Starting phenix.real_space_refine on Thu Mar 21 15:30:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wmr_21851/03_2024/6wmr_21851.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wmr_21851/03_2024/6wmr_21851.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wmr_21851/03_2024/6wmr_21851.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wmr_21851/03_2024/6wmr_21851.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wmr_21851/03_2024/6wmr_21851.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wmr_21851/03_2024/6wmr_21851.pdb" } resolution = 3.46 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= 0.006 sd= 1.641 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 81 5.49 5 Mg 1 5.21 5 S 119 5.16 5 C 18995 2.51 5 N 5281 2.21 5 O 5961 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "S ASP 30": "OD1" <-> "OD2" Residue "S PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 99": "OD1" <-> "OD2" Residue "S ASP 125": "OD1" <-> "OD2" Residue "S PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 42": "OE1" <-> "OE2" Residue "M ASP 59": "OD1" <-> "OD2" Residue "M PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 70": "OE1" <-> "OE2" Residue "M GLU 73": "OE1" <-> "OE2" Residue "M PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 116": "OD1" <-> "OD2" Residue "M GLU 141": "OE1" <-> "OE2" Residue "M GLU 143": "OE1" <-> "OE2" Residue "M PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 186": "OE1" <-> "OE2" Residue "Z ASP 102": "OD1" <-> "OD2" Residue "Z GLU 119": "OE1" <-> "OE2" Residue "Z TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 161": "NH1" <-> "NH2" Residue "Z TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 225": "OE1" <-> "OE2" Residue "Z PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 409": "OD1" <-> "OD2" Residue "Z ARG 429": "NH1" <-> "NH2" Residue "Z ARG 440": "NH1" <-> "NH2" Residue "Z ASP 486": "OD1" <-> "OD2" Residue "Z GLU 521": "OE1" <-> "OE2" Residue "Z GLU 541": "OE1" <-> "OE2" Residue "Z PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 18": "OE1" <-> "OE2" Residue "A PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 45": "NH1" <-> "NH2" Residue "A ARG 46": "NH1" <-> "NH2" Residue "A ASP 78": "OD1" <-> "OD2" Residue "A ASP 98": "OD1" <-> "OD2" Residue "A ARG 99": "NH1" <-> "NH2" Residue "A ARG 139": "NH1" <-> "NH2" Residue "A ASP 174": "OD1" <-> "OD2" Residue "A ARG 180": "NH1" <-> "NH2" Residue "A PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 4": "OE1" <-> "OE2" Residue "B PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 61": "OD1" <-> "OD2" Residue "B GLU 96": "OE1" <-> "OE2" Residue "B GLU 114": "OE1" <-> "OE2" Residue "B GLU 120": "OE1" <-> "OE2" Residue "B GLU 142": "OE1" <-> "OE2" Residue "B ARG 183": "NH1" <-> "NH2" Residue "B ARG 186": "NH1" <-> "NH2" Residue "B ARG 187": "NH1" <-> "NH2" Residue "B GLU 207": "OE1" <-> "OE2" Residue "B ARG 210": "NH1" <-> "NH2" Residue "B GLU 227": "OE1" <-> "OE2" Residue "B GLU 228": "OE1" <-> "OE2" Residue "C PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 75": "OD1" <-> "OD2" Residue "C PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 91": "NH1" <-> "NH2" Residue "C TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 96": "OD1" <-> "OD2" Residue "C TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 362": "OD1" <-> "OD2" Residue "C PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 401": "OD1" <-> "OD2" Residue "C ARG 439": "NH1" <-> "NH2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C TYR 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 507": "OE1" <-> "OE2" Residue "C ASP 519": "OD1" <-> "OD2" Residue "C ARG 543": "NH1" <-> "NH2" Residue "C ASP 544": "OD1" <-> "OD2" Residue "C ARG 551": "NH1" <-> "NH2" Residue "C TYR 581": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 583": "NH1" <-> "NH2" Residue "C TYR 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 615": "OD1" <-> "OD2" Residue "C ARG 652": "NH1" <-> "NH2" Residue "C ASP 657": "OD1" <-> "OD2" Residue "C ARG 713": "NH1" <-> "NH2" Residue "C GLU 729": "OE1" <-> "OE2" Residue "C PHE 806": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 816": "OD1" <-> "OD2" Residue "C PHE 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1156": "NH1" <-> "NH2" Residue "C TYR 1163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1180": "OE1" <-> "OE2" Residue "C ASP 1200": "OD1" <-> "OD2" Residue "C PHE 1225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1234": "OD1" <-> "OD2" Residue "C TYR 1263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1284": "OE1" <-> "OE2" Residue "C ARG 1313": "NH1" <-> "NH2" Residue "C ARG 1343": "NH1" <-> "NH2" Residue "C TYR 1353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 45": "NH1" <-> "NH2" Residue "D GLU 50": "OE1" <-> "OE2" Residue "D PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 99": "NH1" <-> "NH2" Residue "D PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 127": "OD1" <-> "OD2" Residue "D TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 146": "OD1" <-> "OD2" Residue "D GLU 193": "OE1" <-> "OE2" Residue "D ASP 262": "OD1" <-> "OD2" Residue "D ARG 310": "NH1" <-> "NH2" Residue "D TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 384": "NH1" <-> "NH2" Residue "D ARG 397": "NH1" <-> "NH2" Residue "D ARG 429": "NH1" <-> "NH2" Residue "D PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 513": "NH1" <-> "NH2" Residue "D TYR 624": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 646": "OD1" <-> "OD2" Residue "D GLU 656": "OE1" <-> "OE2" Residue "D GLU 673": "OE1" <-> "OE2" Residue "D ARG 728": "NH1" <-> "NH2" Residue "D TYR 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 799": "OD1" <-> "OD2" Residue "D ARG 839": "NH1" <-> "NH2" Residue "D GLU 909": "OE1" <-> "OE2" Residue "D GLU 1242": "OE1" <-> "OE2" Residue "D TYR 1290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1291": "OE1" <-> "OE2" Residue "D ARG 1299": "NH1" <-> "NH2" Residue "D GLU 1315": "OE1" <-> "OE2" Residue "D ARG 1318": "NH1" <-> "NH2" Residue "D ARG 1343": "NH1" <-> "NH2" Residue "D ARG 1354": "NH1" <-> "NH2" Residue "E ASP 11": "OD1" <-> "OD2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "E GLU 57": "OE1" <-> "OE2" Residue "E GLU 63": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 30440 Number of models: 1 Model: "" Number of chains: 13 Chain: "G" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 720 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain: "H" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 487 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "X" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 225 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "J" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 226 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "S" Number of atoms: 1583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1583 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 8, 'TRANS': 193} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 34 Chain: "M" Number of atoms: 1598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1598 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 189} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "Z" Number of atoms: 3772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3772 Classifications: {'peptide': 470} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 13, 'TRANS': 456} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 94 Chain: "A" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1688 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 215} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1769 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 225} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 8922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1186, 8922 Classifications: {'peptide': 1186} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'PTRANS': 42, 'TRANS': 1143} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 374 Unresolved non-hydrogen angles: 458 Unresolved non-hydrogen dihedrals: 305 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 7, 'ARG:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 23, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 214 Chain: "D" Number of atoms: 8880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1159, 8880 Classifications: {'peptide': 1159} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 1117} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 253 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 5, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 110 Chain: "E" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 567 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 71} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 21447 SG CYS D 68 54.808 112.593 78.930 1.00101.55 S ATOM 21461 SG CYS D 70 54.068 114.400 81.620 1.00105.52 S ATOM 21568 SG CYS D 83 53.837 116.395 78.229 1.00101.89 S ATOM 21594 SG CYS D 86 57.024 115.077 79.776 1.00105.62 S ATOM 27252 SG CYS D 811 91.678 91.212 24.655 1.00112.74 S ATOM 27789 SG CYS D 884 91.914 91.954 28.120 1.00102.18 S ATOM 27845 SG CYS D 891 90.163 88.539 26.607 1.00106.21 S ATOM 27865 SG CYS D 894 93.572 89.157 26.499 1.00 98.73 S Time building chain proxies: 15.89, per 1000 atoms: 0.52 Number of scatterers: 30440 At special positions: 0 Unit cell: (161.12, 185.5, 146.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 119 16.00 P 81 15.00 Mg 1 11.99 O 5961 8.00 N 5281 7.00 C 18995 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 11.29 Conformation dependent library (CDL) restraints added in 5.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 83 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 86 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 68 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 884 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 891 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 811 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 894 " Number of angles added : 12 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7034 Finding SS restraints... Secondary structure from input PDB file: 141 helices and 35 sheets defined 43.6% alpha, 9.7% beta 25 base pairs and 58 stacking pairs defined. Time for finding SS restraints: 10.47 Creating SS restraints... Processing helix chain 'S' and resid 12 through 25 Processing helix chain 'S' and resid 38 through 46 removed outlier: 3.916A pdb=" N THR S 46 " --> pdb=" O ILE S 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 66 through 75 removed outlier: 3.539A pdb=" N PHE S 75 " --> pdb=" O ILE S 71 " (cutoff:3.500A) Processing helix chain 'S' and resid 84 through 101 removed outlier: 3.686A pdb=" N ARG S 92 " --> pdb=" O ARG S 88 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU S 101 " --> pdb=" O LYS S 97 " (cutoff:3.500A) Processing helix chain 'S' and resid 102 through 112 removed outlier: 3.774A pdb=" N LEU S 106 " --> pdb=" O TRP S 102 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN S 108 " --> pdb=" O PRO S 104 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ILE S 109 " --> pdb=" O VAL S 105 " (cutoff:3.500A) Processing helix chain 'S' and resid 115 through 135 removed outlier: 3.720A pdb=" N ASP S 125 " --> pdb=" O SER S 121 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS S 135 " --> pdb=" O LEU S 131 " (cutoff:3.500A) Processing helix chain 'S' and resid 149 through 164 removed outlier: 3.691A pdb=" N CYS S 153 " --> pdb=" O THR S 149 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA S 156 " --> pdb=" O ASP S 152 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ALA S 157 " --> pdb=" O CYS S 153 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU S 158 " --> pdb=" O TYR S 154 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU S 162 " --> pdb=" O LEU S 158 " (cutoff:3.500A) Processing helix chain 'S' and resid 182 through 186 removed outlier: 3.541A pdb=" N ALA S 185 " --> pdb=" O ARG S 182 " (cutoff:3.500A) Processing helix chain 'S' and resid 203 through 209 Processing helix chain 'M' and resid 9 through 23 removed outlier: 3.594A pdb=" N LYS M 22 " --> pdb=" O ILE M 18 " (cutoff:3.500A) Processing helix chain 'M' and resid 33 through 35 No H-bonds generated for 'chain 'M' and resid 33 through 35' Processing helix chain 'M' and resid 36 through 47 Processing helix chain 'M' and resid 64 through 76 removed outlier: 3.517A pdb=" N ILE M 68 " --> pdb=" O ARG M 64 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 111 removed outlier: 4.256A pdb=" N GLN M 105 " --> pdb=" O LYS M 101 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ASN M 106 " --> pdb=" O THR M 102 " (cutoff:3.500A) Processing helix chain 'M' and resid 116 through 148 removed outlier: 3.673A pdb=" N ALA M 120 " --> pdb=" O ASP M 116 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ILE M 132 " --> pdb=" O GLN M 128 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N SER M 133 " --> pdb=" O ARG M 129 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER M 148 " --> pdb=" O VAL M 144 " (cutoff:3.500A) Processing helix chain 'M' and resid 156 through 171 removed outlier: 3.829A pdb=" N LEU M 160 " --> pdb=" O ASN M 156 " (cutoff:3.500A) Processing helix chain 'M' and resid 180 through 192 Processing helix chain 'M' and resid 193 through 201 removed outlier: 3.729A pdb=" N LYS M 198 " --> pdb=" O PRO M 194 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N THR M 199 " --> pdb=" O ASN M 195 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE M 200 " --> pdb=" O PHE M 196 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS M 201 " --> pdb=" O ILE M 197 " (cutoff:3.500A) Processing helix chain 'Z' and resid 86 through 96 removed outlier: 3.930A pdb=" N MET Z 90 " --> pdb=" O ASP Z 86 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLU Z 94 " --> pdb=" O MET Z 90 " (cutoff:3.500A) Processing helix chain 'Z' and resid 102 through 125 Processing helix chain 'Z' and resid 128 through 150 removed outlier: 3.975A pdb=" N LYS Z 132 " --> pdb=" O PRO Z 128 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N TYR Z 148 " --> pdb=" O LYS Z 144 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N MET Z 149 " --> pdb=" O ALA Z 145 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASN Z 150 " --> pdb=" O ILE Z 146 " (cutoff:3.500A) Processing helix chain 'Z' and resid 194 through 213 Processing helix chain 'Z' and resid 216 through 229 removed outlier: 3.629A pdb=" N LEU Z 229 " --> pdb=" O GLU Z 225 " (cutoff:3.500A) Processing helix chain 'Z' and resid 233 through 262 Proline residue: Z 246 - end of helix Processing helix chain 'Z' and resid 271 through 276 removed outlier: 3.518A pdb=" N VAL Z 275 " --> pdb=" O GLU Z 271 " (cutoff:3.500A) Processing helix chain 'Z' and resid 285 through 290 Processing helix chain 'Z' and resid 294 through 316 Processing helix chain 'Z' and resid 318 through 321 Processing helix chain 'Z' and resid 322 through 345 Processing helix chain 'Z' and resid 347 through 355 removed outlier: 3.909A pdb=" N VAL Z 351 " --> pdb=" O ASN Z 347 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL Z 352 " --> pdb=" O LEU Z 348 " (cutoff:3.500A) Processing helix chain 'Z' and resid 364 through 381 removed outlier: 3.683A pdb=" N ILE Z 368 " --> pdb=" O HIS Z 364 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA Z 379 " --> pdb=" O GLY Z 375 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ASP Z 381 " --> pdb=" O MET Z 377 " (cutoff:3.500A) Processing helix chain 'Z' and resid 390 through 411 removed outlier: 3.554A pdb=" N TYR Z 394 " --> pdb=" O LYS Z 390 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR Z 396 " --> pdb=" O SER Z 392 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N TRP Z 397 " --> pdb=" O THR Z 393 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N TRP Z 398 " --> pdb=" O TYR Z 394 " (cutoff:3.500A) Processing helix chain 'Z' and resid 417 through 439 Processing helix chain 'Z' and resid 443 through 450 removed outlier: 3.598A pdb=" N HIS Z 450 " --> pdb=" O GLU Z 446 " (cutoff:3.500A) Processing helix chain 'Z' and resid 458 through 463 removed outlier: 3.704A pdb=" N LEU Z 463 " --> pdb=" O LEU Z 459 " (cutoff:3.500A) Processing helix chain 'Z' and resid 483 through 487 Processing helix chain 'Z' and resid 502 through 507 Processing helix chain 'Z' and resid 508 through 513 Processing helix chain 'Z' and resid 514 through 516 No H-bonds generated for 'chain 'Z' and resid 514 through 516' Processing helix chain 'Z' and resid 519 through 530 Processing helix chain 'Z' and resid 538 through 546 removed outlier: 3.722A pdb=" N LYS Z 544 " --> pdb=" O GLU Z 540 " (cutoff:3.500A) Processing helix chain 'Z' and resid 551 through 565 removed outlier: 3.851A pdb=" N GLN Z 555 " --> pdb=" O GLU Z 551 " (cutoff:3.500A) Processing helix chain 'Z' and resid 572 through 577 removed outlier: 3.723A pdb=" N THR Z 575 " --> pdb=" O PHE Z 572 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU Z 577 " --> pdb=" O LYS Z 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 49 removed outlier: 3.825A pdb=" N ASN A 42 " --> pdb=" O HIS A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 88 removed outlier: 3.989A pdb=" N LYS A 88 " --> pdb=" O SER A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 117 No H-bonds generated for 'chain 'A' and resid 115 through 117' Processing helix chain 'A' and resid 205 through 222 Processing helix chain 'B' and resid 32 through 48 removed outlier: 3.730A pdb=" N THR B 36 " --> pdb=" O GLY B 32 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 85 Processing helix chain 'B' and resid 204 through 219 removed outlier: 3.597A pdb=" N ILE B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 231 Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.904A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N TYR C 35 " --> pdb=" O GLN C 31 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS C 36 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS C 37 " --> pdb=" O GLU C 33 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N PHE C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 58 removed outlier: 3.613A pdb=" N GLN C 58 " --> pdb=" O ILE C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 91 removed outlier: 3.500A pdb=" N GLN C 89 " --> pdb=" O GLU C 85 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL C 90 " --> pdb=" O THR C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 212 removed outlier: 3.894A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 354 removed outlier: 4.052A pdb=" N LYS C 354 " --> pdb=" O SER C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 373 removed outlier: 3.569A pdb=" N ALA C 364 " --> pdb=" O ASN C 360 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 365 " --> pdb=" O THR C 361 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS C 370 " --> pdb=" O VAL C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 391 removed outlier: 3.853A pdb=" N GLU C 388 " --> pdb=" O LYS C 384 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE C 391 " --> pdb=" O PHE C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 412 removed outlier: 3.538A pdb=" N ARG C 410 " --> pdb=" O LYS C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 441 Processing helix chain 'C' and resid 450 through 452 No H-bonds generated for 'chain 'C' and resid 450 through 452' Processing helix chain 'C' and resid 458 through 479 removed outlier: 4.080A pdb=" N GLU C 464 " --> pdb=" O GLY C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 512 removed outlier: 3.849A pdb=" N THR C 502 " --> pdb=" O SER C 498 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ALA C 504 " --> pdb=" O PRO C 500 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLU C 507 " --> pdb=" O ALA C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 531 removed outlier: 3.566A pdb=" N GLU C 526 " --> pdb=" O ASN C 522 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL C 527 " --> pdb=" O PRO C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 558 removed outlier: 3.995A pdb=" N TYR C 558 " --> pdb=" O ALA C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 616 Processing helix chain 'C' and resid 651 through 653 No H-bonds generated for 'chain 'C' and resid 651 through 653' Processing helix chain 'C' and resid 673 through 677 Processing helix chain 'C' and resid 679 through 689 removed outlier: 3.738A pdb=" N MET C 684 " --> pdb=" O ASN C 680 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLN C 689 " --> pdb=" O GLY C 685 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 712 removed outlier: 3.877A pdb=" N ALA C 712 " --> pdb=" O GLU C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 715 No H-bonds generated for 'chain 'C' and resid 713 through 715' Processing helix chain 'C' and resid 741 through 744 Processing helix chain 'C' and resid 822 through 827 removed outlier: 3.599A pdb=" N LYS C 826 " --> pdb=" O GLU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 898 through 908 removed outlier: 3.562A pdb=" N PHE C 908 " --> pdb=" O LEU C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 944 through 980 removed outlier: 4.230A pdb=" N ILE C 950 " --> pdb=" O ARG C 946 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASP C 961 " --> pdb=" O LYS C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 1030 through 1046 Processing helix chain 'C' and resid 1095 through 1099 removed outlier: 3.706A pdb=" N MET C1099 " --> pdb=" O VAL C1096 " (cutoff:3.500A) Processing helix chain 'C' and resid 1115 through 1120 removed outlier: 4.374A pdb=" N SER C1119 " --> pdb=" O LEU C1115 " (cutoff:3.500A) Processing helix chain 'C' and resid 1123 through 1147 removed outlier: 3.725A pdb=" N LEU C1127 " --> pdb=" O ILE C1123 " (cutoff:3.500A) Processing helix chain 'C' and resid 1152 through 1165 removed outlier: 3.693A pdb=" N SER C1165 " --> pdb=" O GLU C1161 " (cutoff:3.500A) Processing helix chain 'C' and resid 1172 through 1176 removed outlier: 3.506A pdb=" N ALA C1175 " --> pdb=" O ASN C1172 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU C1176 " --> pdb=" O LEU C1173 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1172 through 1176' Processing helix chain 'C' and resid 1179 through 1188 removed outlier: 3.622A pdb=" N ASP C1186 " --> pdb=" O LEU C1182 " (cutoff:3.500A) Processing helix chain 'C' and resid 1203 through 1215 Processing helix chain 'C' and resid 1284 through 1293 removed outlier: 3.707A pdb=" N TRP C1288 " --> pdb=" O GLU C1284 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA C1289 " --> pdb=" O MET C1285 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU C1290 " --> pdb=" O GLU C1286 " (cutoff:3.500A) Processing helix chain 'C' and resid 1295 through 1301 Processing helix chain 'C' and resid 1309 through 1323 removed outlier: 3.820A pdb=" N SER C1314 " --> pdb=" O ILE C1310 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL C1321 " --> pdb=" O TYR C1317 " (cutoff:3.500A) Processing helix chain 'C' and resid 1333 through 1344 Processing helix chain 'D' and resid 24 through 32 removed outlier: 3.519A pdb=" N SER D 32 " --> pdb=" O ILE D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 96 Processing helix chain 'D' and resid 120 through 127 Processing helix chain 'D' and resid 129 through 138 removed outlier: 3.515A pdb=" N VAL D 136 " --> pdb=" O ASN D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 171 Processing helix chain 'D' and resid 179 through 189 removed outlier: 3.540A pdb=" N ILE D 183 " --> pdb=" O GLY D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 205 removed outlier: 3.567A pdb=" N GLU D 202 " --> pdb=" O LEU D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 229 removed outlier: 3.929A pdb=" N LEU D 219 " --> pdb=" O ALA D 215 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG D 220 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY D 229 " --> pdb=" O PHE D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 234 Processing helix chain 'D' and resid 244 through 248 Processing helix chain 'D' and resid 261 through 284 removed outlier: 3.856A pdb=" N ASP D 265 " --> pdb=" O SER D 261 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU D 266 " --> pdb=" O ASP D 262 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN D 272 " --> pdb=" O ARG D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 307 removed outlier: 3.709A pdb=" N GLN D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 329 Processing helix chain 'D' and resid 335 through 340 removed outlier: 3.659A pdb=" N ASN D 339 " --> pdb=" O ARG D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 375 Processing helix chain 'D' and resid 375 through 387 Processing helix chain 'D' and resid 391 through 400 removed outlier: 3.917A pdb=" N ALA D 395 " --> pdb=" O THR D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 414 removed outlier: 4.021A pdb=" N TRP D 407 " --> pdb=" O GLU D 403 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP D 408 " --> pdb=" O ALA D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 430 No H-bonds generated for 'chain 'D' and resid 428 through 430' Processing helix chain 'D' and resid 448 through 452 Processing helix chain 'D' and resid 473 through 482 removed outlier: 4.183A pdb=" N ARG D 479 " --> pdb=" O GLN D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 487 Processing helix chain 'D' and resid 503 through 512 removed outlier: 3.722A pdb=" N LEU D 508 " --> pdb=" O ILE D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 527 through 537 Processing helix chain 'D' and resid 572 through 577 removed outlier: 3.591A pdb=" N LEU D 576 " --> pdb=" O VAL D 572 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU D 577 " --> pdb=" O GLY D 573 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 572 through 577' Processing helix chain 'D' and resid 586 through 590 Processing helix chain 'D' and resid 595 through 611 removed outlier: 3.635A pdb=" N LYS D 601 " --> pdb=" O LYS D 597 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY D 611 " --> pdb=" O PHE D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 630 removed outlier: 3.696A pdb=" N LYS D 628 " --> pdb=" O TYR D 624 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 668 removed outlier: 3.822A pdb=" N ALA D 655 " --> pdb=" O LYS D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 673 through 700 removed outlier: 3.737A pdb=" N MET D 695 " --> pdb=" O VAL D 691 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N MET D 696 " --> pdb=" O GLY D 692 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASP D 697 " --> pdb=" O ALA D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 725 removed outlier: 3.847A pdb=" N ALA D 723 " --> pdb=" O VAL D 719 " (cutoff:3.500A) Processing helix chain 'D' and resid 730 through 739 removed outlier: 3.513A pdb=" N MET D 734 " --> pdb=" O SER D 730 " (cutoff:3.500A) Processing helix chain 'D' and resid 765 through 785 removed outlier: 3.568A pdb=" N SER D 772 " --> pdb=" O GLN D 768 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N HIS D 774 " --> pdb=" O PHE D 770 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N GLY D 775 " --> pdb=" O THR D 771 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR D 783 " --> pdb=" O GLY D 779 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA D 784 " --> pdb=" O LEU D 780 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 802 Processing helix chain 'D' and resid 831 through 836 Processing helix chain 'D' and resid 865 through 870 removed outlier: 4.464A pdb=" N ASP D 869 " --> pdb=" O VAL D 865 " (cutoff:3.500A) Processing helix chain 'D' and resid 880 through 884 Processing helix chain 'D' and resid 910 through 918 removed outlier: 3.647A pdb=" N ILE D 914 " --> pdb=" O SER D 910 " (cutoff:3.500A) Processing helix chain 'D' and resid 921 through 925 Processing helix chain 'D' and resid 1125 through 1133 Processing helix chain 'D' and resid 1207 through 1212 Processing helix chain 'D' and resid 1212 through 1231 removed outlier: 4.435A pdb=" N GLU D1216 " --> pdb=" O LYS D1212 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N PHE D1217 " --> pdb=" O GLY D1213 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER D1227 " --> pdb=" O ILE D1223 " (cutoff:3.500A) Processing helix chain 'D' and resid 1237 through 1246 removed outlier: 3.970A pdb=" N ILE D1241 " --> pdb=" O ASN D1237 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR D1243 " --> pdb=" O LYS D1239 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE D1244 " --> pdb=" O HIS D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1247 through 1249 No H-bonds generated for 'chain 'D' and resid 1247 through 1249' Processing helix chain 'D' and resid 1268 through 1282 removed outlier: 3.943A pdb=" N GLU D1276 " --> pdb=" O ARG D1272 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU D1280 " --> pdb=" O GLU D1276 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG D1281 " --> pdb=" O ASN D1277 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS D1282 " --> pdb=" O ASP D1278 " (cutoff:3.500A) Processing helix chain 'D' and resid 1296 through 1303 Processing helix chain 'D' and resid 1306 through 1314 removed outlier: 3.659A pdb=" N GLN D1314 " --> pdb=" O ALA D1310 " (cutoff:3.500A) Processing helix chain 'D' and resid 1315 through 1326 removed outlier: 4.053A pdb=" N ILE D1325 " --> pdb=" O THR D1321 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN D1326 " --> pdb=" O GLU D1322 " (cutoff:3.500A) Processing helix chain 'D' and resid 1347 through 1357 removed outlier: 3.637A pdb=" N ALA D1352 " --> pdb=" O GLY D1348 " (cutoff:3.500A) Processing helix chain 'D' and resid 1357 through 1365 removed outlier: 3.627A pdb=" N GLU D1361 " --> pdb=" O SER D1357 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS D1362 " --> pdb=" O ALA D1358 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N MET D1363 " --> pdb=" O LYS D1359 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 10 Processing helix chain 'E' and resid 17 through 33 Processing helix chain 'E' and resid 46 through 57 removed outlier: 4.196A pdb=" N LEU E 52 " --> pdb=" O THR E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 67 removed outlier: 4.180A pdb=" N ARG E 67 " --> pdb=" O GLU E 63 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'S' and resid 5 through 8 Processing sheet with id=AA2, first strand: chain 'M' and resid 27 through 29 removed outlier: 6.249A pdb=" N LEU M 3 " --> pdb=" O VAL M 29 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR M 54 " --> pdb=" O TYR M 4 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Z' and resid 470 through 471 removed outlier: 6.955A pdb=" N ILE Z 470 " --> pdb=" O THR D 260 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 14 through 15 Processing sheet with id=AA5, first strand: chain 'A' and resid 99 through 106 removed outlier: 7.302A pdb=" N SER A 142 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ILE A 62 " --> pdb=" O SER A 142 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N THR A 144 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N VAL A 60 " --> pdb=" O THR A 144 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR A 146 " --> pdb=" O ILE A 58 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 111 through 113 Processing sheet with id=AA7, first strand: chain 'B' and resid 15 through 18 removed outlier: 3.589A pdb=" N TYR B 17 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ALA B 21 " --> pdb=" O TYR B 17 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ASP B 191 " --> pdb=" O ALA B 28 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU B 190 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA B 182 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 98 through 101 removed outlier: 6.784A pdb=" N GLU B 142 " --> pdb=" O ILE B 57 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ILE B 57 " --> pdb=" O GLU B 142 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LYS B 144 " --> pdb=" O THR B 55 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 110 through 112 removed outlier: 7.062A pdb=" N ILE B 111 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 13 through 14 removed outlier: 7.202A pdb=" N LYS C 13 " --> pdb=" O ALA C1195 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 72 through 78 removed outlier: 6.117A pdb=" N TYR C 73 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ARG C 104 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASP C 75 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY C 130 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL C 101 " --> pdb=" O TYR C 128 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N TYR C 128 " --> pdb=" O VAL C 101 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N LEU C 103 " --> pdb=" O TYR C 126 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N TYR C 126 " --> pdb=" O LEU C 103 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AB4, first strand: chain 'C' and resid 454 through 457 Processing sheet with id=AB5, first strand: chain 'C' and resid 175 through 176 removed outlier: 3.826A pdb=" N ILE C 176 " --> pdb=" O LEU C 184 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP C 185 " --> pdb=" O ARG C 197 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG C 197 " --> pdb=" O ASP C 185 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 601 through 609 removed outlier: 5.502A pdb=" N LYS C 596 " --> pdb=" O THR C 603 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N GLU C 605 " --> pdb=" O TYR C 594 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N TYR C 594 " --> pdb=" O GLU C 605 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLU C 607 " --> pdb=" O ALA C 592 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ALA C 592 " --> pdb=" O GLU C 607 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 636 through 640 Processing sheet with id=AB8, first strand: chain 'C' and resid 751 through 754 removed outlier: 7.084A pdb=" N ARG C 734 " --> pdb=" O VAL C 730 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N VAL C 730 " --> pdb=" O ARG C 734 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL C 736 " --> pdb=" O ALA C 728 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY C 725 " --> pdb=" O VAL C 779 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 791 through 792 Processing sheet with id=AC1, first strand: chain 'C' and resid 1110 through 1112 removed outlier: 3.660A pdb=" N LEU C1112 " --> pdb=" O ALA C 805 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE C 806 " --> pdb=" O THR C1238 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N THR C1238 " --> pdb=" O PHE C 806 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 818 through 820 removed outlier: 7.208A pdb=" N ILE C 818 " --> pdb=" O SER C1091 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL C1093 " --> pdb=" O ILE C 818 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU C 820 " --> pdb=" O VAL C1093 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 848 through 849 removed outlier: 3.697A pdb=" N LYS C1062 " --> pdb=" O ALA C 842 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ASP C 844 " --> pdb=" O VAL C1060 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N VAL C1060 " --> pdb=" O ASP C 844 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASN C 932 " --> pdb=" O PHE C1067 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA C1069 " --> pdb=" O VAL C 930 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N VAL C 930 " --> pdb=" O ALA C1069 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 884 through 886 removed outlier: 6.633A pdb=" N LEU C 920 " --> pdb=" O LEU C 885 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 890 through 891 Processing sheet with id=AC6, first strand: chain 'C' and resid 1101 through 1102 Processing sheet with id=AC7, first strand: chain 'C' and resid 1257 through 1258 removed outlier: 6.110A pdb=" N CYS D 364 " --> pdb=" O ARG D 438 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE D 440 " --> pdb=" O CYS D 364 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LEU D 366 " --> pdb=" O ILE D 440 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1257 through 1258 Processing sheet with id=AC9, first strand: chain 'C' and resid 1350 through 1352 removed outlier: 3.534A pdb=" N LYS D 19 " --> pdb=" O ASP C1350 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE D 17 " --> pdb=" O ASP C1352 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE D 18 " --> pdb=" O ASP D1330 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 103 through 110 removed outlier: 11.013A pdb=" N CYS D 107 " --> pdb=" O VAL D 239 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N VAL D 239 " --> pdb=" O CYS D 107 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 142 through 143 Processing sheet with id=AD3, first strand: chain 'D' and resid 524 through 525 Processing sheet with id=AD4, first strand: chain 'D' and resid 701 through 706 Processing sheet with id=AD5, first strand: chain 'D' and resid 806 through 808 Processing sheet with id=AD6, first strand: chain 'D' and resid 817 through 819 removed outlier: 3.506A pdb=" N ILE D 876 " --> pdb=" O PHE D 819 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 845 through 846 removed outlier: 6.722A pdb=" N VAL D 845 " --> pdb=" O LEU D 853 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 1265 through 1267 removed outlier: 4.799A pdb=" N LYS D1251 " --> pdb=" O VAL D1293 " (cutoff:3.500A) 1134 hydrogen bonds defined for protein. 3210 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 62 hydrogen bonds 124 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 58 stacking parallelities Total time for adding SS restraints: 13.49 Time building geometry restraints manager: 12.