residue 187 SER Chi-restraints excluded: chain V residue 21 ILE Chi-restraints excluded: chain V residue 75 ILE Chi-restraints excluded: chain V residue 88 CYS Chi-restraints excluded: chain V residue 147 GLN Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain W residue 27 LEU Chi-restraints excluded: chain W residue 54 ARG Chi-restraints excluded: chain W residue 78 THR Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain S residue 42 LYS Chi-restraints excluded: chain S residue 83 ILE Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 135 LEU Chi-restraints excluded: chain S residue 150 VAL Chi-restraints excluded: chain S residue 191 VAL Chi-restraints excluded: chain S residue 194 CYS Chi-restraints excluded: chain S residue 199 GLN Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 73 VAL Chi-restraints excluded: chain T residue 88 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 412 optimal weight: 8.9990 chunk 434 optimal weight: 30.0000 chunk 396 optimal weight: 5.9990 chunk 423 optimal weight: 8.9990 chunk 254 optimal weight: 0.3980 chunk 184 optimal weight: 0.5980 chunk 332 optimal weight: 8.9990 chunk 129 optimal weight: 9.9990 chunk 382 optimal weight: 7.9990 chunk 400 optimal weight: 5.9990 chunk 421 optimal weight: 0.4980 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 87 ASN A 125 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN B 81 ASN B 317 ASN B 755 GLN B 913 GLN B1010 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 613 GLN C 658 ASN C 913 GLN C 955 ASN U 59 ASN V 166 GLN ** R 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 199 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.114 36997 Z= 0.725 Angle : 0.763 15.905 50455 Z= 0.399 Chirality : 0.055 0.302 5886 Planarity : 0.006 0.066 6480 Dihedral : 6.043 56.360 5864 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.79 % Favored : 93.16 % Rotamer: Outliers : 4.47 % Allowed : 20.88 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.12), residues: 4666 helix: 0.77 (0.19), residues: 707 sheet: -0.28 (0.13), residues: 1422 loop : -1.53 (0.12), residues: 2537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 64 HIS 0.011 0.002 HIS C1064 PHE 0.045 0.003 PHE A 855 TYR 0.056 0.003 TYR A 265 ARG 0.008 0.001 ARG C 498 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 723 residues out of total 4091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 553 time to evaluate : 4.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8433 (mt) cc_final: 0.8188 (mp) REVERT: A 227 VAL cc_start: 0.8601 (p) cc_final: 0.8304 (t) REVERT: A 338 PHE cc_start: 0.7799 (m-80) cc_final: 0.7335 (m-80) REVERT: A 468 ILE cc_start: 0.2653 (OUTLIER) cc_final: 0.2352 (mm) REVERT: A 572 THR cc_start: 0.8393 (m) cc_final: 0.8148 (p) REVERT: A 602 THR cc_start: 0.8015 (p) cc_final: 0.7601 (m) REVERT: A 751 ASN cc_start: 0.8436 (t0) cc_final: 0.8158 (m-40) REVERT: A 796 TYR cc_start: 0.8226 (t80) cc_final: 0.7894 (t80) REVERT: A 820 ASP cc_start: 0.7443 (OUTLIER) cc_final: 0.7205 (m-30) REVERT: A 884 SER cc_start: 0.8466 (m) cc_final: 0.8031 (p) REVERT: A 969 LYS cc_start: 0.8618 (mtpp) cc_final: 0.8388 (mtmt) REVERT: A 975 SER cc_start: 0.8625 (p) cc_final: 0.8308 (t) REVERT: A 995 ARG cc_start: 0.7929 (ttm170) cc_final: 0.7696 (mtt90) REVERT: A 1084 ASP cc_start: 0.7408 (t0) cc_final: 0.6787 (t0) REVERT: B 52 GLN cc_start: 0.7552 (tm-30) cc_final: 0.6836 (tm-30) REVERT: B 196 ASN cc_start: 0.7745 (t0) cc_final: 0.7306 (t0) REVERT: B 239 GLN cc_start: 0.6708 (mt0) cc_final: 0.6417 (tt0) REVERT: B 307 THR cc_start: 0.8653 (m) cc_final: 0.8295 (p) REVERT: B 537 LYS cc_start: 0.8484 (pttp) cc_final: 0.8231 (pttp) REVERT: B 708 SER cc_start: 0.8231 (t) cc_final: 0.8019 (p) REVERT: B 720 ILE cc_start: 0.8404 (mm) cc_final: 0.8074 (mm) REVERT: B 973 ILE cc_start: 0.8751 (tt) cc_final: 0.8340 (tt) REVERT: B 983 ARG cc_start: 0.7666 (mtm110) cc_final: 0.7339 (mtm110) REVERT: B 984 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8247 (mp) REVERT: B 1084 ASP cc_start: 0.7386 (t0) cc_final: 0.7028 (t0) REVERT: C 118 LEU cc_start: 0.7044 (OUTLIER) cc_final: 0.6731 (mt) REVERT: C 198 ASP cc_start: 0.5007 (OUTLIER) cc_final: 0.4690 (p0) REVERT: C 317 ASN cc_start: 0.7444 (m-40) cc_final: 0.7162 (m-40) REVERT: C 349 SER cc_start: 0.7633 (p) cc_final: 0.7241 (p) REVERT: C 378 LYS cc_start: 0.7858 (mtmt) cc_final: 0.7610 (mtmt) REVERT: C 420 ASP cc_start: 0.7213 (OUTLIER) cc_final: 0.6706 (t0) REVERT: C 440 LYS cc_start: 0.8489 (mmtm) cc_final: 0.8118 (mmtm) REVERT: C 453 TYR cc_start: 0.7106 (p90) cc_final: 0.6743 (p90) REVERT: C 466 ARG cc_start: 0.7894 (ttt-90) cc_final: 0.7055 (ttt-90) REVERT: C 471 GLU cc_start: 0.7700 (tm-30) cc_final: 0.7391 (tm-30) REVERT: C 753 LEU cc_start: 0.8554 (tp) cc_final: 0.8346 (tt) REVERT: C 934 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8535 (tt) REVERT: C 964 LYS cc_start: 0.8412 (tttt) cc_final: 0.8116 (mtpt) REVERT: C 976 VAL cc_start: 0.8514 (p) cc_final: 0.8255 (m) REVERT: C 990 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7481 (tp30) REVERT: X 81 MET cc_start: 0.5083 (OUTLIER) cc_final: 0.4468 (tmm) REVERT: X 118 MET cc_start: 0.2608 (tpt) cc_final: 0.2320 (tpt) REVERT: V 147 GLN cc_start: 0.2387 (OUTLIER) cc_final: 0.1492 (tm-30) REVERT: R 118 MET cc_start: 0.0736 (tpt) cc_final: -0.0184 (tpt) REVERT: T 43 MET cc_start: -0.3756 (mmm) cc_final: -0.5101 (tmm) outliers start: 170 outliers final: 132 residues processed: 668 average time/residue: 0.4308 time to fit residues: 498.7704 Evaluate side-chains 682 residues out of total 4091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 541 time to evaluate : 3.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain X residue 5 VAL Chi-restraints excluded: chain X residue 45 LEU Chi-restraints excluded: chain X residue 81 MET Chi-restraints excluded: chain X residue 93 VAL Chi-restraints excluded: chain X residue 152 VAL Chi-restraints excluded: chain Y residue 19 VAL Chi-restraints excluded: chain Y residue 79 GLN Chi-restraints excluded: chain Y residue 115 VAL Chi-restraints excluded: chain Z residue 31 CYS Chi-restraints excluded: chain Z residue 46 PHE Chi-restraints excluded: chain Z residue 92 MET Chi-restraints excluded: chain Z residue 102 VAL Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 37 VAL Chi-restraints excluded: chain U residue 51 ILE Chi-restraints excluded: chain U residue 120 THR Chi-restraints excluded: chain U residue 126 THR Chi-restraints excluded: chain U residue 187 SER Chi-restraints excluded: chain V residue 21 ILE Chi-restraints excluded: chain V residue 22 THR Chi-restraints excluded: chain V residue 75 ILE Chi-restraints excluded: chain V residue 88 CYS Chi-restraints excluded: chain V residue 104 VAL Chi-restraints excluded: chain V residue 147 GLN Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain W residue 27 LEU Chi-restraints excluded: chain W residue 78 THR Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain S residue 42 LYS Chi-restraints excluded: chain S residue 83 ILE Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 135 LEU Chi-restraints excluded: chain S residue 150 VAL Chi-restraints excluded: chain S residue 191 VAL Chi-restraints excluded: chain S residue 199 GLN Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 73 VAL Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain T residue 93 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 277 optimal weight: 0.6980 chunk 447 optimal weight: 5.9990 chunk 273 optimal weight: 3.9990 chunk 212 optimal weight: 1.9990 chunk 310 optimal weight: 7.9990 chunk 469 optimal weight: 8.9990 chunk 431 optimal weight: 9.9990 chunk 373 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 288 optimal weight: 0.7980 chunk 229 optimal weight: 0.