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8531 1.33 - 1.45: 5074 1.45 - 1.57: 17077 1.57 - 1.69: 158 1.69 - 1.81: 206 Bond restraints: 31046 Sorted by residual: bond pdb=" CA GLN D 736 " pdb=" C GLN D 736 " ideal model delta sigma weight residual 1.522 1.468 0.055 1.38e-02 5.25e+03 1.56e+01 bond pdb=" C VAL M 84 " pdb=" N PHE M 85 " ideal model delta sigma weight residual 1.332 1.285 0.047 1.44e-02 4.82e+03 1.08e+01 bond pdb=" CA ALA C1344 " pdb=" C ALA C1344 " ideal model delta sigma weight residual 1.523 1.469 0.054 1.80e-02 3.09e+03 9.14e+00 bond pdb=" CA ASN D1326 " pdb=" C ASN D1326 " ideal model delta sigma weight residual 1.523 1.472 0.051 1.80e-02 3.09e+03 8.10e+00 bond pdb=" C ARG C1073 " pdb=" N ILE C1074 " ideal model delta sigma weight residual 1.334 1.303 0.031 1.29e-02 6.01e+03 5.69e+00 ... (remaining 31041 not shown) Histogram of bond angle deviations from ideal: 98.46 - 105.58: 826 105.58 - 112.71: 17057 112.71 - 119.83: 10388 119.83 - 126.95: 13627 126.95 - 134.07: 379 Bond angle restraints: 42277 Sorted by residual: angle pdb=" N VAL E 49 " pdb=" CA VAL E 49 " pdb=" C VAL E 49 " ideal model delta sigma weight residual 112.96 108.35 4.61 1.00e+00 1.00e+00 2.12e+01 angle pdb=" N GLU Z 271 " pdb=" CA GLU Z 271 " pdb=" C GLU Z 271 " ideal model delta sigma weight residual 112.57 107.61 4.96 1.13e+00 7.83e-01 1.92e+01 angle pdb=" C PRO S 52 " pdb=" N VAL S 53 " pdb=" CA VAL S 53 " ideal model delta sigma weight residual 121.97 115.32 6.65 1.80e+00 3.09e-01 1.37e+01 angle pdb=" C VAL M 84 " pdb=" N PHE M 85 " pdb=" CA PHE M 85 " ideal model delta sigma weight residual 122.28 116.16 6.12 1.77e+00 3.19e-01 1.19e+01 angle pdb=" C ILE C 198 " pdb=" N ASP C 199 " pdb=" CA ASP C 199 " ideal model delta sigma weight residual 121.54 128.14 -6.60 1.91e+00 2.74e-01 1.19e+01 ... (remaining 42272 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.20: 15868 18.20 - 36.40: 2164 36.40 - 54.60: 645 54.60 - 72.79: 148 72.79 - 90.99: 43 Dihedral angle restraints: 18868 sinusoidal: 7999 harmonic: 10869 Sorted by residual: dihedral pdb=" CA LYS Z 213 " pdb=" C LYS Z 213 " pdb=" N PRO Z 214 " pdb=" CA PRO Z 214 " ideal model delta harmonic sigma weight residual -180.00 -148.56 -31.44 0 5.00e+00 4.00e-02 3.95e+01 dihedral pdb=" CA GLN D1283 " pdb=" C GLN D1283 " pdb=" N GLY D1284 " pdb=" CA GLY D1284 " ideal model delta harmonic sigma weight residual 180.00 152.13 27.87 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA THR D 354 " pdb=" C THR D 354 " pdb=" N VAL D 355 " pdb=" CA VAL D 355 " ideal model delta harmonic sigma weight residual -180.00 -152.66 -27.34 0 5.00e+00 4.00e-02 2.99e+01 ... (remaining 18865 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 3210 0.042 - 0.084: 1351 0.084 - 0.126: 333 0.126 - 0.168: 29 0.168 - 0.210: 4 Chirality restraints: 4927 Sorted by residual: chirality pdb=" CA TYR C 812 " pdb=" N TYR C 812 " pdb=" C TYR C 812 " pdb=" CB TYR C 812 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA PRO C 523 " pdb=" N PRO C 523 " pdb=" C PRO C 523 " pdb=" CB PRO C 523 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.59e-01 chirality pdb=" CA PHE C 60 " pdb=" N PHE C 60 " pdb=" C PHE C 60 " pdb=" CB PHE C 60 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.49e-01 ... (remaining 4924 not shown) Planarity restraints: 5167 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR Z 267 " 0.043 5.00e-02 4.00e+02 6.52e-02 6.80e+00 pdb=" N PRO Z 268 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO Z 268 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO Z 268 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 159 " 0.039 5.00e-02 4.00e+02 5.88e-02 5.54e+00 pdb=" N PRO A 160 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 160 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 160 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS Z 566 " 0.037 5.00e-02 4.00e+02 5.68e-02 5.16e+00 pdb=" N PRO Z 567 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO Z 567 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO Z 567 " 0.031 5.00e-02 4.00e+02 ... (remaining 5164 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 662 2.61 - 3.18: 29279 3.18 - 3.76: 45709 3.76 - 4.33: 62370 4.33 - 4.90: 98810 Nonbonded interactions: 236830 Sorted by model distance: nonbonded pdb=" O ILE Z 447 " pdb=" OG1 THR Z 451 " model vdw 2.040 2.440 nonbonded pdb=" O GLU C1161 " pdb=" OG SER C1165 " model vdw 2.058 2.440 nonbonded pdb=" O ASP C 519 " pdb=" OG SER C 525 " model vdw 2.080 2.440 nonbonded pdb=" OD2 ASP M 13 " pdb=" OH TYR M 168 " model vdw 2.110 2.440 nonbonded pdb=" OD1 ASP D 462 " pdb="MG MG D1501 " model vdw 2.112 2.170 ... (remaining 236825 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 3.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 13.880 Check model and map are aligned: 0.480 Set scattering table: 0.280 Process input model: 92.160 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.119 31046 Z= 0.532 Angle : 0.787 9.979 42277 Z= 0.442 Chirality : 0.046 0.210 4927 Planarity : 0.004 0.065 5167 Dihedral : 18.640 90.994 11834 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.67 % Favored : 85.20 % Rotamer: Outliers : 9.74 % Allowed : 22.41 % Favored : 67.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.79 % 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: -4.89 (0.11), residues: 3715 helix: -2.62 (0.11), residues: 1442 sheet: -3.36 (0.22), residues: 367 loop : -3.83 (0.12), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 183 HIS 0.008 0.001 HIS Z 566 PHE 0.020 0.002 PHE A 183 TYR 0.019 0.002 TYR C 35 ARG 0.005 0.000 ARG C 457 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 907 residues out of total 3271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 296 poor density : 611 time to evaluate : 3.990 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: S 44 LYS cc_start: 0.7048 (OUTLIER) cc_final: 0.6741 (mmtt) REVERT: S 54 LEU cc_start: 0.6522 (OUTLIER) cc_final: 0.6251 (tp) REVERT: S 90 LYS cc_start: 0.8212 (mttp) cc_final: 0.7852 (ptpt) REVERT: S 110 ARG cc_start: 0.7591 (ttm110) cc_final: 0.7003 (tpm170) REVERT: S 133 MET cc_start: 0.8912 (mmm) cc_final: 0.8651 (mmt) REVERT: S 154 TYR cc_start: 0.8027 (OUTLIER) cc_final: 0.7296 (m-10) REVERT: M 76 TYR cc_start: 0.8695 (m-80) cc_final: 0.8487 (m-80) REVERT: M 153 GLN cc_start: 0.7809 (pp30) cc_final: 0.7355 (pp30) REVERT: Z 124 ILE cc_start: 0.9030 (mm) cc_final: 0.8821 (mm) REVERT: Z 127 TYR cc_start: 0.7214 (m-80) cc_final: 0.6793 (m-80) REVERT: Z 149 MET cc_start: 0.3731 (ttt) cc_final: 0.3302 (tpp) REVERT: Z 230 ARG cc_start: 0.7394 (tmt-80) cc_final: 0.5571 (mtt90) REVERT: Z 315 MET cc_start: 0.9081 (tpp) cc_final: 0.8578 (tpp) REVERT: Z 343 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8511 (ttt) REVERT: Z 366 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8097 (mp) REVERT: Z 458 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8346 (ttmm) REVERT: Z 467 HIS cc_start: 0.6387 (t-170) cc_final: 0.5402 (t-90) REVERT: Z 472 MET cc_start: 0.8098 (ptp) cc_final: 0.7883 (ptt) REVERT: Z 521 GLU cc_start: 0.7384 (mt-10) cc_final: 0.7181 (mt-10) REVERT: Z 523 LYS cc_start: 0.8502 (mmtp) cc_final: 0.8245 (mttt) REVERT: Z 541 GLU cc_start: 0.8397 (tp30) cc_final: 0.7907 (tp30) REVERT: Z 569 ARG cc_start: 0.8272 (mpp80) cc_final: 0.7875 (mpt-90) REVERT: A 121 GLN cc_start: 0.5629 (OUTLIER) cc_final: 0.5237 (pp30) REVERT: A 128 LYS cc_start: 0.8615 (mmtt) cc_final: 0.8374 (mtmm) REVERT: B 31 ARG cc_start: 0.8432 (ttp-170) cc_final: 0.8173 (ttp80) REVERT: B 75 GLU cc_start: 0.8333 (mp0) cc_final: 0.8129 (mp0) REVERT: B 133 TYR cc_start: 0.7489 (t80) cc_final: 0.6462 (t80) REVERT: B 206 GLU cc_start: 0.9018 (tm-30) cc_final: 0.8811 (tm-30) REVERT: B 221 ARG cc_start: 0.8838 (ttm170) cc_final: 0.8343 (ptt180) REVERT: C 185 ASP cc_start: 0.6280 (p0) cc_final: 0.6066 (p0) REVERT: C 405 MET cc_start: 0.7937 (ttp) cc_final: 0.7698 (ptp) REVERT: C 634 GLU cc_start: 0.8031 (tp30) cc_final: 0.7544 (tp30) REVERT: C 697 LYS cc_start: 0.9105 (tttm) cc_final: 0.8817 (ptpt) REVERT: C 738 LYS cc_start: 0.8560 (pttp) cc_final: 0.8308 (ptmm) REVERT: C 815 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7681 (tp30) REVERT: C 852 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8728 (mt) REVERT: C 1256 HIS cc_start: 0.7853 (t70) cc_final: 0.7630 (t70) REVERT: C 1271 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7245 (mt) REVERT: C 1286 GLU cc_start: 0.8298 (mp0) cc_final: 0.7914 (mp0) REVERT: C 1351 PHE cc_start: 0.8081 (m-80) cc_final: 0.7668 (m-80) REVERT: D 48 LYS cc_start: 0.8805 (mtpt) cc_final: 0.8309 (mptt) REVERT: D 76 LEU cc_start: 0.8779 (mp) cc_final: 0.8567 (mp) REVERT: D 135 LYS cc_start: 0.8720 (mttt) cc_final: 0.8474 (mtpt) REVERT: D 279 LYS cc_start: 0.8197 (tttt) cc_final: 0.7865 (mmtt) REVERT: D 328 MET cc_start: 0.8774 (mtm) cc_final: 0.8491 (mtp) REVERT: D 556 ASP cc_start: 0.7203 (m-30) cc_final: 0.6368 (m-30) REVERT: D 562 TYR cc_start: 0.7396 (p90) cc_final: 0.6597 (p90) REVERT: D 571 THR cc_start: 0.9419 (m) cc_final: 0.9178 (p) REVERT: D 849 LYS cc_start: 0.7248 (mttt) cc_final: 0.6887 (tmtt) REVERT: D 899 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8036 (tt) REVERT: D 1230 ARG cc_start: 0.8435 (mmt90) cc_final: 0.8023 (mmm160) REVERT: D 1269 GLU cc_start: 0.7650 (tp30) cc_final: 0.7340 (tm-30) REVERT: D 1279 LYS cc_start: 0.8189 (tptm) cc_final: 0.7672 (tptp) REVERT: E 26 ARG cc_start: 0.8682 (tpt170) cc_final: 0.8199 (tpp80) outliers start: 296 outliers final: 200 residues processed: 853 average time/residue: 0.4283 time to fit residues: 575.3475 Evaluate side-chains 707 residues out of total 3271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 497 time to evaluate : 3.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 29 THR Chi-restraints excluded: chain S residue 44 LYS Chi-restraints excluded: chain S residue 54 LEU Chi-restraints excluded: chain S residue 68 LEU Chi-restraints excluded: chain S residue 125 ASP Chi-restraints excluded: chain S residue 149 THR Chi-restraints excluded: chain S residue 154 TYR Chi-restraints excluded: chain S residue 155 ILE Chi-restraints excluded: chain S residue 191 LYS Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 52 ILE Chi-restraints excluded: chain M residue 74 ASP Chi-restraints excluded: chain M residue 82 PHE Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 106 ASN Chi-restraints excluded: chain M residue 108 ILE Chi-restraints excluded: chain M residue 112 SER Chi-restraints excluded: chain M residue 154 ASN Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain M residue 166 PHE Chi-restraints excluded: chain M residue 170 ILE Chi-restraints excluded: chain M residue 182 ASN Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain Z residue 99 ASP Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain Z residue 143 GLU Chi-restraints excluded: chain Z residue 233 THR Chi-restraints excluded: chain Z residue 265 SER Chi-restraints excluded: chain Z residue 271 GLU Chi-restraints excluded: chain Z residue 275 VAL Chi-restraints excluded: chain Z residue 278 VAL Chi-restraints excluded: chain Z residue 297 THR Chi-restraints excluded: chain Z residue 305 THR Chi-restraints excluded: chain Z residue 343 MET Chi-restraints excluded: chain Z residue 344 ILE Chi-restraints excluded: chain Z residue 358 TYR Chi-restraints excluded: chain Z residue 366 LEU Chi-restraints excluded: chain Z residue 389 PHE Chi-restraints excluded: chain Z residue 392 SER Chi-restraints excluded: chain Z residue 421 ILE Chi-restraints excluded: chain Z residue 423 THR Chi-restraints excluded: chain Z residue 427 VAL Chi-restraints excluded: chain Z residue 453 ASN Chi-restraints excluded: chain Z residue 458 LYS Chi-restraints excluded: chain Z residue 468 THR Chi-restraints excluded: chain Z residue 512 LEU Chi-restraints excluded: chain Z residue 534 ASN Chi-restraints excluded: chain Z residue 542 VAL Chi-restraints excluded: chain Z residue 549 THR Chi-restraints excluded: chain Z residue 553 ILE Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 157 ASN Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 426 SER Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 495 ILE Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 515 SER Chi-restraints excluded: chain C residue 548 PHE Chi-restraints excluded: chain C residue 556 THR Chi-restraints excluded: chain C residue 576 ASN Chi-restraints excluded: chain C residue 580 SER Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 613 ASP Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 652 ARG Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 700 LYS Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain C residue 744 SER Chi-restraints excluded: chain C residue 748 ASN Chi-restraints excluded: chain C residue 754 SER Chi-restraints excluded: chain C residue 756 THR Chi-restraints excluded: chain C residue 831 THR Chi-restraints excluded: chain C residue 832 SER Chi-restraints excluded: chain C residue 837 GLU Chi-restraints excluded: chain C residue 839 THR Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 856 ILE Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 867 LEU Chi-restraints excluded: chain C residue 870 SER Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 889 ILE Chi-restraints excluded: chain C residue 929 THR Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain C residue 1091 SER Chi-restraints excluded: chain C residue 1098 ASP Chi-restraints excluded: chain C residue 1119 SER Chi-restraints excluded: chain C residue 1123 ILE Chi-restraints excluded: chain C residue 1145 THR Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 1168 ASP Chi-restraints excluded: chain C residue 1206 ASP Chi-restraints excluded: chain C residue 1229 THR Chi-restraints excluded: chain C residue 1234 ASP Chi-restraints excluded: chain C residue 1241 TYR Chi-restraints excluded: chain C residue 1245 LEU Chi-restraints excluded: chain C residue 1258 ARG Chi-restraints excluded: chain C residue 1266 VAL Chi-restraints excluded: chain C residue 1271 LEU Chi-restraints excluded: chain C residue 1350 ASP Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 68 CYS Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 112 ILE Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 160 ASP Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 272 ASN Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 350 ARG Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 388 HIS Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 398 MET Chi-restraints excluded: chain D residue 463 GLN Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 530 ASP Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 569 ASN Chi-restraints excluded: chain D residue 570 THR Chi-restraints excluded: chain D residue 652 ILE Chi-restraints excluded: chain D residue 674 ASN Chi-restraints excluded: chain D residue 680 ILE Chi-restraints excluded: chain D residue 748 ASP Chi-restraints excluded: chain D residue 750 THR Chi-restraints excluded: chain D residue 773 THR Chi-restraints excluded: chain D residue 786 LYS Chi-restraints excluded: chain D residue 823 VAL Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 871 ASN Chi-restraints excluded: chain D residue 891 CYS Chi-restraints excluded: chain D residue 899 LEU Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain D residue 1136 ARG Chi-restraints excluded: chain D residue 1197 VAL Chi-restraints excluded: chain D residue 1203 THR Chi-restraints excluded: chain D residue 1228 VAL Chi-restraints excluded: chain D residue 1256 ASP Chi-restraints excluded: chain D residue 1274 LEU Chi-restraints excluded: chain D residue 1341 ILE Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 35 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 320 optimal weight: 9.9990 chunk 287 optimal weight: 0.2980 chunk 159 optimal weight: 0.3980 chunk 98 optimal weight: 0.8980 chunk 193 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 297 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 180 optimal weight: 20.0000 chunk 221 optimal weight: 9.9990 chunk 344 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 100 ASN S 112 HIS M 88 GLN ** M 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 128 GLN M 154 ASN ** Z 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 347 ASN ** Z 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 464 ASN A 85 ASN ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 ASN B 230 ASN C 31 GLN C 66 ASN C 144 ASN C 631 HIS C 717 ASN C1122 ASN C1130 HIS C1172 ASN C1268 GLN C1319 ASN C1336 ASN D 102 HIS ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 362 HIS D 428 HIS D 433 GLN D 475 GLN D 487 ASN D 553 GLN D 563 ASN D 679 ASN D 774 HIS D1206 HIS ** D1277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1331 ASN ** D1338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 31046 Z= 0.181 Angle : 0.631 9.761 42277 Z= 0.337 Chirality : 0.043 0.170 4927 Planarity : 0.004 0.079 5167 Dihedral : 16.032 88.735 5272 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer: Outliers : 5.63 % Allowed : 26.92 % Favored : 67.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -3.27 (0.13), residues: 3715 helix: -0.93 (0.13), residues: 1453 sheet: -2.71 (0.23), residues: 399 loop : -3.16 (0.13), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 183 HIS 0.006 0.001 HIS Z 364 PHE 0.027 0.001 PHE D 607 TYR 0.028 0.001 TYR M 168 ARG 0.006 0.000 ARG S 182 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 771 residues out of total 3271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 600 time to evaluate : 3.736 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: S 90 LYS cc_start: 0.8256 (mttp) cc_final: 0.7968 (ttmm) REVERT: S 133 MET cc_start: 0.8957 (mmm) cc_final: 0.8660 (mmt) REVERT: S 154 TYR cc_start: 0.7659 (OUTLIER) cc_final: 0.7256 (m-10) REVERT: S 207 ARG cc_start: 0.7040 (mpt-90) cc_final: 0.5710 (ptt180) REVERT: M 103 PHE cc_start: 0.8198 (m-80) cc_final: 0.7957 (m-80) REVERT: M 121 ASN cc_start: 0.6457 (m-40) cc_final: 0.5754 (m110) REVERT: M 169 PHE cc_start: 0.8230 (OUTLIER) cc_final: 0.7836 (t80) REVERT: M 193 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6852 (tm-30) REVERT: Z 149 MET cc_start: 0.3750 (ttt) cc_final: 0.3245 (mmp) REVERT: Z 230 ARG cc_start: 0.7410 (tmt-80) cc_final: 0.5488 (mtt90) REVERT: Z 283 TRP cc_start: 0.5880 (OUTLIER) cc_final: 0.4139 (t60) REVERT: Z 295 GLU cc_start: 0.6256 (OUTLIER) cc_final: 0.5898 (pp20) REVERT: Z 315 MET cc_start: 0.8803 (tpp) cc_final: 0.8335 (tpp) REVERT: Z 457 GLU cc_start: 0.8830 (tt0) cc_final: 0.8281 (tp30) REVERT: Z 472 MET cc_start: 0.8003 (ptp) cc_final: 0.7756 (ptt) REVERT: Z 476 ILE cc_start: 0.5448 (OUTLIER) cc_final: 0.5239 (pt) REVERT: Z 521 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7054 (mt-10) REVERT: Z 541 GLU cc_start: 0.8345 (tp30) cc_final: 0.7819 (tp30) REVERT: Z 569 ARG cc_start: 0.8248 (mpp80) cc_final: 0.7696 (mtt90) REVERT: A 121 GLN cc_start: 0.5838 (OUTLIER) cc_final: 0.5586 (pp30) REVERT: A 128 LYS cc_start: 0.8640 (mmtt) cc_final: 0.8374 (mtmm) REVERT: B 75 GLU cc_start: 0.8060 (mp0) cc_final: 0.7821 (mp0) REVERT: B 133 TYR cc_start: 0.7394 (t80) cc_final: 0.6465 (t80) REVERT: B 221 ARG cc_start: 0.8780 (ttm170) cc_final: 0.8281 (ptt180) REVERT: C 49 HIS cc_start: 0.8339 (m-70) cc_final: 0.8114 (m-70) REVERT: C 434 GLU cc_start: 0.9055 (mm-30) cc_final: 0.8782 (mm-30) REVERT: C 442 LYS cc_start: 0.7171 (mppt) cc_final: 0.5910 (tptp) REVERT: C 475 GLU cc_start: 0.8681 (pp20) cc_final: 0.8283 (tp30) REVERT: C 556 THR cc_start: 0.9318 (p) cc_final: 0.9023 (p) REVERT: C 634 GLU cc_start: 0.7941 (tp30) cc_final: 0.7464 (tp30) REVERT: C 697 LYS cc_start: 0.9071 (tttm) cc_final: 0.8747 (ptpt) REVERT: C 852 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8623 (mt) REVERT: C 1256 HIS cc_start: 0.7404 (t70) cc_final: 0.7039 (t70) REVERT: C 1286 GLU cc_start: 0.8323 (mp0) cc_final: 0.7986 (mp0) REVERT: C 1351 PHE cc_start: 0.7955 (m-80) cc_final: 0.7435 (m-80) REVERT: D 48 LYS cc_start: 0.8875 (mtpt) cc_final: 0.8394 (mptt) REVERT: D 76 LEU cc_start: 0.8749 (mp) cc_final: 0.8513 (mp) REVERT: D 135 LYS cc_start: 0.8759 (mttt) cc_final: 0.8442 (mtpt) REVERT: D 163 TYR cc_start: 0.7528 (OUTLIER) cc_final: 0.7162 (t80) REVERT: D 165 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7112 (mm-30) REVERT: D 195 GLU cc_start: 0.8294 (tp30) cc_final: 0.7914 (tp30) REVERT: D 279 LYS cc_start: 0.8202 (tttt) cc_final: 0.7875 (mmtt) REVERT: D 327 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.8001 (t0) REVERT: D 403 GLU cc_start: 0.7967 (tm-30) cc_final: 0.6926 (mm-30) REVERT: D 734 MET cc_start: 0.8604 (mtp) cc_final: 0.8364 (mtm) REVERT: D 746 LYS cc_start: 0.7779 (ptpt) cc_final: 0.7566 (pttt) REVERT: D 796 ARG cc_start: 0.8653 (mtm-85) cc_final: 0.8057 (mtm-85) REVERT: D 849 LYS cc_start: 0.7217 (mttt) cc_final: 0.6793 (tmtt) REVERT: D 1132 PHE cc_start: 0.8708 (m-80) cc_final: 0.8302 (m-80) REVERT: D 1230 ARG cc_start: 0.8388 (mmt90) cc_final: 0.7873 (mmm160) REVERT: D 1269 GLU cc_start: 0.7684 (tp30) cc_final: 0.7302 (tm-30) REVERT: D 1279 LYS cc_start: 0.8185 (tptm) cc_final: 0.7771 (tptp) REVERT: E 26 ARG cc_start: 0.8657 (tpt170) cc_final: 0.8272 (tpp-160) REVERT: E 35 TYR cc_start: 0.4240 (OUTLIER) cc_final: 0.2826 (p90) outliers start: 171 outliers final: 107 residues processed: 730 average time/residue: 0.4297 time to fit residues: 502.0526 Evaluate side-chains 632 residues out of total 3271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 514 time to evaluate : 3.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 100 ASN Chi-restraints excluded: chain S residue 154 TYR Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 74 ASP Chi-restraints excluded: chain M residue 99 VAL Chi-restraints excluded: chain M residue 106 ASN Chi-restraints excluded: chain M residue 147 GLU Chi-restraints excluded: chain M residue 154 ASN Chi-restraints excluded: chain M residue 169 PHE Chi-restraints excluded: chain M residue 170 ILE Chi-restraints excluded: chain M residue 182 ASN Chi-restraints excluded: chain M residue 193 GLU Chi-restraints excluded: chain M residue 199 THR Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain Z residue 99 ASP Chi-restraints excluded: chain Z residue 134 TYR Chi-restraints excluded: chain Z residue 143 GLU Chi-restraints excluded: chain Z residue 235 HIS Chi-restraints excluded: chain Z residue 283 TRP Chi-restraints excluded: chain Z residue 295 GLU Chi-restraints excluded: chain Z residue 392 SER Chi-restraints excluded: chain Z residue 421 ILE Chi-restraints excluded: chain Z residue 468 THR Chi-restraints excluded: chain Z residue 476 ILE Chi-restraints excluded: chain Z residue 488 ILE Chi-restraints excluded: chain Z residue 518 THR Chi-restraints excluded: chain Z residue 542 VAL Chi-restraints excluded: chain Z residue 557 GLU Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 73 TYR Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 548 PHE Chi-restraints excluded: chain C residue 562 CYS Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 700 LYS Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain C residue 748 ASN Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 856 ILE Chi-restraints excluded: chain C residue 898 THR Chi-restraints excluded: chain C residue 929 THR Chi-restraints excluded: chain C residue 1098 ASP Chi-restraints excluded: chain C residue 1122 ASN Chi-restraints excluded: chain C residue 1166 VAL Chi-restraints excluded: chain C residue 1168 ASP Chi-restraints excluded: chain C residue 1229 THR Chi-restraints excluded: chain C residue 1234 ASP Chi-restraints excluded: chain C residue 1241 TYR Chi-restraints excluded: chain C residue 1245 LEU Chi-restraints excluded: chain C residue 1251 VAL Chi-restraints excluded: chain C residue 1258 ARG Chi-restraints excluded: chain C residue 1266 VAL Chi-restraints excluded: chain C residue 1327 MET Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 160 ASP Chi-restraints excluded: chain D residue 163 TYR Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 318 ASN Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 350 ARG Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 504 ILE Chi-restraints excluded: chain D residue 530 ASP Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 569 ASN Chi-restraints excluded: chain D residue 570 THR Chi-restraints excluded: chain D residue 748 ASP Chi-restraints excluded: chain D residue 766 VAL Chi-restraints excluded: chain D residue 863 ASN Chi-restraints excluded: chain D residue 1136 ARG Chi-restraints excluded: chain D residue 1156 ASP Chi-restraints excluded: chain D residue 1197 VAL Chi-restraints excluded: chain D residue 1203 THR Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 35 TYR Chi-restraints excluded: chain E residue 70 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 191 optimal weight: 10.0000 chunk 106 optimal weight: 5.9990 chunk 286 optimal weight: 0.3980 chunk 234 optimal weight: 7.9990 chunk 94 optimal weight: 6.9990 chunk 344 optimal weight: 0.7980 chunk 372 optimal weight: 7.9990 chunk 307 optimal weight: 8.9990 chunk 341 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 chunk 276 optimal weight: 7.9990 overall best weight: 4.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 ASN ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1236 HIS ** C1256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 ASN ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 264 ASN ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 HIS ** D1277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1338 ASN E 68 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 31046 Z= 0.309 Angle : 0.655 10.709 42277 Z= 0.348 Chirality : 0.044 0.167 4927 Planarity : 0.004 0.060 5167 Dihedral : 15.686 87.348 5057 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.36 % Favored : 88.61 % Rotamer: Outliers : 6.91 % Allowed : 27.02 % Favored : 66.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.79 % 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: -2.90 (0.13), residues: 3715 helix: -0.56 (0.13), residues: 1459 sheet: -2.38 (0.24), residues: 395 loop : -3.04 (0.13), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 183 HIS 0.011 0.001 HIS Z 467 PHE 0.020 0.002 PHE C 172 TYR 0.028 0.002 TYR M 168 ARG 0.011 0.000 ARG D 257 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 742 residues out of total 3271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 532 time to evaluate : 3.914 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: S 90 LYS cc_start: 0.8303 (mttp) cc_final: 0.7957 (ttmm) REVERT: S 133 MET cc_start: 0.8955 (mmm) cc_final: 0.8650 (mmt) REVERT: S 154 TYR cc_start: 0.7788 (OUTLIER) cc_final: 0.7393 (m-10) REVERT: S 191 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8436 (mptp) REVERT: S 207 ARG cc_start: 0.7114 (mpt-90) cc_final: 0.6255 (tpp80) REVERT: M 19 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8346 (mm) REVERT: M 63 TYR cc_start: 0.8678 (p90) cc_final: 0.8206 (p90) REVERT: M 87 LYS cc_start: 0.8141 (mtpt) cc_final: 0.7916 (mtpp) REVERT: M 121 ASN cc_start: 0.5960 (m-40) cc_final: 0.5682 (m110) REVERT: M 127 MET cc_start: 0.8632 (mpp) cc_final: 0.8102 (mpp) REVERT: M 153 GLN cc_start: 0.7860 (pp30) cc_final: 0.7282 (pp30) REVERT: M 169 PHE cc_start: 0.8252 (OUTLIER) cc_final: 0.7939 (t80) REVERT: M 193 GLU cc_start: 0.7005 (OUTLIER) cc_final: 0.6690 (tm-30) REVERT: Z 149 MET cc_start: 0.3646 (ttt) cc_final: 0.3234 (mmp) REVERT: Z 230 ARG cc_start: 0.7356 (tmt-80) cc_final: 0.5532 (mtt90) REVERT: Z 366 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.7925 (mp) REVERT: Z 401 GLN cc_start: 0.8335 (tm-30) cc_final: 0.8076 (pp30) REVERT: Z 457 GLU cc_start: 0.8857 (tt0) cc_final: 0.8441 (tp30) REVERT: Z 472 MET cc_start: 0.8091 (ptp) cc_final: 0.7851 (ptt) REVERT: Z 506 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.7398 (tpt-90) REVERT: Z 521 GLU cc_start: 0.7367 (mt-10) cc_final: 0.6945 (mt-10) REVERT: Z 541 GLU cc_start: 0.8257 (tp30) cc_final: 0.7775 (tp30) REVERT: Z 569 ARG cc_start: 0.8271 (mpp80) cc_final: 0.7978 (mpt-90) REVERT: A 77 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.6684 (mp0) REVERT: A 121 GLN cc_start: 0.5721 (OUTLIER) cc_final: 0.5475 (pp30) REVERT: A 128 LYS cc_start: 0.8640 (mmtt) cc_final: 0.8406 (mtmm) REVERT: B 75 GLU cc_start: 0.8137 (mp0) cc_final: 0.7908 (mp0) REVERT: B 80 ILE cc_start: 0.9284 (OUTLIER) cc_final: 0.9047 (tp) REVERT: B 133 TYR cc_start: 0.7438 (t80) cc_final: 0.6512 (t80) REVERT: B 221 ARG cc_start: 0.8818 (ttm170) cc_final: 0.8618 (mtm110) REVERT: C 35 TYR cc_start: 0.8878 (OUTLIER) cc_final: 0.7807 (t80) REVERT: C 49 HIS cc_start: 0.8403 (m-70) cc_final: 0.8006 (m-70) REVERT: C 185 ASP cc_start: 0.6421 (p0) cc_final: 0.6111 (p0) REVERT: C 394 GLU cc_start: 0.6965 (OUTLIER) cc_final: 0.6559 (pp20) REVERT: C 442 LYS cc_start: 0.7539 (mppt) cc_final: 0.6215 (tptm) REVERT: C 457 ARG cc_start: 0.8617 (ttp-170) cc_final: 0.8171 (ttm170) REVERT: C 556 THR cc_start: 0.9319 (p) cc_final: 0.9013 (p) REVERT: C 634 GLU cc_start: 0.7989 (tp30) cc_final: 0.7487 (tp30) REVERT: C 852 ILE cc_start: 0.8993 (OUTLIER) cc_final: 0.8790 (mt) REVERT: C 1122 ASN cc_start: 0.8787 (p0) cc_final: 0.8511 (p0) REVERT: C 1182 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8689 (mm) REVERT: C 1256 HIS cc_start: 0.7559 (t70) cc_final: 0.7244 (t70) REVERT: C 1258 ARG cc_start: 0.9130 (OUTLIER) cc_final: 0.8793 (ttt180) REVERT: C 1286 GLU cc_start: 0.8348 (mp0) cc_final: 0.7966 (mp0) REVERT: C 1351 PHE cc_start: 0.7952 (m-80) cc_final: 0.7342 (m-80) REVERT: D 48 LYS cc_start: 0.8859 (mtpt) cc_final: 0.8352 (mptt) REVERT: D 76 LEU cc_start: 0.8799 (mp) cc_final: 0.8584 (mp) REVERT: D 135 LYS cc_start: 0.8788 (mttt) cc_final: 0.8458 (mtpt) REVERT: D 163 TYR cc_start: 0.7571 (OUTLIER) cc_final: 0.7193 (t80) REVERT: D 165 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7165 (mm-30) REVERT: D 195 GLU cc_start: 0.8292 (tp30) cc_final: 0.7925 (tp30) REVERT: D 219 LEU cc_start: 0.8812 (mm) cc_final: 0.8379 (tp) REVERT: D 279 LYS cc_start: 0.8194 (tttt) cc_final: 0.7893 (mmtt) REVERT: D 327 ASP cc_start: 0.8222 (OUTLIER) cc_final: 0.8017 (t0) REVERT: D 403 GLU cc_start: 0.8074 (tm-30) cc_final: 0.6966 (mm-30) REVERT: D 598 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7683 (mm-30) REVERT: D 746 LYS cc_start: 0.7829 (ptpt) cc_final: 0.7620 (pttt) REVERT: D 796 ARG cc_start: 0.8783 (mtm-85) cc_final: 0.8214 (mtm-85) REVERT: D 818 MET cc_start: 0.7309 (mmt) cc_final: 0.7107 (mmt) REVERT: D 849 LYS cc_start: 0.7254 (mttt) cc_final: 0.6829 (tmtt) REVERT: D 1132 PHE cc_start: 0.8737 (m-80) cc_final: 0.8364 (m-80) REVERT: D 1230 ARG cc_start: 0.8441 (mmt90) cc_final: 0.7855 (mmm160) REVERT: D 1269 GLU cc_start: 0.7658 (tp30) cc_final: 0.7302 (tm-30) REVERT: D 1279 LYS cc_start: 0.8240 (tptm) cc_final: 0.7824 (tptp) REVERT: E 26 ARG cc_start: 0.8665 (tpt170) cc_final: 0.8318 (tpp-160) outliers start: 210 outliers final: 143 residues processed: 688 average time/residue: 0.4119 time to fit residues: 452.9659 Evaluate side-chains 657 residues out of total 3271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 497 time to evaluate : 3.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 29 THR Chi-restraints excluded: chain S residue 30 ASP Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 115 ASP Chi-restraints excluded: chain S residue 149 THR Chi-restraints excluded: chain S residue 154 TYR Chi-restraints excluded: chain S residue 191 LYS Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 10 ILE Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 74 ASP Chi-restraints excluded: chain M residue 82 PHE Chi-restraints excluded: chain M residue 99 VAL Chi-restraints excluded: chain M residue 106 ASN Chi-restraints excluded: chain M residue 147 GLU Chi-restraints excluded: chain M residue 154 ASN Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain M residue 169 PHE Chi-restraints excluded: chain M residue 182 ASN Chi-restraints excluded: chain M residue 193 GLU Chi-restraints excluded: chain M residue 199 THR Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain Z residue 99 ASP Chi-restraints excluded: chain Z residue 134 TYR Chi-restraints excluded: chain Z residue 143 GLU Chi-restraints excluded: chain Z residue 199 PHE Chi-restraints excluded: chain Z residue 235 HIS Chi-restraints excluded: chain Z residue 308 ILE Chi-restraints excluded: chain Z residue 344 ILE Chi-restraints excluded: chain Z residue 358 TYR Chi-restraints excluded: chain Z residue 366 LEU Chi-restraints excluded: chain Z residue 421 ILE Chi-restraints excluded: chain Z residue 423 THR Chi-restraints excluded: chain Z residue 468 THR Chi-restraints excluded: chain Z residue 488 ILE Chi-restraints excluded: chain Z residue 506 ARG Chi-restraints excluded: chain Z residue 512 LEU Chi-restraints excluded: chain Z residue 542 VAL Chi-restraints excluded: chain Z residue 549 THR Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 35 TYR Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 394 GLU Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 515 SER Chi-restraints excluded: chain C residue 548 PHE Chi-restraints excluded: chain C residue 562 CYS Chi-restraints excluded: chain C residue 568 GLU Chi-restraints excluded: chain C residue 576 ASN Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 639 CYS Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 700 LYS Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 730 VAL Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain C residue 748 ASN Chi-restraints excluded: chain C residue 756 THR Chi-restraints excluded: chain C residue 766 CYS Chi-restraints excluded: chain C residue 828 ASP Chi-restraints excluded: chain C residue 832 SER Chi-restraints excluded: chain C residue 837 GLU Chi-restraints excluded: chain C residue 840 CYS Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 856 ILE Chi-restraints excluded: chain C residue 863 SER Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 888 LYS Chi-restraints excluded: chain C residue 889 ILE Chi-restraints excluded: chain C residue 897 LEU Chi-restraints excluded: chain C residue 898 THR Chi-restraints excluded: chain C residue 927 SER Chi-restraints excluded: chain C residue 929 THR Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain C residue 1166 VAL Chi-restraints excluded: chain C residue 1168 ASP Chi-restraints excluded: chain C residue 1182 LEU Chi-restraints excluded: chain C residue 1229 THR Chi-restraints excluded: chain C residue 1234 ASP Chi-restraints excluded: chain C residue 1241 TYR Chi-restraints excluded: chain C residue 1251 VAL Chi-restraints excluded: chain C residue 1258 ARG Chi-restraints excluded: chain C residue 1266 VAL Chi-restraints excluded: chain C residue 1327 MET Chi-restraints excluded: chain C residue 1350 ASP Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 160 ASP Chi-restraints excluded: chain D residue 163 TYR Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 284 ASN Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 318 ASN Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 350 ARG Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 398 MET Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 504 ILE Chi-restraints excluded: chain D residue 530 ASP Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 569 ASN Chi-restraints excluded: chain D residue 570 THR Chi-restraints excluded: chain D residue 580 ILE Chi-restraints excluded: chain D residue 646 ASP Chi-restraints excluded: chain D residue 748 ASP Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 823 VAL Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 863 ASN Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain D residue 1136 ARG Chi-restraints excluded: chain D residue 1156 ASP Chi-restraints excluded: chain D residue 1197 VAL Chi-restraints excluded: chain D residue 1203 THR Chi-restraints excluded: chain D residue 1357 SER Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 70 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 340 optimal weight: 0.2980 chunk 259 optimal weight: 5.9990 chunk 178 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 164 optimal weight: 10.0000 chunk 231 optimal weight: 6.9990 chunk 346 optimal weight: 10.0000 chunk 366 optimal weight: 3.9990 chunk 180 optimal weight: 0.1980 chunk 327 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 100 ASN ** M 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 467 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1122 ASN ** C1256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1206 HIS D1277 ASN E 68 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 31046 Z= 0.213 Angle : 0.609 9.353 42277 Z= 0.323 Chirality : 0.043 0.189 4927 Planarity : 0.004 0.058 5167 Dihedral : 15.442 87.293 5044 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.91 % Favored : 90.07 % Rotamer: Outliers : 6.98 % Allowed : 26.98 % Favored : 66.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -2.50 (0.13), residues: 3715 helix: -0.17 (0.14), residues: 1472 sheet: -2.13 (0.24), residues: 398 loop : -2.89 (0.13), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 183 HIS 0.006 0.001 HIS Z 467 PHE 0.021 0.001 PHE C 172 TYR 0.031 0.001 TYR M 168 ARG 0.005 0.000 ARG E 53 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 3271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 556 time to evaluate : 3.482 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: S 90 LYS cc_start: 0.8244 (mttp) cc_final: 0.7972 (ttmm) REVERT: S 92 ARG cc_start: 0.8561 (mtt90) cc_final: 0.8238 (mtm180) REVERT: S 133 MET cc_start: 0.8915 (mmm) cc_final: 0.8575 (mmt) REVERT: S 154 TYR cc_start: 0.7730 (OUTLIER) cc_final: 0.7357 (m-10) REVERT: S 207 ARG cc_start: 0.7181 (mpt-90) cc_final: 0.6284 (tpp80) REVERT: M 13 ASP cc_start: 0.7988 (m-30) cc_final: 0.7767 (m-30) REVERT: M 19 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8351 (mm) REVERT: M 52 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8247 (mm) REVERT: M 63 TYR cc_start: 0.8650 (p90) cc_final: 0.8260 (p90) REVERT: M 127 MET cc_start: 0.8752 (mpp) cc_final: 0.8291 (mpp) REVERT: M 153 GLN cc_start: 0.7880 (pp30) cc_final: 0.7390 (pp30) REVERT: M 168 TYR cc_start: 0.6967 (m-80) cc_final: 0.6192 (m-10) REVERT: M 169 PHE cc_start: 0.8292 (OUTLIER) cc_final: 0.7951 (t80) REVERT: M 193 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6668 (tm-30) REVERT: Z 149 MET cc_start: 0.3729 (ttt) cc_final: 0.3453 (mmp) REVERT: Z 230 ARG cc_start: 0.7285 (tmt-80) cc_final: 0.5422 (mtt90) REVERT: Z 245 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8117 (mm) REVERT: Z 295 GLU cc_start: 0.6328 (OUTLIER) cc_final: 0.5990 (pp20) REVERT: Z 366 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.7953 (mp) REVERT: Z 401 GLN cc_start: 0.8338 (tm-30) cc_final: 0.8119 (pp30) REVERT: Z 457 GLU cc_start: 0.8783 (tt0) cc_final: 0.8373 (tp30) REVERT: Z 472 MET cc_start: 0.8148 (ptp) cc_final: 0.7804 (ptt) REVERT: Z 476 ILE cc_start: 0.5275 (OUTLIER) cc_final: 0.5039 (pt) REVERT: Z 541 GLU cc_start: 0.8258 (tp30) cc_final: 0.7714 (tp30) REVERT: Z 569 ARG cc_start: 0.8280 (mpp80) cc_final: 0.7976 (mpt-90) REVERT: A 77 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.6675 (mp0) REVERT: A 128 LYS cc_start: 0.8659 (mmtt) cc_final: 0.8380 (mtmm) REVERT: B 80 ILE cc_start: 0.9261 (OUTLIER) cc_final: 0.9006 (tp) REVERT: B 133 TYR cc_start: 0.7376 (t80) cc_final: 0.6516 (t80) REVERT: B 221 ARG cc_start: 0.8768 (ttm170) cc_final: 0.8565 (mtm110) REVERT: C 3 TYR cc_start: 0.6127 (OUTLIER) cc_final: 0.5843 (m-10) REVERT: C 35 TYR cc_start: 0.8880 (OUTLIER) cc_final: 0.7819 (t80) REVERT: C 87 GLU cc_start: 0.8342 (mm-30) cc_final: 0.8046 (tp30) REVERT: C 394 GLU cc_start: 0.6924 (OUTLIER) cc_final: 0.6489 (pp20) REVERT: C 442 LYS cc_start: 0.7624 (mppt) cc_final: 0.6127 (tptm) REVERT: C 457 ARG cc_start: 0.8571 (ttp-170) cc_final: 0.7778 (ttp-110) REVERT: C 556 THR cc_start: 0.9331 (p) cc_final: 0.9026 (p) REVERT: C 634 GLU cc_start: 0.8001 (tp30) cc_final: 0.7506 (tp30) REVERT: C 803 MET cc_start: 0.8323 (tpp) cc_final: 0.7932 (tpp) REVERT: C 852 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8678 (mt) REVERT: C 1078 ASP cc_start: 0.8700 (m-30) cc_final: 0.8481 (m-30) REVERT: C 1182 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8658 (mm) REVERT: C 1189 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.7936 (ttmt) REVERT: C 1256 HIS cc_start: 0.7278 (t70) cc_final: 0.7020 (t70) REVERT: C 1351 PHE cc_start: 0.7904 (m-80) cc_final: 0.7127 (m-80) REVERT: D 48 LYS cc_start: 0.8822 (mtpt) cc_final: 0.8269 (mptt) REVERT: D 76 LEU cc_start: 0.8727 (mp) cc_final: 0.8500 (mp) REVERT: D 100 MET cc_start: 0.7277 (mtt) cc_final: 0.6930 (mtt) REVERT: D 135 LYS cc_start: 0.8775 (mttt) cc_final: 0.8460 (mtpt) REVERT: D 165 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7180 (mm-30) REVERT: D 195 GLU cc_start: 0.8272 (tp30) cc_final: 0.7875 (tp30) REVERT: D 219 LEU cc_start: 0.8766 (mm) cc_final: 0.8439 (tp) REVERT: D 279 LYS cc_start: 0.8235 (tttt) cc_final: 0.7931 (mmtt) REVERT: D 350 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7738 (ptm160) REVERT: D 397 ARG cc_start: 0.8332 (tpp80) cc_final: 0.7601 (tpp80) REVERT: D 403 GLU cc_start: 0.8007 (tm-30) cc_final: 0.6971 (mm-30) REVERT: D 598 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7689 (mm-30) REVERT: D 782 ASP cc_start: 0.7930 (OUTLIER) cc_final: 0.7644 (m-30) REVERT: D 796 ARG cc_start: 0.8771 (mtm-85) cc_final: 0.8092 (mtm-85) REVERT: D 849 LYS cc_start: 0.7208 (mttt) cc_final: 0.6779 (tmtt) REVERT: D 1132 PHE cc_start: 0.8677 (m-80) cc_final: 0.8302 (m-80) REVERT: D 1269 GLU cc_start: 0.7619 (tp30) cc_final: 0.7266 (tm-30) REVERT: D 1279 LYS cc_start: 0.8254 (tptm) cc_final: 0.7891 (mmmt) REVERT: D 1363 MET cc_start: 0.7403 (mmp) cc_final: 0.7176 (mmp) REVERT: E 26 ARG cc_start: 0.8637 (tpt170) cc_final: 0.8318 (tpp-160) REVERT: E 35 TYR cc_start: 0.4142 (OUTLIER) cc_final: 0.2495 (p90) outliers start: 212 outliers final: 144 residues processed: 708 average time/residue: 0.4083 time to fit residues: 464.1645 Evaluate side-chains 670 residues out of total 3271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 506 time to evaluate : 3.