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 125 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN B 81 ASN B 755 GLN B1010 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 ASN C 658 ASN ** R 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.227 36997 Z= 0.596 Angle : 0.958 59.197 50455 Z= 0.531 Chirality : 0.053 0.754 5886 Planarity : 0.006 0.144 6480 Dihedral : 6.080 56.244 5864 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.82 % Favored : 93.14 % Rotamer: Outliers : 3.81 % Allowed : 21.77 % Favored : 74.41 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.12), residues: 4666 helix: 0.77 (0.19), residues: 707 sheet: -0.29 (0.13), residues: 1412 loop : -1.53 (0.12), residues: 2547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 64 HIS 0.009 0.001 HIS C 66 PHE 0.048 0.003 PHE B 58 TYR 0.048 0.002 TYR B 265 ARG 0.008 0.001 ARG B 815 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 4091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 541 time to evaluate : 3.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8433 (mt) cc_final: 0.8191 (mp) REVERT: A 227 VAL cc_start: 0.8593 (p) cc_final: 0.8291 (t) REVERT: A 338 PHE cc_start: 0.7834 (m-80) cc_final: 0.7319 (m-80) REVERT: A 468 ILE cc_start: 0.2659 (OUTLIER) cc_final: 0.2351 (mm) REVERT: A 572 THR cc_start: 0.8388 (m) cc_final: 0.8147 (p) REVERT: A 602 THR cc_start: 0.8024 (p) cc_final: 0.7593 (m) REVERT: A 751 ASN cc_start: 0.8421 (t0) cc_final: 0.8143 (m-40) REVERT: A 796 TYR cc_start: 0.8216 (t80) cc_final: 0.7890 (t80) REVERT: A 820 ASP cc_start: 0.7425 (OUTLIER) cc_final: 0.7189 (m-30) REVERT: A 884 SER cc_start: 0.8474 (m) cc_final: 0.8024 (p) REVERT: A 969 LYS cc_start: 0.8661 (mtpp) cc_final: 0.8390 (mtmt) REVERT: A 975 SER cc_start: 0.8627 (p) cc_final: 0.8300 (t) REVERT: A 995 ARG cc_start: 0.7890 (ttm170) cc_final: 0.7654 (mtt90) REVERT: A 1084 ASP cc_start: 0.7396 (t0) cc_final: 0.6779 (t0) REVERT: B 52 GLN cc_start: 0.7536 (tm-30) cc_final: 0.6800 (tm-30) REVERT: B 196 ASN cc_start: 0.7726 (t0) cc_final: 0.7298 (t0) REVERT: B 239 GLN cc_start: 0.6694 (mt0) cc_final: 0.6373 (tt0) REVERT: B 307 THR cc_start: 0.8652 (m) cc_final: 0.8299 (p) REVERT: B 537 LYS cc_start: 0.8466 (pttp) cc_final: 0.8215 (pttp) REVERT: B 708 SER cc_start: 0.8212 (t) cc_final: 0.7984 (p) REVERT: B 720 ILE cc_start: 0.8395 (mm) cc_final: 0.8066 (mm) REVERT: B 973 ILE cc_start: 0.8737 (tt) cc_final: 0.8322 (tt) REVERT: B 983 ARG cc_start: 0.7649 (mtm110) cc_final: 0.7328 (mtm110) REVERT: B 984 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8239 (mp) REVERT: B 1084 ASP cc_start: 0.7377 (t0) cc_final: 0.7025 (t0) REVERT: C 118 LEU cc_start: 0.7028 (OUTLIER) cc_final: 0.6714 (mt) REVERT: C 198 ASP cc_start: 0.4996 (OUTLIER) cc_final: 0.4675 (p0) REVERT: C 349 SER cc_start: 0.7620 (p) cc_final: 0.7234 (p) REVERT: C 378 LYS cc_start: 0.7855 (mtmt) cc_final: 0.7602 (mtmt) REVERT: C 420 ASP cc_start: 0.7200 (OUTLIER) cc_final: 0.6699 (t0) REVERT: C 440 LYS cc_start: 0.8471 (mmtm) cc_final: 0.8098 (mmtm) REVERT: C 466 ARG cc_start: 0.7898 (ttt-90) cc_final: 0.7053 (ttt-90) REVERT: C 471 GLU cc_start: 0.7699 (tm-30) cc_final: 0.7382 (tm-30) REVERT: C 753 LEU cc_start: 0.8566 (tp) cc_final: 0.8359 (tt) REVERT: C 934 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8529 (tt) REVERT: C 964 LYS cc_start: 0.8382 (tttt) cc_final: 0.8110 (mtpt) REVERT: C 976 VAL cc_start: 0.8526 (p) cc_final: 0.8253 (m) REVERT: X 81 MET cc_start: 0.4992 (OUTLIER) cc_final: 0.4424 (tmm) REVERT: X 118 MET cc_start: 0.2604 (tpt) cc_final: 0.2332 (tpt) REVERT: V 147 GLN cc_start: 0.2384 (OUTLIER) cc_final: 0.1490 (tm-30) REVERT: R 118 MET cc_start: 0.0733 (tpt) cc_final: -0.0184 (tpt) REVERT: T 43 MET cc_start: -0.3759 (mmm) cc_final: -0.5102 (tmm) outliers start: 145 outliers final: 131 residues processed: 642 average time/residue: 0.4424 time to fit residues: 481.7152 Evaluate side-chains 681 residues out of total 4091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 541 time to evaluate : 3.