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 24 GLU Chi-restraints excluded: chain S residue 29 THR Chi-restraints excluded: chain S residue 30 ASP Chi-restraints excluded: chain S residue 41 MET Chi-restraints excluded: chain S residue 68 LEU Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 100 ASN Chi-restraints excluded: chain S residue 115 ASP Chi-restraints excluded: chain S residue 130 LEU Chi-restraints excluded: chain S residue 154 TYR Chi-restraints excluded: chain S residue 158 LEU Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 10 ILE Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 52 ILE Chi-restraints excluded: chain M residue 74 ASP Chi-restraints excluded: chain M residue 82 PHE Chi-restraints excluded: chain M residue 99 VAL Chi-restraints excluded: chain M residue 106 ASN Chi-restraints excluded: chain M residue 147 GLU Chi-restraints excluded: chain M residue 159 THR Chi-restraints excluded: chain M residue 169 PHE Chi-restraints excluded: chain M residue 182 ASN Chi-restraints excluded: chain M residue 193 GLU Chi-restraints excluded: chain M residue 199 THR Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain Z residue 99 ASP Chi-restraints excluded: chain Z residue 134 TYR Chi-restraints excluded: chain Z residue 143 GLU Chi-restraints excluded: chain Z residue 199 PHE Chi-restraints excluded: chain Z residue 233 THR Chi-restraints excluded: chain Z residue 235 HIS Chi-restraints excluded: chain Z residue 245 LEU Chi-restraints excluded: chain Z residue 295 GLU Chi-restraints excluded: chain Z residue 358 TYR Chi-restraints excluded: chain Z residue 366 LEU Chi-restraints excluded: chain Z residue 392 SER Chi-restraints excluded: chain Z residue 421 ILE Chi-restraints excluded: chain Z residue 468 THR Chi-restraints excluded: chain Z residue 476 ILE Chi-restraints excluded: chain Z residue 483 THR Chi-restraints excluded: chain Z residue 488 ILE Chi-restraints excluded: chain Z residue 512 LEU Chi-restraints excluded: chain Z residue 542 VAL Chi-restraints excluded: chain Z residue 548 VAL Chi-restraints excluded: chain Z residue 549 THR Chi-restraints excluded: chain Z residue 553 ILE Chi-restraints excluded: chain Z residue 557 GLU Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain C residue 3 TYR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 35 TYR Chi-restraints excluded: chain C residue 73 TYR Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 394 GLU Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 478 ILE Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 515 SER Chi-restraints excluded: chain C residue 516 GLN Chi-restraints excluded: chain C residue 548 PHE Chi-restraints excluded: chain C residue 562 CYS Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 700 LYS Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 730 VAL Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain C residue 748 ASN Chi-restraints excluded: chain C residue 766 CYS Chi-restraints excluded: chain C residue 775 VAL Chi-restraints excluded: chain C residue 828 ASP Chi-restraints excluded: chain C residue 832 SER Chi-restraints excluded: chain C residue 840 CYS Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 856 ILE Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 897 LEU Chi-restraints excluded: chain C residue 898 THR Chi-restraints excluded: chain C residue 929 THR Chi-restraints excluded: chain C residue 1098 ASP Chi-restraints excluded: chain C residue 1122 ASN Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 1166 VAL Chi-restraints excluded: chain C residue 1168 ASP Chi-restraints excluded: chain C residue 1182 LEU Chi-restraints excluded: chain C residue 1189 LYS Chi-restraints excluded: chain C residue 1229 THR Chi-restraints excluded: chain C residue 1234 ASP Chi-restraints excluded: chain C residue 1241 TYR Chi-restraints excluded: chain C residue 1251 VAL Chi-restraints excluded: chain C residue 1266 VAL Chi-restraints excluded: chain C residue 1301 GLU Chi-restraints excluded: chain C residue 1327 MET Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 56 CYS Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 160 ASP Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 350 ARG Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 398 MET Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 504 ILE Chi-restraints excluded: chain D residue 530 ASP Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 570 THR Chi-restraints excluded: chain D residue 646 ASP Chi-restraints excluded: chain D residue 748 ASP Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 863 ASN Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain D residue 1136 ARG Chi-restraints excluded: chain D residue 1156 ASP Chi-restraints excluded: chain D residue 1197 VAL Chi-restraints excluded: chain D residue 1203 THR Chi-restraints excluded: chain D residue 1341 ILE Chi-restraints excluded: chain E residue 35 TYR Chi-restraints excluded: chain E residue 70 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 305 optimal weight: 0.0370 chunk 207 optimal weight: 1.9990 chunk 5 optimal weight: 20.0000 chunk 272 optimal weight: 0.7980 chunk 151 optimal weight: 20.0000 chunk 312 optimal weight: 10.0000 chunk 253 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 187 optimal weight: 7.9990 chunk 328 optimal weight: 9.9990 chunk 92 optimal weight: 7.9990 overall best weight: 3.7664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 182 ASN ** Z 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 453 ASN Z 467 HIS ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN C 631 HIS ** C1256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 388 HIS ** D 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 31046 Z= 0.287 Angle : 0.636 10.469 42277 Z= 0.336 Chirality : 0.043 0.191 4927 Planarity : 0.004 0.059 5167 Dihedral : 15.345 86.437 5026 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.12 % Favored : 88.86 % Rotamer: Outliers : 7.70 % Allowed : 26.95 % Favored : 65.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -2.43 (0.13), residues: 3715 helix: -0.13 (0.14), residues: 1475 sheet: -2.00 (0.25), residues: 385 loop : -2.87 (0.13), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 183 HIS 0.004 0.001 HIS Z 566 PHE 0.026 0.002 PHE Z 200 TYR 0.027 0.001 TYR M 168 ARG 0.005 0.000 ARG D 257 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 3271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 509 time to evaluate : 3.246 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: S 90 LYS cc_start: 0.8314 (mttp) cc_final: 0.8000 (ttmm) REVERT: S 133 MET cc_start: 0.9003 (mmm) cc_final: 0.8656 (mmt) REVERT: S 154 TYR cc_start: 0.7724 (OUTLIER) cc_final: 0.7335 (m-10) REVERT: S 191 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8458 (mptp) REVERT: S 207 ARG cc_start: 0.7196 (mpt-90) cc_final: 0.6325 (tpp80) REVERT: M 13 ASP cc_start: 0.8018 (m-30) cc_final: 0.7720 (m-30) REVERT: M 19 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8327 (mm) REVERT: M 63 TYR cc_start: 0.8671 (p90) cc_final: 0.8340 (p90) REVERT: M 153 GLN cc_start: 0.7962 (pp30) cc_final: 0.7448 (pp30) REVERT: M 168 TYR cc_start: 0.6995 (m-80) cc_final: 0.6206 (m-10) REVERT: M 169 PHE cc_start: 0.8278 (OUTLIER) cc_final: 0.7984 (t80) REVERT: M 193 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6667 (tm-30) REVERT: Z 123 THR cc_start: 0.8255 (OUTLIER) cc_final: 0.7971 (p) REVERT: Z 136 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7849 (tp30) REVERT: Z 230 ARG cc_start: 0.7332 (tmt-80) cc_final: 0.5493 (mtt90) REVERT: Z 245 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8155 (mm) REVERT: Z 295 GLU cc_start: 0.6308 (OUTLIER) cc_final: 0.5987 (pp20) REVERT: Z 298 ILE cc_start: 0.7973 (OUTLIER) cc_final: 0.7752 (mt) REVERT: Z 366 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.7942 (mp) REVERT: Z 401 GLN cc_start: 0.8392 (tm-30) cc_final: 0.8177 (pp30) REVERT: Z 457 GLU cc_start: 0.8815 (tt0) cc_final: 0.8415 (tp30) REVERT: Z 472 MET cc_start: 0.8166 (ptp) cc_final: 0.7911 (ptt) REVERT: Z 476 ILE cc_start: 0.5432 (OUTLIER) cc_final: 0.5206 (pt) REVERT: Z 541 GLU cc_start: 0.8292 (tp30) cc_final: 0.7756 (tp30) REVERT: Z 569 ARG cc_start: 0.8248 (mpp80) cc_final: 0.7978 (mpt-90) REVERT: A 77 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.6691 (mp0) REVERT: A 121 GLN cc_start: 0.5849 (OUTLIER) cc_final: 0.5576 (pp30) REVERT: A 128 LYS cc_start: 0.8677 (mmtt) cc_final: 0.8406 (mtmm) REVERT: B 75 GLU cc_start: 0.7984 (mp0) cc_final: 0.7473 (mp0) REVERT: B 80 ILE cc_start: 0.9282 (OUTLIER) cc_final: 0.9021 (tp) REVERT: B 133 TYR cc_start: 0.7338 (t80) cc_final: 0.6495 (t80) REVERT: B 221 ARG cc_start: 0.8769 (ttm170) cc_final: 0.8553 (mtm110) REVERT: C 3 TYR cc_start: 0.6144 (OUTLIER) cc_final: 0.5874 (m-10) REVERT: C 35 TYR cc_start: 0.8889 (OUTLIER) cc_final: 0.7824 (t80) REVERT: C 87 GLU cc_start: 0.8364 (mm-30) cc_final: 0.8078 (tp30) REVERT: C 161 PHE cc_start: 0.7981 (m-10) cc_final: 0.7779 (m-10) REVERT: C 185 ASP cc_start: 0.6451 (p0) cc_final: 0.6165 (p0) REVERT: C 394 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.6448 (pp20) REVERT: C 442 LYS cc_start: 0.7629 (mppt) cc_final: 0.6209 (tptp) REVERT: C 457 ARG cc_start: 0.8598 (ttp-170) cc_final: 0.7695 (ttp-110) REVERT: C 556 THR cc_start: 0.9328 (p) cc_final: 0.9021 (p) REVERT: C 634 GLU cc_start: 0.8006 (tp30) cc_final: 0.7506 (tp30) REVERT: C 803 MET cc_start: 0.8311 (tpp) cc_final: 0.7928 (tpp) REVERT: C 1078 ASP cc_start: 0.8672 (m-30) cc_final: 0.8465 (m-30) REVERT: C 1182 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8655 (mm) REVERT: C 1189 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.7912 (ttmt) REVERT: C 1258 ARG cc_start: 0.9083 (OUTLIER) cc_final: 0.8795 (ttt180) REVERT: C 1271 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7196 (mt) REVERT: C 1351 PHE cc_start: 0.7938 (m-80) cc_final: 0.7091 (m-80) REVERT: D 76 LEU cc_start: 0.8772 (mp) cc_final: 0.8545 (mp) REVERT: D 100 MET cc_start: 0.7327 (mtt) cc_final: 0.6989 (mtt) REVERT: D 135 LYS cc_start: 0.8784 (mttt) cc_final: 0.8465 (mtpt) REVERT: D 165 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7185 (mm-30) REVERT: D 195 GLU cc_start: 0.8286 (tp30) cc_final: 0.7892 (tp30) REVERT: D 219 LEU cc_start: 0.8781 (mm) cc_final: 0.8451 (tp) REVERT: D 279 LYS cc_start: 0.8231 (tttt) cc_final: 0.7899 (mmtt) REVERT: D 397 ARG cc_start: 0.8382 (tpp80) cc_final: 0.8122 (mmm-85) REVERT: D 403 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7004 (mm-30) REVERT: D 796 ARG cc_start: 0.8797 (mtm-85) cc_final: 0.8007 (mtm-85) REVERT: D 849 LYS cc_start: 0.7234 (mttt) cc_final: 0.6798 (tmtt) REVERT: D 1132 PHE cc_start: 0.8671 (m-80) cc_final: 0.8316 (m-80) REVERT: D 1269 GLU cc_start: 0.7614 (tp30) cc_final: 0.7268 (tm-30) REVERT: D 1279 LYS cc_start: 0.8267 (tptm) cc_final: 0.7881 (tptp) outliers start: 234 outliers final: 185 residues processed: 686 average time/residue: 0.4030 time to fit residues: 449.5741 Evaluate side-chains 693 residues out of total 3271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 487 time to evaluate : 3.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 24 GLU Chi-restraints excluded: chain S residue 29 THR Chi-restraints excluded: chain S residue 30 ASP Chi-restraints excluded: chain S residue 41 MET Chi-restraints excluded: chain S residue 68 LEU Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 115 ASP Chi-restraints excluded: chain S residue 130 LEU Chi-restraints excluded: chain S residue 149 THR Chi-restraints excluded: chain S residue 154 TYR Chi-restraints excluded: chain S residue 158 LEU Chi-restraints excluded: chain S residue 191 LYS Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 32 SER Chi-restraints excluded: chain M residue 52 ILE Chi-restraints excluded: chain M residue 74 ASP Chi-restraints excluded: chain M residue 82 PHE Chi-restraints excluded: chain M residue 99 VAL Chi-restraints excluded: chain M residue 106 ASN Chi-restraints excluded: chain M residue 147 GLU Chi-restraints excluded: chain M residue 159 THR Chi-restraints excluded: chain M residue 169 PHE Chi-restraints excluded: chain M residue 182 ASN Chi-restraints excluded: chain M residue 193 GLU Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain Z residue 99 ASP Chi-restraints excluded: chain Z residue 123 THR Chi-restraints excluded: chain Z residue 134 TYR Chi-restraints excluded: chain Z residue 143 GLU Chi-restraints excluded: chain Z residue 199 PHE Chi-restraints excluded: chain Z residue 219 TYR Chi-restraints excluded: chain Z residue 233 THR Chi-restraints excluded: chain Z residue 235 HIS Chi-restraints excluded: chain Z residue 245 LEU Chi-restraints excluded: chain Z residue 278 VAL Chi-restraints excluded: chain Z residue 295 GLU Chi-restraints excluded: chain Z residue 298 ILE Chi-restraints excluded: chain Z residue 358 TYR Chi-restraints excluded: chain Z residue 366 LEU Chi-restraints excluded: chain Z residue 392 SER Chi-restraints excluded: chain Z residue 421 ILE Chi-restraints excluded: chain Z residue 453 ASN Chi-restraints excluded: chain Z residue 468 THR Chi-restraints excluded: chain Z residue 476 ILE Chi-restraints excluded: chain Z residue 483 THR Chi-restraints excluded: chain Z residue 488 ILE Chi-restraints excluded: chain Z residue 512 LEU Chi-restraints excluded: chain Z residue 518 THR Chi-restraints excluded: chain Z residue 534 ASN Chi-restraints excluded: chain Z residue 548 VAL Chi-restraints excluded: chain Z residue 549 THR Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 157 ASN Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain C residue 3 TYR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 35 TYR Chi-restraints excluded: chain C residue 73 TYR Chi-restraints excluded: chain C residue 135 MET Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 394 GLU Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 515 SER Chi-restraints excluded: chain C residue 516 GLN Chi-restraints excluded: chain C residue 548 PHE Chi-restraints excluded: chain C residue 562 CYS Chi-restraints excluded: chain C residue 568 GLU Chi-restraints excluded: chain C residue 576 ASN Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 700 LYS Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 730 VAL Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain C residue 748 ASN Chi-restraints excluded: chain C residue 756 THR Chi-restraints excluded: chain C residue 766 CYS Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 828 ASP Chi-restraints excluded: chain C residue 831 THR Chi-restraints excluded: chain C residue 832 SER Chi-restraints excluded: chain C residue 837 GLU Chi-restraints excluded: chain C residue 840 CYS Chi-restraints excluded: chain C residue 856 ILE Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 863 SER Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 888 LYS Chi-restraints excluded: chain C residue 889 ILE Chi-restraints excluded: chain C residue 897 LEU Chi-restraints excluded: chain C residue 898 THR Chi-restraints excluded: chain C residue 929 THR Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain C residue 1145 THR Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 1166 VAL Chi-restraints excluded: chain C residue 1168 ASP Chi-restraints excluded: chain C residue 1182 LEU Chi-restraints excluded: chain C residue 1189 LYS Chi-restraints excluded: chain C residue 1229 THR Chi-restraints excluded: chain C residue 1234 ASP Chi-restraints excluded: chain C residue 1241 TYR Chi-restraints excluded: chain C residue 1245 LEU Chi-restraints excluded: chain C residue 1251 VAL Chi-restraints excluded: chain C residue 1258 ARG Chi-restraints excluded: chain C residue 1266 VAL Chi-restraints excluded: chain C residue 1267 THR Chi-restraints excluded: chain C residue 1271 LEU Chi-restraints excluded: chain C residue 1301 GLU Chi-restraints excluded: chain C residue 1327 MET Chi-restraints excluded: chain C residue 1350 ASP Chi-restraints excluded: chain D residue 56 CYS Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 160 ASP Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 225 PHE Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 284 ASN Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 318 ASN Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 398 MET Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 504 ILE Chi-restraints excluded: chain D residue 530 ASP Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 569 ASN Chi-restraints excluded: chain D residue 570 THR Chi-restraints excluded: chain D residue 580 ILE Chi-restraints excluded: chain D residue 646 ASP Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 748 ASP Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 823 VAL Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 852 VAL Chi-restraints excluded: chain D residue 863 ASN Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain D residue 1136 ARG Chi-restraints excluded: chain D residue 1156 ASP Chi-restraints excluded: chain D residue 1197 VAL Chi-restraints excluded: chain D residue 1203 THR Chi-restraints excluded: chain D residue 1231 MET Chi-restraints excluded: chain D residue 1256 ASP Chi-restraints excluded: chain D residue 1274 LEU Chi-restraints excluded: chain D residue 1341 ILE Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 70 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 123 optimal weight: 2.9990 chunk 329 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 chunk 215 optimal weight: 9.9990 chunk 90 optimal weight: 0.9990 chunk 366 optimal weight: 0.8980 chunk 304 optimal weight: 2.9990 chunk 169 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 chunk 192 optimal weight: 5.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1125 GLN ** C1256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1226 GLN E 68 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31046 Z= 0.181 Angle : 0.596 11.166 42277 Z= 0.315 Chirality : 0.042 0.176 4927 Planarity : 0.004 0.057 5167 Dihedral : 15.182 86.130 5017 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.29 % Favored : 90.69 % Rotamer: Outliers : 6.98 % Allowed : 27.74 % Favored : 65.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -2.14 (0.13), residues: 3715 helix: 0.12 (0.14), residues: 1480 sheet: -1.86 (0.25), residues: 403 loop : -2.72 (0.13), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 183 HIS 0.005 0.001 HIS Z 364 PHE 0.030 0.001 PHE M 196 TYR 0.024 0.001 TYR M 168 ARG 0.005 0.000 ARG E 53 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 3271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 550 time to evaluate : 3.508 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: S 56 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7512 (mm-30) REVERT: S 90 LYS cc_start: 0.8262 (mttp) cc_final: 0.7872 (ttmm) REVERT: S 133 MET cc_start: 0.9011 (mmm) cc_final: 0.8645 (mmt) REVERT: S 154 TYR cc_start: 0.7550 (OUTLIER) cc_final: 0.7326 (m-10) REVERT: S 207 ARG cc_start: 0.7248 (mpt-90) cc_final: 0.6567 (tpp80) REVERT: M 13 ASP cc_start: 0.8008 (m-30) cc_final: 0.7713 (m-30) REVERT: M 19 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8461 (mm) REVERT: M 52 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.8203 (mm) REVERT: M 60 PHE cc_start: 0.7865 (p90) cc_final: 0.7155 (p90) REVERT: M 63 TYR cc_start: 0.8544 (p90) cc_final: 0.8238 (p90) REVERT: M 127 MET cc_start: 0.8108 (mtt) cc_final: 0.7906 (mpp) REVERT: M 153 GLN cc_start: 0.7962 (pp30) cc_final: 0.7503 (pp30) REVERT: M 168 TYR cc_start: 0.6884 (m-80) cc_final: 0.6055 (m-10) REVERT: M 169 PHE cc_start: 0.8270 (OUTLIER) cc_final: 0.7985 (t80) REVERT: M 193 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6634 (tm-30) REVERT: Z 123 THR cc_start: 0.8134 (OUTLIER) cc_final: 0.7914 (p) REVERT: Z 136 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7871 (tp30) REVERT: Z 143 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.6618 (tt0) REVERT: Z 230 ARG cc_start: 0.7363 (tmt-80) cc_final: 0.5528 (mtt90) REVERT: Z 245 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8143 (mm) REVERT: Z 256 LYS cc_start: 0.8540 (mttt) cc_final: 0.7627 (tptt) REVERT: Z 295 GLU cc_start: 0.6245 (OUTLIER) cc_final: 0.5935 (pp20) REVERT: Z 366 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.7776 (mp) REVERT: Z 401 GLN cc_start: 0.8392 (tm-30) cc_final: 0.8190 (pp30) REVERT: Z 457 GLU cc_start: 0.8747 (tt0) cc_final: 0.8375 (tp30) REVERT: Z 472 MET cc_start: 0.8170 (ptp) cc_final: 0.7842 (ptt) REVERT: Z 476 ILE cc_start: 0.5225 (OUTLIER) cc_final: 0.4992 (pt) REVERT: Z 541 GLU cc_start: 0.8283 (tp30) cc_final: 0.7734 (tp30) REVERT: Z 569 ARG cc_start: 0.8278 (mpp80) cc_final: 0.8011 (mpt-90) REVERT: A 77 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.6628 (mp0) REVERT: A 128 LYS cc_start: 0.8678 (mmtt) cc_final: 0.8409 (mtmm) REVERT: B 75 GLU cc_start: 0.7915 (mp0) cc_final: 0.7399 (mp0) REVERT: B 80 ILE cc_start: 0.9249 (OUTLIER) cc_final: 0.8996 (tp) REVERT: B 133 TYR cc_start: 0.7333 (t80) cc_final: 0.6492 (t80) REVERT: B 221 ARG cc_start: 0.8739 (ttm170) cc_final: 0.8527 (mtm110) REVERT: C 3 TYR cc_start: 0.6148 (OUTLIER) cc_final: 0.5885 (m-10) REVERT: C 35 TYR cc_start: 0.8865 (OUTLIER) cc_final: 0.7895 (t80) REVERT: C 87 GLU cc_start: 0.8291 (mm-30) cc_final: 0.8063 (tp30) REVERT: C 185 ASP cc_start: 0.6497 (p0) cc_final: 0.6157 (p0) REVERT: C 394 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6568 (pp20) REVERT: C 442 LYS cc_start: 0.7651 (mppt) cc_final: 0.6261 (tptp) REVERT: C 457 ARG cc_start: 0.8663 (ttp-170) cc_final: 0.7870 (ttp-110) REVERT: C 556 THR cc_start: 0.9336 (p) cc_final: 0.9019 (p) REVERT: C 634 GLU cc_start: 0.7945 (tp30) cc_final: 0.7449 (tp30) REVERT: C 803 MET cc_start: 0.8219 (tpp) cc_final: 0.7845 (tpp) REVERT: C 1078 ASP cc_start: 0.8663 (m-30) cc_final: 0.8444 (m-30) REVERT: C 1079 LYS cc_start: 0.9315 (tttt) cc_final: 0.9079 (tttt) REVERT: C 1182 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8604 (mm) REVERT: C 1189 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.7935 (ttmt) REVERT: C 1338 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8661 (tp) REVERT: C 1351 PHE cc_start: 0.7900 (m-80) cc_final: 0.6894 (m-80) REVERT: D 76 LEU cc_start: 0.8718 (mp) cc_final: 0.8497 (mp) REVERT: D 100 MET cc_start: 0.7290 (mtt) cc_final: 0.6942 (mtt) REVERT: D 135 LYS cc_start: 0.8792 (mttt) cc_final: 0.8465 (mtpt) REVERT: D 195 GLU cc_start: 0.8262 (tp30) cc_final: 0.7842 (tp30) REVERT: D 219 LEU cc_start: 0.8744 (mm) cc_final: 0.8455 (tp) REVERT: D 279 LYS cc_start: 0.8263 (tttt) cc_final: 0.7851 (mmtt) REVERT: D 397 ARG cc_start: 0.8375 (tpp80) cc_final: 0.8106 (mmm-85) REVERT: D 403 GLU cc_start: 0.7908 (tm-30) cc_final: 0.6974 (mm-30) REVERT: D 782 ASP cc_start: 0.7927 (OUTLIER) cc_final: 0.7642 (m-30) REVERT: D 796 ARG cc_start: 0.8736 (mtm-85) cc_final: 0.8049 (mtm-85) REVERT: D 849 LYS cc_start: 0.7197 (mttt) cc_final: 0.6760 (tmtt) REVERT: D 899 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8356 (mp) REVERT: D 1132 PHE cc_start: 0.8527 (m-80) cc_final: 0.8206 (m-80) REVERT: D 1269 GLU cc_start: 0.7592 (tp30) cc_final: 0.7250 (tm-30) REVERT: D 1279 LYS cc_start: 0.8268 (tptm) cc_final: 0.7929 (mmmt) REVERT: E 35 TYR cc_start: 0.4214 (OUTLIER) cc_final: 0.2332 (p90) outliers start: 212 outliers final: 153 residues processed: 710 average time/residue: 0.3930 time to fit residues: 451.8559 Evaluate side-chains 691 residues out of total 3271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 516 time to evaluate : 3.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 24 GLU Chi-restraints excluded: chain S residue 29 THR Chi-restraints excluded: chain S residue 30 ASP Chi-restraints excluded: chain S residue 41 MET Chi-restraints excluded: chain S residue 68 LEU Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 115 ASP Chi-restraints excluded: chain S residue 130 LEU Chi-restraints excluded: chain S residue 154 TYR Chi-restraints excluded: chain S residue 158 LEU Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 10 ILE Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 32 SER Chi-restraints excluded: chain M residue 52 ILE Chi-restraints excluded: chain M residue 82 PHE Chi-restraints excluded: chain M residue 169 PHE Chi-restraints excluded: chain M residue 182 ASN Chi-restraints excluded: chain M residue 193 GLU Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain Z residue 99 ASP Chi-restraints excluded: chain Z residue 123 THR Chi-restraints excluded: chain Z residue 134 TYR Chi-restraints excluded: chain Z residue 143 GLU Chi-restraints excluded: chain Z residue 199 PHE Chi-restraints excluded: chain Z residue 218 LEU Chi-restraints excluded: chain Z residue 219 TYR Chi-restraints excluded: chain Z residue 235 HIS Chi-restraints excluded: chain Z residue 245 LEU Chi-restraints excluded: chain Z residue 278 VAL Chi-restraints excluded: chain Z residue 295 GLU Chi-restraints excluded: chain Z residue 308 ILE Chi-restraints excluded: chain Z residue 366 LEU Chi-restraints excluded: chain Z residue 392 SER Chi-restraints excluded: chain Z residue 421 ILE Chi-restraints excluded: chain Z residue 451 THR Chi-restraints excluded: chain Z residue 453 ASN Chi-restraints excluded: chain Z residue 468 THR Chi-restraints excluded: chain Z residue 476 ILE Chi-restraints excluded: chain Z residue 488 ILE Chi-restraints excluded: chain Z residue 512 LEU Chi-restraints excluded: chain Z residue 549 THR Chi-restraints excluded: chain Z residue 553 ILE Chi-restraints excluded: chain Z residue 557 GLU Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 157 ASN Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain C residue 3 TYR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 35 TYR Chi-restraints excluded: chain C residue 60 PHE Chi-restraints excluded: chain C residue 73 TYR Chi-restraints excluded: chain C residue 135 MET Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 394 GLU Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 478 ILE Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 515 SER Chi-restraints excluded: chain C residue 516 GLN Chi-restraints excluded: chain C residue 548 PHE Chi-restraints excluded: chain C residue 562 CYS Chi-restraints excluded: chain C residue 577 SER Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 700 LYS Chi-restraints excluded: chain C residue 730 VAL Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain C residue 766 CYS Chi-restraints excluded: chain C residue 831 THR Chi-restraints excluded: chain C residue 832 SER Chi-restraints excluded: chain C residue 840 CYS Chi-restraints excluded: chain C residue 856 ILE Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 863 SER Chi-restraints excluded: chain C residue 889 ILE Chi-restraints excluded: chain C residue 897 LEU Chi-restraints excluded: chain C residue 898 THR Chi-restraints excluded: chain C residue 929 THR Chi-restraints excluded: chain C residue 1098 ASP Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 1168 ASP Chi-restraints excluded: chain C residue 1182 LEU Chi-restraints excluded: chain C residue 1189 LYS Chi-restraints excluded: chain C residue 1229 THR Chi-restraints excluded: chain C residue 1234 ASP Chi-restraints excluded: chain C residue 1241 TYR Chi-restraints excluded: chain C residue 1245 LEU Chi-restraints excluded: chain C residue 1251 VAL Chi-restraints excluded: chain C residue 1266 VAL Chi-restraints excluded: chain C residue 1267 THR Chi-restraints excluded: chain C residue 1301 GLU Chi-restraints excluded: chain C residue 1327 MET Chi-restraints excluded: chain C residue 1338 LEU Chi-restraints excluded: chain C residue 1350 ASP Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 56 CYS Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 160 ASP Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 225 PHE Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 284 ASN Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 318 ASN Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 501 THR Chi-restraints excluded: chain D residue 504 ILE Chi-restraints excluded: chain D residue 530 ASP Chi-restraints excluded: chain D residue 532 SER Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 569 ASN Chi-restraints excluded: chain D residue 570 THR Chi-restraints excluded: chain D residue 646 ASP Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 748 ASP Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 863 ASN Chi-restraints excluded: chain D residue 899 LEU Chi-restraints excluded: chain D residue 1136 ARG Chi-restraints excluded: chain D residue 1156 ASP Chi-restraints excluded: chain D residue 1197 VAL Chi-restraints excluded: chain D residue 1203 THR Chi-restraints excluded: chain D residue 1231 MET Chi-restraints excluded: chain D residue 1256 ASP Chi-restraints excluded: chain D residue 1274 LEU Chi-restraints excluded: chain D residue 1295 MET Chi-restraints excluded: chain D residue 1341 ILE Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 35 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 353 optimal weight: 30.0000 chunk 41 optimal weight: 4.9990 chunk 208 optimal weight: 6.9990 chunk 267 optimal weight: 5.9990 chunk 207 optimal weight: 0.9980 chunk 308 optimal weight: 10.0000 chunk 204 optimal weight: 10.0000 chunk 365 optimal weight: 10.0000 chunk 228 optimal weight: 3.9990 chunk 222 optimal weight: 10.0000 chunk 168 optimal weight: 6.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 453 ASN ** C1256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 HIS ** D 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1226 GLN D1232 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 31046 Z= 0.337 Angle : 0.674 11.630 42277 Z= 0.352 Chirality : 0.044 0.181 4927 Planarity : 0.004 0.057 5167 Dihedral : 15.240 85.635 5008 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.49 % Favored : 88.51 % Rotamer: Outliers : 7.77 % Allowed : 27.48 % Favored : 64.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -2.22 (0.13), residues: 3715 helix: 0.01 (0.14), residues: 1477 sheet: -1.81 (0.25), residues: 412 loop : -2.75 (0.13), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 183 HIS 0.005 0.001 HIS Z 566 PHE 0.031 0.002 PHE M 196 TYR 0.021 0.002 TYR M 168 ARG 0.011 0.000 ARG D 257 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 3271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 502 time to evaluate : 3.539 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: S 90 LYS cc_start: 0.8361 (mttp) cc_final: 0.8040 (ttmm) REVERT: S 133 MET cc_start: 0.8987 (mmm) cc_final: 0.8659 (mmt) REVERT: S 154 TYR cc_start: 0.7721 (OUTLIER) cc_final: 0.7362 (m-10) REVERT: S 191 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8474 (mptp) REVERT: S 207 ARG cc_start: 0.7248 (mpt-90) cc_final: 0.6583 (tpp80) REVERT: M 13 ASP cc_start: 0.8028 (m-30) cc_final: 0.7666 (m-30) REVERT: M 19 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8335 (mm) REVERT: M 60 PHE cc_start: 0.7957 (p90) cc_final: 0.7247 (p90) REVERT: M 63 TYR cc_start: 0.8596 (p90) cc_final: 0.8331 (p90) REVERT: M 153 GLN cc_start: 0.7889 (pp30) cc_final: 0.7457 (pp30) REVERT: M 168 TYR cc_start: 0.6978 (m-80) cc_final: 0.6116 (m-10) REVERT: M 169 PHE cc_start: 0.8294 (OUTLIER) cc_final: 0.7989 (t80) REVERT: M 193 GLU cc_start: 0.6883 (OUTLIER) cc_final: 0.6594 (tm-30) REVERT: Z 136 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7787 (tp30) REVERT: Z 230 ARG cc_start: 0.7341 (tmt-80) cc_final: 0.5495 (mtt90) REVERT: Z 283 TRP cc_start: 0.5824 (t60) cc_final: 0.5394 (t-100) REVERT: Z 298 ILE cc_start: 0.7889 (OUTLIER) cc_final: 0.7626 (mm) REVERT: Z 315 MET cc_start: 0.8884 (tpp) cc_final: 0.8398 (tpp) REVERT: Z 366 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.7924 (mp) REVERT: Z 457 GLU cc_start: 0.8840 (tt0) cc_final: 0.8421 (tp30) REVERT: Z 472 MET cc_start: 0.8217 (ptp) cc_final: 0.7883 (ptt) REVERT: Z 476 ILE cc_start: 0.5631 (OUTLIER) cc_final: 0.5389 (pt) REVERT: Z 541 GLU cc_start: 0.8299 (tp30) cc_final: 0.7753 (tp30) REVERT: Z 569 ARG cc_start: 0.8231 (mpp80) cc_final: 0.7939 (mtt-85) REVERT: A 77 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.6739 (mp0) REVERT: A 128 LYS cc_start: 0.8669 (mmtt) cc_final: 0.8378 (mtmm) REVERT: B 75 GLU cc_start: 0.8011 (mp0) cc_final: 0.7404 (mp0) REVERT: B 80 ILE cc_start: 0.9288 (OUTLIER) cc_final: 0.9025 (tp) REVERT: B 133 TYR cc_start: 0.7267 (t80) cc_final: 0.6456 (t80) REVERT: B 221 ARG cc_start: 0.8766 (ttm170) cc_final: 0.8544 (mtm110) REVERT: C 3 TYR cc_start: 0.6245 (OUTLIER) cc_final: 0.5951 (m-10) REVERT: C 35 TYR cc_start: 0.8886 (OUTLIER) cc_final: 0.7879 (t80) REVERT: C 185 ASP cc_start: 0.6625 (p0) cc_final: 0.6186 (p0) REVERT: C 394 GLU cc_start: 0.6930 (OUTLIER) cc_final: 0.6554 (pp20) REVERT: C 442 LYS cc_start: 0.7718 (mppt) cc_final: 0.6318 (tptp) REVERT: C 457 ARG cc_start: 0.8645 (ttp-170) cc_final: 0.7760 (ttp-110) REVERT: C 556 THR cc_start: 0.9315 (p) cc_final: 0.8996 (p) REVERT: C 634 GLU cc_start: 0.8016 (tp30) cc_final: 0.7492 (tp30) REVERT: C 803 MET cc_start: 0.8219 (tpp) cc_final: 0.7780 (tpp) REVERT: C 1078 ASP cc_start: 0.8655 (m-30) cc_final: 0.8451 (m-30) REVERT: C 1182 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8592 (mm) REVERT: C 1189 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.7919 (ttmt) REVERT: C 1271 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7248 (mt) REVERT: C 1338 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8704 (tp) REVERT: C 1351 PHE cc_start: 0.7922 (m-80) cc_final: 0.7058 (m-80) REVERT: D 48 LYS cc_start: 0.8591 (mtpt) cc_final: 0.8080 (mptt) REVERT: D 50 GLU cc_start: 0.7916 (mp0) cc_final: 0.7689 (mp0) REVERT: D 76 LEU cc_start: 0.8758 (mp) cc_final: 0.8528 (mp) REVERT: D 100 MET cc_start: 0.7339 (mtt) cc_final: 0.6998 (mtt) REVERT: D 135 LYS cc_start: 0.8805 (mttt) cc_final: 0.8503 (mtpt) REVERT: D 165 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7167 (mm-30) REVERT: D 195 GLU cc_start: 0.8315 (tp30) cc_final: 0.7901 (tp30) REVERT: D 219 LEU cc_start: 0.8799 (mm) cc_final: 0.8472 (tp) REVERT: D 279 LYS cc_start: 0.8269 (tttt) cc_final: 0.7931 (mmtt) REVERT: D 751 MET cc_start: 0.7929 (mmt) cc_final: 0.7720 (mmt) REVERT: D 849 LYS cc_start: 0.7292 (mttt) cc_final: 0.6854 (tmtt) REVERT: D 1132 PHE cc_start: 0.8681 (m-80) cc_final: 0.8334 (m-80) REVERT: D 1269 GLU cc_start: 0.7662 (tp30) cc_final: 0.7290 (tm-30) REVERT: D 1279 LYS cc_start: 0.8275 (tptm) cc_final: 0.7874 (tptp) outliers start: 236 outliers final: 189 residues processed: 679 average time/residue: 0.4065 time to fit residues: 446.5780 Evaluate side-chains 694 residues out of total 3271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 488 time to evaluate : 3.