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain X residue 5 VAL Chi-restraints excluded: chain X residue 45 LEU Chi-restraints excluded: chain X residue 81 MET Chi-restraints excluded: chain X residue 93 VAL Chi-restraints excluded: chain X residue 152 VAL Chi-restraints excluded: chain Y residue 19 VAL Chi-restraints excluded: chain Y residue 79 GLN Chi-restraints excluded: chain Y residue 115 VAL Chi-restraints excluded: chain Z residue 31 CYS Chi-restraints excluded: chain Z residue 46 PHE Chi-restraints excluded: chain Z residue 92 MET Chi-restraints excluded: chain Z residue 102 VAL Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 37 VAL Chi-restraints excluded: chain U residue 51 ILE Chi-restraints excluded: chain U residue 120 THR Chi-restraints excluded: chain U residue 126 THR Chi-restraints excluded: chain U residue 187 SER Chi-restraints excluded: chain V residue 21 ILE Chi-restraints excluded: chain V residue 22 THR Chi-restraints excluded: chain V residue 75 ILE Chi-restraints excluded: chain V residue 88 CYS Chi-restraints excluded: chain V residue 104 VAL Chi-restraints excluded: chain V residue 147 GLN Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain W residue 27 LEU Chi-restraints excluded: chain W residue 78 THR Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain S residue 42 LYS Chi-restraints excluded: chain S residue 83 ILE Chi-restraints excluded: chain S residue 109 THR Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 135 LEU Chi-restraints excluded: chain S residue 150 VAL Chi-restraints excluded: chain S residue 191 VAL Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 73 VAL Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain T residue 93 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 296 optimal weight: 0.6980 chunk 398 optimal weight: 0.0980 chunk 114 optimal weight: 0.4980 chunk 344 optimal weight: 10.0000 chunk 55 optimal weight: 0.6980 chunk 103 optimal weight: 0.7980 chunk 374 optimal weight: 6.9990 chunk 156 optimal weight: 0.9980 chunk 384 optimal weight: 0.1980 chunk 47 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN B 81 ASN B 317 ASN B 755 GLN B1010 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN ** R 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.207246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.145606 restraints weight = 59756.149| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.49 r_work: 0.3496 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.227 36997 Z= 0.596 Angle : 0.952 51.813 50455 Z= 0.533 Chirality : 0.053 0.754 5886 Planarity : 0.007 0.144 6480 Dihedral : 6.080 56.244 5864 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.82 % Favored : 93.14 % Rotamer: Outliers : 3.68 % Allowed : 21.90 % Favored : 74.41 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.12), residues: 4666 helix: 0.77 (0.19), residues: 707 sheet: -0.29 (0.13), residues: 1412 loop : -1.53 (0.12), residues: 2547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 64 HIS 0.009 0.001 HIS C 66 PHE 0.048 0.003 PHE B 58 TYR 0.048 0.002 TYR B 265 ARG 0.008 0.001 ARG B 815 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11761.27 seconds wall clock time: 208 minutes 20.76 seconds (12500.76 seconds total)