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 24 GLU Chi-restraints excluded: chain S residue 29 THR Chi-restraints excluded: chain S residue 30 ASP Chi-restraints excluded: chain S residue 41 MET Chi-restraints excluded: chain S residue 68 LEU Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 115 ASP Chi-restraints excluded: chain S residue 130 LEU Chi-restraints excluded: chain S residue 149 THR Chi-restraints excluded: chain S residue 154 TYR Chi-restraints excluded: chain S residue 158 LEU Chi-restraints excluded: chain S residue 159 ILE Chi-restraints excluded: chain S residue 191 LYS Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 10 ILE Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 32 SER Chi-restraints excluded: chain M residue 52 ILE Chi-restraints excluded: chain M residue 70 GLU Chi-restraints excluded: chain M residue 82 PHE Chi-restraints excluded: chain M residue 106 ASN Chi-restraints excluded: chain M residue 159 THR Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain M residue 169 PHE Chi-restraints excluded: chain M residue 182 ASN Chi-restraints excluded: chain M residue 193 GLU Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain Z residue 99 ASP Chi-restraints excluded: chain Z residue 134 TYR Chi-restraints excluded: chain Z residue 143 GLU Chi-restraints excluded: chain Z residue 199 PHE Chi-restraints excluded: chain Z residue 218 LEU Chi-restraints excluded: chain Z residue 219 TYR Chi-restraints excluded: chain Z residue 223 VAL Chi-restraints excluded: chain Z residue 233 THR Chi-restraints excluded: chain Z residue 235 HIS Chi-restraints excluded: chain Z residue 278 VAL Chi-restraints excluded: chain Z residue 298 ILE Chi-restraints excluded: chain Z residue 308 ILE Chi-restraints excluded: chain Z residue 344 ILE Chi-restraints excluded: chain Z residue 366 LEU Chi-restraints excluded: chain Z residue 392 SER Chi-restraints excluded: chain Z residue 421 ILE Chi-restraints excluded: chain Z residue 423 THR Chi-restraints excluded: chain Z residue 451 THR Chi-restraints excluded: chain Z residue 453 ASN Chi-restraints excluded: chain Z residue 468 THR Chi-restraints excluded: chain Z residue 476 ILE Chi-restraints excluded: chain Z residue 483 THR Chi-restraints excluded: chain Z residue 512 LEU Chi-restraints excluded: chain Z residue 534 ASN Chi-restraints excluded: chain Z residue 548 VAL Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 157 ASN Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain C residue 3 TYR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 35 TYR Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 135 MET Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 394 GLU Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 515 SER Chi-restraints excluded: chain C residue 516 GLN Chi-restraints excluded: chain C residue 548 PHE Chi-restraints excluded: chain C residue 562 CYS Chi-restraints excluded: chain C residue 576 ASN Chi-restraints excluded: chain C residue 577 SER Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 639 CYS Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 700 LYS Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain C residue 756 THR Chi-restraints excluded: chain C residue 766 CYS Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 828 ASP Chi-restraints excluded: chain C residue 831 THR Chi-restraints excluded: chain C residue 832 SER Chi-restraints excluded: chain C residue 840 CYS Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 856 ILE Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 863 SER Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 889 ILE Chi-restraints excluded: chain C residue 898 THR Chi-restraints excluded: chain C residue 927 SER Chi-restraints excluded: chain C residue 929 THR Chi-restraints excluded: chain C residue 1098 ASP Chi-restraints excluded: chain C residue 1143 GLU Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 1166 VAL Chi-restraints excluded: chain C residue 1168 ASP Chi-restraints excluded: chain C residue 1171 VAL Chi-restraints excluded: chain C residue 1182 LEU Chi-restraints excluded: chain C residue 1189 LYS Chi-restraints excluded: chain C residue 1229 THR Chi-restraints excluded: chain C residue 1234 ASP Chi-restraints excluded: chain C residue 1241 TYR Chi-restraints excluded: chain C residue 1245 LEU Chi-restraints excluded: chain C residue 1251 VAL Chi-restraints excluded: chain C residue 1258 ARG Chi-restraints excluded: chain C residue 1266 VAL Chi-restraints excluded: chain C residue 1267 THR Chi-restraints excluded: chain C residue 1271 LEU Chi-restraints excluded: chain C residue 1301 GLU Chi-restraints excluded: chain C residue 1327 MET Chi-restraints excluded: chain C residue 1338 LEU Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 56 CYS Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 160 ASP Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 225 PHE Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 318 ASN Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 398 MET Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 501 THR Chi-restraints excluded: chain D residue 504 ILE Chi-restraints excluded: chain D residue 530 ASP Chi-restraints excluded: chain D residue 532 SER Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 569 ASN Chi-restraints excluded: chain D residue 570 THR Chi-restraints excluded: chain D residue 616 VAL Chi-restraints excluded: chain D residue 646 ASP Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 748 ASP Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 823 VAL Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 852 VAL Chi-restraints excluded: chain D residue 863 ASN Chi-restraints excluded: chain D residue 1136 ARG Chi-restraints excluded: chain D residue 1156 ASP Chi-restraints excluded: chain D residue 1197 VAL Chi-restraints excluded: chain D residue 1203 THR Chi-restraints excluded: chain D residue 1231 MET Chi-restraints excluded: chain D residue 1256 ASP Chi-restraints excluded: chain D residue 1274 LEU Chi-restraints excluded: chain D residue 1341 ILE Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 13 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 225 optimal weight: 8.9990 chunk 145 optimal weight: 7.9990 chunk 218 optimal weight: 0.0770 chunk 110 optimal weight: 9.9990 chunk 71 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 232 optimal weight: 3.9990 chunk 248 optimal weight: 2.9990 chunk 180 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 287 optimal weight: 9.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1226 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31046 Z= 0.224 Angle : 0.632 12.540 42277 Z= 0.331 Chirality : 0.043 0.183 4927 Planarity : 0.004 0.058 5167 Dihedral : 15.152 85.735 5008 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.66 % Favored : 90.28 % Rotamer: Outliers : 6.68 % Allowed : 28.50 % Favored : 64.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -2.03 (0.14), residues: 3715 helix: 0.15 (0.14), residues: 1477 sheet: -1.65 (0.25), residues: 399 loop : -2.64 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 183 HIS 0.005 0.001 HIS Z 364 PHE 0.033 0.001 PHE M 196 TYR 0.021 0.001 TYR M 168 ARG 0.008 0.000 ARG D 257 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 731 residues out of total 3271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 528 time to evaluate : 3.531 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: S 88 ARG cc_start: 0.7560 (ttm170) cc_final: 0.7025 (mtm-85) REVERT: S 90 LYS cc_start: 0.8333 (mttp) cc_final: 0.7917 (ttmm) REVERT: S 133 MET cc_start: 0.8977 (mmm) cc_final: 0.8649 (mmt) REVERT: S 154 TYR cc_start: 0.7578 (OUTLIER) cc_final: 0.7351 (m-10) REVERT: S 191 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8517 (mmtt) REVERT: S 207 ARG cc_start: 0.7283 (mpt-90) cc_final: 0.6624 (tpp80) REVERT: M 13 ASP cc_start: 0.8061 (m-30) cc_final: 0.7785 (m-30) REVERT: M 19 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8452 (mm) REVERT: M 52 ILE cc_start: 0.8502 (OUTLIER) cc_final: 0.8211 (mm) REVERT: M 60 PHE cc_start: 0.7998 (p90) cc_final: 0.7340 (p90) REVERT: M 127 MET cc_start: 0.8600 (mpp) cc_final: 0.8226 (mpp) REVERT: M 153 GLN cc_start: 0.7914 (pp30) cc_final: 0.7490 (pp30) REVERT: M 169 PHE cc_start: 0.8304 (OUTLIER) cc_final: 0.8005 (t80) REVERT: M 193 GLU cc_start: 0.6876 (OUTLIER) cc_final: 0.6577 (tm-30) REVERT: Z 136 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7877 (tp30) REVERT: Z 143 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.6604 (tt0) REVERT: Z 230 ARG cc_start: 0.7376 (tmt-80) cc_final: 0.5536 (mtt90) REVERT: Z 256 LYS cc_start: 0.8590 (mttt) cc_final: 0.7806 (tptt) REVERT: Z 283 TRP cc_start: 0.5862 (t60) cc_final: 0.5434 (t-100) REVERT: Z 298 ILE cc_start: 0.7806 (OUTLIER) cc_final: 0.7538 (mm) REVERT: Z 366 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7949 (mp) REVERT: Z 401 GLN cc_start: 0.8423 (tm-30) cc_final: 0.8131 (pp30) REVERT: Z 457 GLU cc_start: 0.8864 (tt0) cc_final: 0.8456 (tp30) REVERT: Z 472 MET cc_start: 0.8245 (ptp) cc_final: 0.7917 (ptt) REVERT: Z 476 ILE cc_start: 0.5306 (OUTLIER) cc_final: 0.5102 (pt) REVERT: Z 506 ARG cc_start: 0.7183 (OUTLIER) cc_final: 0.6965 (ttt-90) REVERT: Z 541 GLU cc_start: 0.8281 (tp30) cc_final: 0.7723 (tp30) REVERT: Z 569 ARG cc_start: 0.8266 (mpp80) cc_final: 0.7937 (mtt-85) REVERT: A 19 ASP cc_start: 0.8554 (t0) cc_final: 0.8333 (t0) REVERT: A 74 ASP cc_start: 0.8330 (m-30) cc_final: 0.7659 (t70) REVERT: A 77 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.6659 (mp0) REVERT: A 128 LYS cc_start: 0.8645 (mmtt) cc_final: 0.8420 (mtmm) REVERT: B 80 ILE cc_start: 0.9238 (OUTLIER) cc_final: 0.8970 (tp) REVERT: B 133 TYR cc_start: 0.7275 (t80) cc_final: 0.6475 (t80) REVERT: B 221 ARG cc_start: 0.8750 (ttm170) cc_final: 0.8539 (mtm110) REVERT: C 35 TYR cc_start: 0.8872 (OUTLIER) cc_final: 0.7836 (t80) REVERT: C 185 ASP cc_start: 0.6653 (p0) cc_final: 0.6197 (p0) REVERT: C 394 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6507 (pp20) REVERT: C 442 LYS cc_start: 0.7670 (mppt) cc_final: 0.6161 (tptp) REVERT: C 457 ARG cc_start: 0.8576 (ttp-170) cc_final: 0.7789 (ttp-110) REVERT: C 519 ASP cc_start: 0.7883 (OUTLIER) cc_final: 0.7630 (p0) REVERT: C 556 THR cc_start: 0.9321 (p) cc_final: 0.8999 (p) REVERT: C 634 GLU cc_start: 0.7998 (tp30) cc_final: 0.7483 (tp30) REVERT: C 803 MET cc_start: 0.8216 (tpp) cc_final: 0.7804 (tpp) REVERT: C 1078 ASP cc_start: 0.8653 (m-30) cc_final: 0.8446 (m-30) REVERT: C 1079 LYS cc_start: 0.9301 (tttt) cc_final: 0.9055 (tttt) REVERT: C 1122 ASN cc_start: 0.8684 (p0) cc_final: 0.8365 (p0) REVERT: C 1182 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8659 (mm) REVERT: C 1189 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.7822 (ttmt) REVERT: C 1258 ARG cc_start: 0.9113 (OUTLIER) cc_final: 0.8889 (ttt180) REVERT: C 1271 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7191 (mt) REVERT: C 1338 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8676 (tp) REVERT: C 1351 PHE cc_start: 0.7862 (m-80) cc_final: 0.7021 (m-80) REVERT: D 37 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8602 (mtmm) REVERT: D 48 LYS cc_start: 0.8559 (mtpt) cc_final: 0.8060 (mptt) REVERT: D 76 LEU cc_start: 0.8748 (mp) cc_final: 0.8532 (mp) REVERT: D 100 MET cc_start: 0.7289 (mtt) cc_final: 0.6935 (mtt) REVERT: D 135 LYS cc_start: 0.8811 (mttt) cc_final: 0.8479 (mtpt) REVERT: D 165 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7313 (mm-30) REVERT: D 195 GLU cc_start: 0.8294 (tp30) cc_final: 0.7868 (tp30) REVERT: D 219 LEU cc_start: 0.8765 (mm) cc_final: 0.8485 (tp) REVERT: D 279 LYS cc_start: 0.8267 (tttt) cc_final: 0.7865 (mmtt) REVERT: D 397 ARG cc_start: 0.8374 (tpp80) cc_final: 0.8116 (mmm-85) REVERT: D 403 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7047 (mt-10) REVERT: D 409 ILE cc_start: 0.9253 (mm) cc_final: 0.9046 (mm) REVERT: D 657 LYS cc_start: 0.7790 (mmmt) cc_final: 0.6880 (ptmt) REVERT: D 751 MET cc_start: 0.7946 (mmt) cc_final: 0.7739 (mmt) REVERT: D 782 ASP cc_start: 0.7826 (OUTLIER) cc_final: 0.7521 (m-30) REVERT: D 849 LYS cc_start: 0.7269 (mttt) cc_final: 0.6825 (tmtt) REVERT: D 1132 PHE cc_start: 0.8658 (m-80) cc_final: 0.8344 (m-80) REVERT: D 1269 GLU cc_start: 0.7572 (tp30) cc_final: 0.7234 (tm-30) REVERT: D 1279 LYS cc_start: 0.8269 (tptm) cc_final: 0.7803 (mtpp) outliers start: 203 outliers final: 159 residues processed: 681 average time/residue: 0.3993 time to fit residues: 440.3336 Evaluate side-chains 696 residues out of total 3271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 514 time to evaluate : 3.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 24 GLU Chi-restraints excluded: chain S residue 29 THR Chi-restraints excluded: chain S residue 30 ASP Chi-restraints excluded: chain S residue 41 MET Chi-restraints excluded: chain S residue 68 LEU Chi-restraints excluded: chain S residue 115 ASP Chi-restraints excluded: chain S residue 130 LEU Chi-restraints excluded: chain S residue 154 TYR Chi-restraints excluded: chain S residue 158 LEU Chi-restraints excluded: chain S residue 159 ILE Chi-restraints excluded: chain S residue 191 LYS Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 10 ILE Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 32 SER Chi-restraints excluded: chain M residue 52 ILE Chi-restraints excluded: chain M residue 82 PHE Chi-restraints excluded: chain M residue 159 THR Chi-restraints excluded: chain M residue 169 PHE Chi-restraints excluded: chain M residue 182 ASN Chi-restraints excluded: chain M residue 193 GLU Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain Z residue 99 ASP Chi-restraints excluded: chain Z residue 134 TYR Chi-restraints excluded: chain Z residue 143 GLU Chi-restraints excluded: chain Z residue 199 PHE Chi-restraints excluded: chain Z residue 218 LEU Chi-restraints excluded: chain Z residue 219 TYR Chi-restraints excluded: chain Z residue 233 THR Chi-restraints excluded: chain Z residue 235 HIS Chi-restraints excluded: chain Z residue 278 VAL Chi-restraints excluded: chain Z residue 298 ILE Chi-restraints excluded: chain Z residue 308 ILE Chi-restraints excluded: chain Z residue 366 LEU Chi-restraints excluded: chain Z residue 392 SER Chi-restraints excluded: chain Z residue 421 ILE Chi-restraints excluded: chain Z residue 451 THR Chi-restraints excluded: chain Z residue 468 THR Chi-restraints excluded: chain Z residue 476 ILE Chi-restraints excluded: chain Z residue 506 ARG Chi-restraints excluded: chain Z residue 512 LEU Chi-restraints excluded: chain Z residue 518 THR Chi-restraints excluded: chain Z residue 548 VAL Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 157 ASN Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 35 TYR Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 135 MET Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 394 GLU Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 515 SER Chi-restraints excluded: chain C residue 516 GLN Chi-restraints excluded: chain C residue 519 ASP Chi-restraints excluded: chain C residue 548 PHE Chi-restraints excluded: chain C residue 562 CYS Chi-restraints excluded: chain C residue 577 SER Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 639 CYS Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 700 LYS Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 766 CYS Chi-restraints excluded: chain C residue 831 THR Chi-restraints excluded: chain C residue 832 SER Chi-restraints excluded: chain C residue 840 CYS Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 856 ILE Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 863 SER Chi-restraints excluded: chain C residue 898 THR Chi-restraints excluded: chain C residue 927 SER Chi-restraints excluded: chain C residue 929 THR Chi-restraints excluded: chain C residue 1098 ASP Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 1166 VAL Chi-restraints excluded: chain C residue 1168 ASP Chi-restraints excluded: chain C residue 1182 LEU Chi-restraints excluded: chain C residue 1189 LYS Chi-restraints excluded: chain C residue 1229 THR Chi-restraints excluded: chain C residue 1234 ASP Chi-restraints excluded: chain C residue 1241 TYR Chi-restraints excluded: chain C residue 1245 LEU Chi-restraints excluded: chain C residue 1251 VAL Chi-restraints excluded: chain C residue 1258 ARG Chi-restraints excluded: chain C residue 1266 VAL Chi-restraints excluded: chain C residue 1267 THR Chi-restraints excluded: chain C residue 1271 LEU Chi-restraints excluded: chain C residue 1301 GLU Chi-restraints excluded: chain C residue 1327 MET Chi-restraints excluded: chain C residue 1338 LEU Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 37 LYS Chi-restraints excluded: chain D residue 56 CYS Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 160 ASP Chi-restraints excluded: chain D residue 225 PHE Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 318 ASN Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 501 THR Chi-restraints excluded: chain D residue 504 ILE Chi-restraints excluded: chain D residue 530 ASP Chi-restraints excluded: chain D residue 532 SER Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 569 ASN Chi-restraints excluded: chain D residue 570 THR Chi-restraints excluded: chain D residue 616 VAL Chi-restraints excluded: chain D residue 646 ASP Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 748 ASP Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 863 ASN Chi-restraints excluded: chain D residue 1136 ARG Chi-restraints excluded: chain D residue 1156 ASP Chi-restraints excluded: chain D residue 1197 VAL Chi-restraints excluded: chain D residue 1203 THR Chi-restraints excluded: chain D residue 1231 MET Chi-restraints excluded: chain D residue 1256 ASP Chi-restraints excluded: chain D residue 1274 LEU Chi-restraints excluded: chain D residue 1341 ILE Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 13 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 332 optimal weight: 8.9990 chunk 349 optimal weight: 0.5980 chunk 319 optimal weight: 0.0870 chunk 340 optimal weight: 6.9990 chunk 204 optimal weight: 10.0000 chunk 148 optimal weight: 9.9990 chunk 267 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 307 optimal weight: 9.9990 chunk 321 optimal weight: 7.9990 chunk 339 optimal weight: 0.9990 overall best weight: 2.5364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 100 ASN M 44 ASN ** M 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1226 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 31046 Z= 0.222 Angle : 0.631 12.116 42277 Z= 0.329 Chirality : 0.042 0.168 4927 Planarity : 0.004 0.058 5167 Dihedral : 15.069 84.641 5005 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.23 % Favored : 89.77 % Rotamer: Outliers : 6.78 % Allowed : 28.56 % Favored : 64.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -1.92 (0.14), residues: 3715 helix: 0.24 (0.14), residues: 1474 sheet: -1.59 (0.26), residues: 387 loop : -2.56 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 183 HIS 0.005 0.001 HIS Z 364 PHE 0.030 0.001 PHE M 196 TYR 0.018 0.001 TYR M 168 ARG 0.006 0.000 ARG D 257 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 742 residues out of total 3271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 536 time to evaluate : 3.794 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: S 90 LYS cc_start: 0.8282 (mttp) cc_final: 0.7895 (ttmm) REVERT: S 133 MET cc_start: 0.8909 (mmm) cc_final: 0.8604 (mmt) REVERT: S 154 TYR cc_start: 0.7563 (OUTLIER) cc_final: 0.7328 (m-10) REVERT: S 191 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8473 (mmtt) REVERT: S 207 ARG cc_start: 0.7306 (mpt-90) cc_final: 0.6650 (tpp80) REVERT: M 19 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8396 (mm) REVERT: M 52 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.8197 (mm) REVERT: M 60 PHE cc_start: 0.8018 (p90) cc_final: 0.7361 (p90) REVERT: M 121 ASN cc_start: 0.6701 (m-40) cc_final: 0.6285 (m110) REVERT: M 127 MET cc_start: 0.8618 (mpp) cc_final: 0.8185 (mpp) REVERT: M 153 GLN cc_start: 0.7887 (pp30) cc_final: 0.7469 (pp30) REVERT: M 169 PHE cc_start: 0.8384 (OUTLIER) cc_final: 0.8117 (t80) REVERT: M 193 GLU cc_start: 0.6868 (OUTLIER) cc_final: 0.6579 (tm-30) REVERT: Z 136 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7882 (tp30) REVERT: Z 143 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6538 (tt0) REVERT: Z 230 ARG cc_start: 0.7383 (tmt-80) cc_final: 0.5531 (mtt90) REVERT: Z 256 LYS cc_start: 0.8592 (mttt) cc_final: 0.7810 (tptt) REVERT: Z 283 TRP cc_start: 0.5911 (t60) cc_final: 0.5482 (t-100) REVERT: Z 366 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7967 (mp) REVERT: Z 398 TRP cc_start: 0.7392 (m100) cc_final: 0.6911 (m100) REVERT: Z 401 GLN cc_start: 0.8448 (tm-30) cc_final: 0.8246 (pp30) REVERT: Z 457 GLU cc_start: 0.8844 (tt0) cc_final: 0.8433 (tp30) REVERT: Z 472 MET cc_start: 0.8248 (ptp) cc_final: 0.7930 (ptt) REVERT: Z 533 MET cc_start: 0.8057 (tpp) cc_final: 0.7826 (tpp) REVERT: Z 541 GLU cc_start: 0.8288 (tp30) cc_final: 0.7727 (tp30) REVERT: Z 569 ARG cc_start: 0.8272 (mpp80) cc_final: 0.8049 (mtt-85) REVERT: A 74 ASP cc_start: 0.8312 (m-30) cc_final: 0.7686 (t70) REVERT: A 77 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.6685 (mp0) REVERT: A 128 LYS cc_start: 0.8636 (mmtt) cc_final: 0.8387 (mtmm) REVERT: B 17 TYR cc_start: 0.7131 (p90) cc_final: 0.6713 (p90) REVERT: B 80 ILE cc_start: 0.9301 (OUTLIER) cc_final: 0.8991 (tp) REVERT: B 133 TYR cc_start: 0.7236 (t80) cc_final: 0.6434 (t80) REVERT: B 221 ARG cc_start: 0.8756 (ttm170) cc_final: 0.8543 (mtm110) REVERT: C 35 TYR cc_start: 0.8865 (OUTLIER) cc_final: 0.7820 (t80) REVERT: C 185 ASP cc_start: 0.6649 (p0) cc_final: 0.6236 (p0) REVERT: C 394 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6548 (pp20) REVERT: C 442 LYS cc_start: 0.7691 (mppt) cc_final: 0.6348 (tptp) REVERT: C 519 ASP cc_start: 0.7991 (OUTLIER) cc_final: 0.7733 (p0) REVERT: C 556 THR cc_start: 0.9328 (p) cc_final: 0.9001 (p) REVERT: C 609 LEU cc_start: 0.8767 (tp) cc_final: 0.8231 (mm) REVERT: C 634 GLU cc_start: 0.7958 (tp30) cc_final: 0.7373 (tp30) REVERT: C 803 MET cc_start: 0.8201 (tpp) cc_final: 0.7779 (tpp) REVERT: C 1078 ASP cc_start: 0.8629 (m-30) cc_final: 0.8424 (m-30) REVERT: C 1079 LYS cc_start: 0.9301 (tttt) cc_final: 0.9055 (tttt) REVERT: C 1182 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8639 (mm) REVERT: C 1189 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.7830 (ttmt) REVERT: C 1200 ASP cc_start: 0.6922 (t0) cc_final: 0.6620 (t0) REVERT: C 1258 ARG cc_start: 0.9100 (OUTLIER) cc_final: 0.8840 (ttt180) REVERT: C 1338 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8670 (tp) REVERT: C 1351 PHE cc_start: 0.7851 (m-80) cc_final: 0.6897 (m-80) REVERT: D 37 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8591 (mtmm) REVERT: D 48 LYS cc_start: 0.8623 (mtpt) cc_final: 0.8118 (mptt) REVERT: D 100 MET cc_start: 0.7348 (mtt) cc_final: 0.7046 (mtt) REVERT: D 135 LYS cc_start: 0.8814 (mttt) cc_final: 0.8503 (mtpt) REVERT: D 165 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7358 (mm-30) REVERT: D 195 GLU cc_start: 0.8253 (tp30) cc_final: 0.7777 (tp30) REVERT: D 219 LEU cc_start: 0.8755 (mm) cc_final: 0.8431 (tp) REVERT: D 279 LYS cc_start: 0.8258 (tttt) cc_final: 0.7846 (mmtt) REVERT: D 397 ARG cc_start: 0.8413 (tpp80) cc_final: 0.7753 (tpp80) REVERT: D 657 LYS cc_start: 0.7724 (mmmt) cc_final: 0.6884 (ptmt) REVERT: D 722 MET cc_start: 0.8647 (tpp) cc_final: 0.8369 (mtp) REVERT: D 782 ASP cc_start: 0.7844 (OUTLIER) cc_final: 0.7541 (m-30) REVERT: D 849 LYS cc_start: 0.7250 (mttt) cc_final: 0.6826 (tmtt) REVERT: D 1132 PHE cc_start: 0.8577 (m-80) cc_final: 0.8271 (m-80) REVERT: D 1266 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7606 (mm-30) REVERT: D 1269 GLU cc_start: 0.7547 (tp30) cc_final: 0.7216 (tm-30) REVERT: D 1279 LYS cc_start: 0.8211 (tptm) cc_final: 0.7803 (mtpp) outliers start: 206 outliers final: 167 residues processed: 690 average time/residue: 0.4146 time to fit residues: 459.3004 Evaluate side-chains 702 residues out of total 3271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 516 time to evaluate : 3.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 24 GLU Chi-restraints excluded: chain S residue 29 THR Chi-restraints excluded: chain S residue 30 ASP Chi-restraints excluded: chain S residue 41 MET Chi-restraints excluded: chain S residue 68 LEU Chi-restraints excluded: chain S residue 115 ASP Chi-restraints excluded: chain S residue 130 LEU Chi-restraints excluded: chain S residue 154 TYR Chi-restraints excluded: chain S residue 158 LEU Chi-restraints excluded: chain S residue 159 ILE Chi-restraints excluded: chain S residue 191 LYS Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 10 ILE Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 32 SER Chi-restraints excluded: chain M residue 52 ILE Chi-restraints excluded: chain M residue 82 PHE Chi-restraints excluded: chain M residue 159 THR Chi-restraints excluded: chain M residue 169 PHE Chi-restraints excluded: chain M residue 182 ASN Chi-restraints excluded: chain M residue 193 GLU Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain Z residue 99 ASP Chi-restraints excluded: chain Z residue 134 TYR Chi-restraints excluded: chain Z residue 143 GLU Chi-restraints excluded: chain Z residue 199 PHE Chi-restraints excluded: chain Z residue 218 LEU Chi-restraints excluded: chain Z residue 219 TYR Chi-restraints excluded: chain Z residue 233 THR Chi-restraints excluded: chain Z residue 235 HIS Chi-restraints excluded: chain Z residue 278 VAL Chi-restraints excluded: chain Z residue 308 ILE Chi-restraints excluded: chain Z residue 366 LEU Chi-restraints excluded: chain Z residue 392 SER Chi-restraints excluded: chain Z residue 421 ILE Chi-restraints excluded: chain Z residue 423 THR Chi-restraints excluded: chain Z residue 451 THR Chi-restraints excluded: chain Z residue 483 THR Chi-restraints excluded: chain Z residue 512 LEU Chi-restraints excluded: chain Z residue 518 THR Chi-restraints excluded: chain Z residue 534 ASN Chi-restraints excluded: chain Z residue 548 VAL Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 157 ASN Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 35 TYR Chi-restraints excluded: chain C residue 60 PHE Chi-restraints excluded: chain C residue 73 TYR Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 135 MET Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 394 GLU Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 515 SER Chi-restraints excluded: chain C residue 516 GLN Chi-restraints excluded: chain C residue 519 ASP Chi-restraints excluded: chain C residue 548 PHE Chi-restraints excluded: chain C residue 577 SER Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 639 CYS Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 700 LYS Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain C residue 756 THR Chi-restraints excluded: chain C residue 766 CYS Chi-restraints excluded: chain C residue 831 THR Chi-restraints excluded: chain C residue 832 SER Chi-restraints excluded: chain C residue 840 CYS Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 856 ILE Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 863 SER Chi-restraints excluded: chain C residue 889 ILE Chi-restraints excluded: chain C residue 898 THR Chi-restraints excluded: chain C residue 927 SER Chi-restraints excluded: chain C residue 929 THR Chi-restraints excluded: chain C residue 1098 ASP Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 1166 VAL Chi-restraints excluded: chain C residue 1168 ASP Chi-restraints excluded: chain C residue 1182 LEU Chi-restraints excluded: chain C residue 1189 LYS Chi-restraints excluded: chain C residue 1229 THR Chi-restraints excluded: chain C residue 1234 ASP Chi-restraints excluded: chain C residue 1241 TYR Chi-restraints excluded: chain C residue 1245 LEU Chi-restraints excluded: chain C residue 1251 VAL Chi-restraints excluded: chain C residue 1258 ARG Chi-restraints excluded: chain C residue 1266 VAL Chi-restraints excluded: chain C residue 1267 THR Chi-restraints excluded: chain C residue 1301 GLU Chi-restraints excluded: chain C residue 1327 MET Chi-restraints excluded: chain C residue 1338 LEU Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 37 LYS Chi-restraints excluded: chain D residue 56 CYS Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 160 ASP Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 225 PHE Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 284 ASN Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 318 ASN Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 398 MET Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 501 THR Chi-restraints excluded: chain D residue 504 ILE Chi-restraints excluded: chain D residue 530 ASP Chi-restraints excluded: chain D residue 532 SER Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 569 ASN Chi-restraints excluded: chain D residue 570 THR Chi-restraints excluded: chain D residue 616 VAL Chi-restraints excluded: chain D residue 646 ASP Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 748 ASP Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 823 VAL Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 852 VAL Chi-restraints excluded: chain D residue 863 ASN Chi-restraints excluded: chain D residue 1136 ARG Chi-restraints excluded: chain D residue 1156 ASP Chi-restraints excluded: chain D residue 1197 VAL Chi-restraints excluded: chain D residue 1203 THR Chi-restraints excluded: chain D residue 1231 MET Chi-restraints excluded: chain D residue 1256 ASP Chi-restraints excluded: chain D residue 1274 LEU Chi-restraints excluded: chain D residue 1341 ILE Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 13 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 223 optimal weight: 30.0000 chunk 359 optimal weight: 7.9990 chunk 219 optimal weight: 0.0670 chunk 170 optimal weight: 3.9990 chunk 250 optimal weight: 5.9990 chunk 377 optimal weight: 6.9990 chunk 347 optimal weight: 0.7980 chunk 300 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 232 optimal weight: 0.9990 chunk 184 optimal weight: 0.9980 overall best weight: 1.3722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 100 ASN ** M 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1226 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31046 Z= 0.175 Angle : 0.619 13.756 42277 Z= 0.321 Chirality : 0.042 0.166 4927 Planarity : 0.004 0.056 5167 Dihedral : 14.937 83.255 5002 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 5.59 % Allowed : 30.08 % Favored : 64.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -1.76 (0.14), residues: 3715 helix: 0.37 (0.14), residues: 1481 sheet: -1.49 (0.26), residues: 381 loop : -2.48 (0.14), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 183 HIS 0.005 0.001 HIS Z 364 PHE 0.035 0.001 PHE M 196 TYR 0.034 0.001 TYR M 168 ARG 0.009 0.000 ARG E 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 723 residues out of total 3271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 553 time to evaluate : 3.817 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: S 88 ARG cc_start: 0.7495 (ttm170) cc_final: 0.6858 (mtm-85) REVERT: S 90 LYS cc_start: 0.8341 (mttp) cc_final: 0.7909 (ttmm) REVERT: S 133 MET cc_start: 0.8911 (mmm) cc_final: 0.8593 (mmt) REVERT: S 207 ARG cc_start: 0.7299 (mpt-90) cc_final: 0.6630 (tpp80) REVERT: M 52 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.8172 (mm) REVERT: M 153 GLN cc_start: 0.7923 (pp30) cc_final: 0.7484 (pp30) REVERT: M 169 PHE cc_start: 0.8217 (OUTLIER) cc_final: 0.7949 (t80) REVERT: M 193 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.6685 (tm-30) REVERT: Z 136 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7935 (tp30) REVERT: Z 143 GLU cc_start: 0.6904 (pp20) cc_final: 0.6479 (tt0) REVERT: Z 256 LYS cc_start: 0.8528 (mttt) cc_final: 0.7612 (tptt) REVERT: Z 315 MET cc_start: 0.8872 (tpp) cc_final: 0.8538 (tpp) REVERT: Z 366 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7907 (mp) REVERT: Z 398 TRP cc_start: 0.7366 (m100) cc_final: 0.6893 (m100) REVERT: Z 457 GLU cc_start: 0.8771 (tt0) cc_final: 0.8416 (tp30) REVERT: Z 472 MET cc_start: 0.8218 (ptp) cc_final: 0.7916 (ptt) REVERT: Z 533 MET cc_start: 0.8121 (tpp) cc_final: 0.7840 (tpp) REVERT: Z 569 ARG cc_start: 0.8208 (mpp80) cc_final: 0.7899 (mtt-85) REVERT: A 74 ASP cc_start: 0.8362 (m-30) cc_final: 0.7697 (t70) REVERT: A 77 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.6644 (mp0) REVERT: B 17 TYR cc_start: 0.7113 (p90) cc_final: 0.6725 (p90) REVERT: B 80 ILE cc_start: 0.9272 (OUTLIER) cc_final: 0.8956 (tp) REVERT: B 133 TYR cc_start: 0.7298 (t80) cc_final: 0.6471 (t80) REVERT: B 206 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8506 (tm-30) REVERT: B 221 ARG cc_start: 0.8757 (ttm170) cc_final: 0.8535 (mtm110) REVERT: C 17 VAL cc_start: 0.8281 (p) cc_final: 0.7853 (m) REVERT: C 35 TYR cc_start: 0.8823 (OUTLIER) cc_final: 0.7864 (t80) REVERT: C 185 ASP cc_start: 0.6663 (p0) cc_final: 0.6336 (p0) REVERT: C 394 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6501 (pp20) REVERT: C 434 GLU cc_start: 0.8942 (mm-30) cc_final: 0.8565 (mm-30) REVERT: C 442 LYS cc_start: 0.7700 (mppt) cc_final: 0.6370 (tptp) REVERT: C 457 ARG cc_start: 0.8352 (mtp180) cc_final: 0.8099 (mtm110) REVERT: C 475 GLU cc_start: 0.8550 (pp20) cc_final: 0.8103 (pp20) REVERT: C 519 ASP cc_start: 0.7783 (OUTLIER) cc_final: 0.7500 (p0) REVERT: C 549 GLU cc_start: 0.7337 (tt0) cc_final: 0.7068 (tm-30) REVERT: C 556 THR cc_start: 0.9326 (p) cc_final: 0.8926 (p) REVERT: C 609 LEU cc_start: 0.8599 (tp) cc_final: 0.8210 (mm) REVERT: C 634 GLU cc_start: 0.7945 (tp30) cc_final: 0.7363 (tp30) REVERT: C 803 MET cc_start: 0.8169 (tpp) cc_final: 0.7768 (tpp) REVERT: C 1078 ASP cc_start: 0.8644 (m-30) cc_final: 0.8428 (m-30) REVERT: C 1079 LYS cc_start: 0.9293 (tttt) cc_final: 0.9038 (tttt) REVERT: C 1182 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8591 (mm) REVERT: C 1189 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.7828 (ttmt) REVERT: C 1200 ASP cc_start: 0.6694 (t0) cc_final: 0.6461 (t0) REVERT: C 1213 ILE cc_start: 0.9020 (mt) cc_final: 0.8819 (mt) REVERT: C 1258 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.8692 (ttt180) REVERT: C 1338 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8639 (tp) REVERT: C 1351 PHE cc_start: 0.7783 (m-80) cc_final: 0.6834 (m-80) REVERT: D 48 LYS cc_start: 0.8634 (mtpt) cc_final: 0.8126 (mptt) REVERT: D 100 MET cc_start: 0.7320 (mtt) cc_final: 0.7046 (mtt) REVERT: D 135 LYS cc_start: 0.8821 (mttt) cc_final: 0.8480 (mtpt) REVERT: D 165 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7288 (mm-30) REVERT: D 195 GLU cc_start: 0.8269 (tp30) cc_final: 0.7784 (tp30) REVERT: D 214 LYS cc_start: 0.7164 (ptpt) cc_final: 0.6854 (pttt) REVERT: D 219 LEU cc_start: 0.8744 (mm) cc_final: 0.8466 (tp) REVERT: D 279 LYS cc_start: 0.8243 (tttt) cc_final: 0.7829 (mmtt) REVERT: D 397 ARG cc_start: 0.8416 (tpp80) cc_final: 0.8104 (mmm-85) REVERT: D 403 GLU cc_start: 0.7902 (tm-30) cc_final: 0.6708 (mt-10) REVERT: D 598 GLU cc_start: 0.7364 (mm-30) cc_final: 0.7120 (mm-30) REVERT: D 601 LYS cc_start: 0.7967 (ttmt) cc_final: 0.7522 (tttt) REVERT: D 657 LYS cc_start: 0.7842 (mmmt) cc_final: 0.7020 (ptmt) REVERT: D 722 MET cc_start: 0.8632 (tpp) cc_final: 0.8288 (mtp) REVERT: D 782 ASP cc_start: 0.7771 (OUTLIER) cc_final: 0.7488 (m-30) REVERT: D 786 LYS cc_start: 0.8198 (tmmt) cc_final: 0.7979 (tmmt) REVERT: D 849 LYS cc_start: 0.7205 (mttt) cc_final: 0.6789 (tmtt) REVERT: D 1132 PHE cc_start: 0.8530 (m-80) cc_final: 0.8212 (m-10) REVERT: D 1266 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7434 (mm-30) REVERT: D 1269 GLU cc_start: 0.7526 (tp30) cc_final: 0.7197 (tm-30) REVERT: D 1279 LYS cc_start: 0.8204 (tptm) cc_final: 0.7782 (mtpp) REVERT: E 7 GLU cc_start: 0.8366 (tp30) cc_final: 0.7510 (tt0) REVERT: E 67 ARG cc_start: 0.8895 (mtp-110) cc_final: 0.8506 (mtp-110) outliers start: 170 outliers final: 138 residues processed: 677 average time/residue: 0.4146 time to fit residues: 453.5844 Evaluate side-chains 685 residues out of total 3271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 533 time to evaluate : 3.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 24 GLU Chi-restraints excluded: chain S residue 29 THR Chi-restraints excluded: chain S residue 30 ASP Chi-restraints excluded: chain S residue 41 MET Chi-restraints excluded: chain S residue 68 LEU Chi-restraints excluded: chain S residue 100 ASN Chi-restraints excluded: chain S residue 115 ASP Chi-restraints excluded: chain S residue 130 LEU Chi-restraints excluded: chain S residue 159 ILE Chi-restraints excluded: chain M residue 10 ILE Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 32 SER Chi-restraints excluded: chain M residue 52 ILE Chi-restraints excluded: chain M residue 82 PHE Chi-restraints excluded: chain M residue 159 THR Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain M residue 169 PHE Chi-restraints excluded: chain M residue 182 ASN Chi-restraints excluded: chain M residue 193 GLU Chi-restraints excluded: chain Z residue 99 ASP Chi-restraints excluded: chain Z residue 134 TYR Chi-restraints excluded: chain Z residue 199 PHE Chi-restraints excluded: chain Z residue 218 LEU Chi-restraints excluded: chain Z residue 219 TYR Chi-restraints excluded: chain Z residue 233 THR Chi-restraints excluded: chain Z residue 235 HIS Chi-restraints excluded: chain Z residue 278 VAL Chi-restraints excluded: chain Z residue 366 LEU Chi-restraints excluded: chain Z residue 392 SER Chi-restraints excluded: chain Z residue 421 ILE Chi-restraints excluded: chain Z residue 451 THR Chi-restraints excluded: chain Z residue 512 LEU Chi-restraints excluded: chain Z residue 518 THR Chi-restraints excluded: chain Z residue 534 ASN Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 157 ASN Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 35 TYR Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 394 GLU Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 515 SER Chi-restraints excluded: chain C residue 519 ASP Chi-restraints excluded: chain C residue 548 PHE Chi-restraints excluded: chain C residue 577 SER Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 639 CYS Chi-restraints excluded: chain C residue 700 LYS Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain C residue 756 THR Chi-restraints excluded: chain C residue 766 CYS Chi-restraints excluded: chain C residue 832 SER Chi-restraints excluded: chain C residue 840 CYS Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 856 ILE Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 863 SER Chi-restraints excluded: chain C residue 898 THR Chi-restraints excluded: chain C residue 929 THR Chi-restraints excluded: chain C residue 1098 ASP Chi-restraints excluded: chain C residue 1155 LEU Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 1166 VAL Chi-restraints excluded: chain C residue 1168 ASP Chi-restraints excluded: chain C residue 1182 LEU Chi-restraints excluded: chain C residue 1189 LYS Chi-restraints excluded: chain C residue 1229 THR Chi-restraints excluded: chain C residue 1234 ASP Chi-restraints excluded: chain C residue 1241 TYR Chi-restraints excluded: chain C residue 1245 LEU Chi-restraints excluded: chain C residue 1251 VAL Chi-restraints excluded: chain C residue 1258 ARG Chi-restraints excluded: chain C residue 1266 VAL Chi-restraints excluded: chain C residue 1267 THR Chi-restraints excluded: chain C residue 1301 GLU Chi-restraints excluded: chain C residue 1327 MET Chi-restraints excluded: chain C residue 1338 LEU Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 56 CYS Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 160 ASP Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 225 PHE Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 318 ASN Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 501 THR Chi-restraints excluded: chain D residue 504 ILE Chi-restraints excluded: chain D residue 530 ASP Chi-restraints excluded: chain D residue 532 SER Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 569 ASN Chi-restraints excluded: chain D residue 616 VAL Chi-restraints excluded: chain D residue 646 ASP Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 748 ASP Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 823 VAL Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 863 ASN Chi-restraints excluded: chain D residue 1136 ARG Chi-restraints excluded: chain D residue 1156 ASP Chi-restraints excluded: chain D residue 1197 VAL Chi-restraints excluded: chain D residue 1203 THR Chi-restraints excluded: chain D residue 1256 ASP Chi-restraints excluded: chain D residue 1274 LEU Chi-restraints excluded: chain D residue 1341 ILE Chi-restraints excluded: chain E residue 39 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 238 optimal weight: 6.9990 chunk 320 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 277 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 chunk 301 optimal weight: 1.9990 chunk 126 optimal weight: 20.0000 chunk 309 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 433 GLN B 230 ASN ** C1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.147994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.112969 restraints weight = 55963.090| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.78 r_work: 0.3247 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 31046 Z= 0.307 Angle : 0.671 12.623 42277 Z= 0.349 Chirality : 0.044 0.202 4927 Planarity : 0.004 0.056 5167 Dihedral : 14.930 82.611 4987 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.42 % Favored : 89.58 % Rotamer: Outliers : 5.73 % Allowed : 29.88 % Favored : 64.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -1.90 (0.14), residues: 3715 helix: 0.21 (0.14), residues: 1484 sheet: -1.45 (0.26), residues: 375 loop : -2.55 (0.14), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP S 102 HIS 0.005 0.001 HIS Z 566 PHE 0.053 0.002 PHE M 196 TYR 0.039 0.002 TYR Z 385 ARG 0.007 0.000 ARG D 257 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8536.51 seconds wall clock time: 156 minutes 31.71 seconds (9391.71 seconds total)