Starting phenix.real_space_refine on Tue Feb 20 10:15:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7asm_11900/02_2024/7asm_11900_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7asm_11900/02_2024/7asm_11900.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7asm_11900/02_2024/7asm_11900_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7asm_11900/02_2024/7asm_11900_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7asm_11900/02_2024/7asm_11900_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7asm_11900/02_2024/7asm_11900.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7asm_11900/02_2024/7asm_11900.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7asm_11900/02_2024/7asm_11900_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7asm_11900/02_2024/7asm_11900_updated.pdb" } resolution = 2.48 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= -0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians P 2949 5.49 5 Mg 1 5.21 5 S 55 5.16 5 C 42553 2.51 5 N 15980 2.21 5 O 24611 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "N GLU 8": "OE1" <-> "OE2" Residue "N ARG 16": "NH1" <-> "NH2" Residue "N ARG 23": "NH1" <-> "NH2" Residue "N ARG 33": "NH1" <-> "NH2" Residue "N GLU 59": "OE1" <-> "OE2" Residue "N PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 90": "NH1" <-> "NH2" Residue "N ARG 91": "NH1" <-> "NH2" Residue "N GLU 114": "OE1" <-> "OE2" Residue "E GLU 27": "OE1" <-> "OE2" Residue "E ARG 45": "NH1" <-> "NH2" Residue "E ARG 106": "NH1" <-> "NH2" Residue "E ARG 107": "NH1" <-> "NH2" Residue "E GLU 147": "OE1" <-> "OE2" Residue "E ARG 168": "NH1" <-> "NH2" Residue "E GLU 204": "OE1" <-> "OE2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C ARG 69": "NH1" <-> "NH2" Residue "C ARG 243": "NH1" <-> "NH2" Residue "G ARG 3": "NH1" <-> "NH2" Residue "G ARG 54": "NH1" <-> "NH2" Residue "G ARG 62": "NH1" <-> "NH2" Residue "G ARG 69": "NH1" <-> "NH2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G ARG 163": "NH1" <-> "NH2" Residue "G ARG 170": "NH1" <-> "NH2" Residue "H ARG 2": "NH1" <-> "NH2" Residue "H ARG 14": "NH1" <-> "NH2" Residue "H GLU 64": "OE1" <-> "OE2" Residue "H GLU 99": "OE1" <-> "OE2" Residue "H ARG 100": "NH1" <-> "NH2" Residue "H GLU 103": "OE1" <-> "OE2" Residue "H GLU 130": "OE1" <-> "OE2" Residue "H GLU 139": "OE1" <-> "OE2" Residue "J ARG 21": "NH1" <-> "NH2" Residue "J GLU 73": "OE1" <-> "OE2" Residue "K ARG 10": "NH1" <-> "NH2" Residue "K ARG 20": "NH1" <-> "NH2" Residue "K ARG 45": "NH1" <-> "NH2" Residue "K ARG 51": "NH1" <-> "NH2" Residue "K ARG 56": "NH1" <-> "NH2" Residue "K TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 82": "NH1" <-> "NH2" Residue "K ARG 115": "NH1" <-> "NH2" Residue "M ARG 11": "NH1" <-> "NH2" Residue "M ARG 14": "NH1" <-> "NH2" Residue "M ARG 35": "NH1" <-> "NH2" Residue "M ARG 96": "NH1" <-> "NH2" Residue "M ARG 104": "NH1" <-> "NH2" Residue "O ARG 48": "NH1" <-> "NH2" Residue "P GLU 6": "OE1" <-> "OE2" Residue "P GLU 23": "OE1" <-> "OE2" Residue "P ARG 67": "NH1" <-> "NH2" Residue "R GLU 14": "OE1" <-> "OE2" Residue "R ARG 64": "NH1" <-> "NH2" Residue "R ARG 76": "NH1" <-> "NH2" Residue "S ARG 32": "NH1" <-> "NH2" Residue "T ARG 9": "NH1" <-> "NH2" Residue "T ARG 22": "NH1" <-> "NH2" Residue "T GLU 47": "OE1" <-> "OE2" Residue "T ARG 53": "NH1" <-> "NH2" Residue "T ARG 57": "NH1" <-> "NH2" Residue "U ARG 22": "NH1" <-> "NH2" Residue "U ARG 28": "NH1" <-> "NH2" Residue "U ARG 33": "NH1" <-> "NH2" Residue "U ARG 49": "NH1" <-> "NH2" Residue "U ARG 82": "NH1" <-> "NH2" Residue "W GLU 23": "OE1" <-> "OE2" Residue "W ARG 44": "NH1" <-> "NH2" Residue "W ARG 47": "NH1" <-> "NH2" Residue "W ARG 52": "NH1" <-> "NH2" Residue "W ARG 58": "NH1" <-> "NH2" Residue "W GLU 59": "OE1" <-> "OE2" Residue "W ARG 60": "NH1" <-> "NH2" Residue "3 ARG 24": "NH1" <-> "NH2" Residue "3 ARG 42": "NH1" <-> "NH2" Residue "3 ARG 57": "NH1" <-> "NH2" Residue "1 ARG 24": "NH1" <-> "NH2" Residue "2 ARG 20": "NH1" <-> "NH2" Residue "2 ARG 22": "NH1" <-> "NH2" Residue "2 ARG 40": "NH1" <-> "NH2" Residue "4 ARG 19": "NH1" <-> "NH2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D ARG 89": "NH1" <-> "NH2" Residue "D GLU 191": "OE1" <-> "OE2" Residue "I ARG 17": "NH1" <-> "NH2" Residue "I ARG 88": "NH1" <-> "NH2" Residue "I GLU 120": "OE1" <-> "OE2" Residue "Q ARG 8": "NH1" <-> "NH2" Residue "Q ARG 11": "NH1" <-> "NH2" Residue "Q GLU 48": "OE1" <-> "OE2" Residue "Q GLU 73": "OE1" <-> "OE2" Residue "Q ARG 86": "NH1" <-> "NH2" Residue "Q ARG 88": "NH1" <-> "NH2" Residue "V ARG 37": "NH1" <-> "NH2" Residue "X ARG 10": "NH1" <-> "NH2" Residue "X GLU 38": "OE1" <-> "OE2" Residue "Z ARG 6": "NH1" <-> "NH2" Residue "Z ARG 7": "NH1" <-> "NH2" Residue "Z GLU 29": "OE1" <-> "OE2" Residue "L GLU 31": "OE1" <-> "OE2" Residue "L GLU 34": "OE1" <-> "OE2" Residue "L GLU 45": "OE1" <-> "OE2" Residue "L ARG 67": "NH1" <-> "NH2" Residue "L ARG 110": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 86149 Number of models: 1 Model: "" Number of chains: 30 Chain: "N" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 889 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 109} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1572 Classifications: {'peptide': 206} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 9, 'TRANS': 196} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 60769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2834, 60769 Classifications: {'DNA': 1, 'RNA': 2833} Modifications used: {'rna2p': 2, 'rna2p_pur': 300, 'rna2p_pyr': 155, 'rna3p': 1, 'rna3p_pur': 1324, 'rna3p_pyr': 1051} Link IDs: {'rna2p': 457, 'rna3p': 2376} Chain breaks: 8 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' C:plan': 1, ' C:plan2': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 2448 Classifications: {'RNA': 115} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 8, 'rna3p_pur': 53, 'rna3p_pyr': 48} Link IDs: {'rna2p': 14, 'rna3p': 100} Chain: "C" Number of atoms: 2094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2094 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 17, 'TRANS': 256} Chain: "G" Number of atoms: 1263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1263 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 7, 'TRANS': 167} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 12, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 72 Chain: "H" Number of atoms: 1149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1149 Classifications: {'peptide': 145} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 6, 'TRANS': 138} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "J" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1086 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 140} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "K" Number of atoms: 1071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1071 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 129} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "M" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 882 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 1, 'TRANS': 117} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "O" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 942 Classifications: {'peptide': 116} Link IDs: {'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "P" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 790 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 99} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 715 Classifications: {'peptide': 89} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 86} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "S" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 755 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "T" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 722 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "U" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 597 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "W" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 541 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 66} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "3" Number of atoms: 521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 521 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "1" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 390 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 44} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "2" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 367 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "4" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 295 Classifications: {'peptide': 37} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 3, 'TRANS': 33} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1627 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 8, 'TRANS': 206} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 778 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 137} Link IDs: {'PTRANS': 6, 'TRANS': 151} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 475 Unresolved non-hydrogen angles: 598 Unresolved non-hydrogen dihedrals: 384 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 4, 'ASN:plan1': 7, 'ASP:plan': 10, 'PHE:plan': 7, 'GLU:plan': 12, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 230 Chain: "I" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 918 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "Q" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 854 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 107} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "V" Number of atoms: 379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 379 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 47} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "X" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "Z" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 360 Classifications: {'peptide': 48} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 3, 'TRANS': 44} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 17 Chain: "L" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 925 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 118} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 33.11, per 1000 atoms: 0.38 Number of scatterers: 86149 At special positions: 0 Unit cell: (214.5, 207.636, 227.37, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 55 16.00 P 2949 15.00 Mg 1 11.99 O 24611 8.00 N 15980 7.00 C 42553 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS 1 9 " - pdb=" SG CYS 1 12 " distance=2.03 Simple disulfide: pdb=" SG CYS 1 12 " - pdb=" SG CYS 1 36 " distance=2.03 Simple disulfide: pdb=" SG CYS 4 11 " - pdb=" SG CYS 4 14 " distance=2.04 Simple disulfide: pdb=" SG CYS 4 11 " - pdb=" SG CYS 4 27 " distance=2.04 Simple disulfide: pdb=" SG CYS 4 14 " - pdb=" SG CYS 4 27 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 32.72 Conformation dependent library (CDL) restraints added in 3.7 seconds 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5530 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 78 helices and 47 sheets defined 23.9% alpha, 17.6% beta 883 base pairs and 1504 stacking pairs defined. Time for finding SS restraints: 38.40 Creating SS restraints... Processing helix chain 'N' and resid 5 through 14 removed outlier: 5.264A pdb=" N SER N 13 " --> pdb=" O ALA N 9 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N GLN N 14 " --> pdb=" O VAL N 10 " (cutoff:3.500A) Processing helix chain 'N' and resid 56 through 58 No H-bonds generated for 'chain 'N' and resid 56 through 58' Processing helix chain 'N' and resid 100 through 103 Processing helix chain 'N' and resid 107 through 109 No H-bonds generated for 'chain 'N' and resid 107 through 109' Processing helix chain 'E' and resid 30 through 44 removed outlier: 3.772A pdb=" N LEU E 44 " --> pdb=" O GLN E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 119 removed outlier: 3.672A pdb=" N LYS E 117 " --> pdb=" O ALA E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 145 Processing helix chain 'E' and resid 161 through 166 Processing helix chain 'E' and resid 183 through 188 Processing helix chain 'E' and resid 196 through 205 Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 132 through 134 No H-bonds generated for 'chain 'C' and resid 132 through 134' Processing helix chain 'C' and resid 198 through 202 removed outlier: 4.413A pdb=" N GLU C 201 " --> pdb=" O LEU C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 214 removed outlier: 3.604A pdb=" N LYS C 214 " --> pdb=" O ARG C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 224 No H-bonds generated for 'chain 'C' and resid 222 through 224' Processing helix chain 'C' and resid 265 through 269 removed outlier: 4.061A pdb=" N LYS C 268 " --> pdb=" O SER C 265 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 6 No H-bonds generated for 'chain 'G' and resid 3 through 6' Processing helix chain 'G' and resid 59 through 80 removed outlier: 4.085A pdb=" N GLY G 66 " --> pdb=" O ARG G 62 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR G 67 " --> pdb=" O THR G 63 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL G 79 " --> pdb=" O MET G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 151 removed outlier: 4.111A pdb=" N VAL G 151 " --> pdb=" O ASN G 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 37 removed outlier: 3.858A pdb=" N GLU H 32 " --> pdb=" O ARG H 28 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE H 36 " --> pdb=" O GLU H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 41 No H-bonds generated for 'chain 'H' and resid 39 through 41' Processing helix chain 'H' and resid 90 through 95 Processing helix chain 'H' and resid 98 through 109 removed outlier: 3.510A pdb=" N ILE H 102 " --> pdb=" O PRO H 98 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N MET H 109 " --> pdb=" O SER H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 121 removed outlier: 3.573A pdb=" N LYS H 118 " --> pdb=" O ARG H 114 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS H 121 " --> pdb=" O GLU H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 134 through 136 No H-bonds generated for 'chain 'H' and resid 134 through 136' Processing helix chain 'J' and resid 38 through 40 No H-bonds generated for 'chain 'J' and resid 38 through 40' Processing helix chain 'J' and resid 57 through 60 No H-bonds generated for 'chain 'J' and resid 57 through 60' Processing helix chain 'J' and resid 79 through 81 No H-bonds generated for 'chain 'J' and resid 79 through 81' Processing helix chain 'J' and resid 93 through 98 removed outlier: 3.572A pdb=" N GLU J 98 " --> pdb=" O ALA J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 130 through 138 removed outlier: 3.671A pdb=" N ALA J 138 " --> pdb=" O GLU J 134 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 57 removed outlier: 3.827A pdb=" N TYR K 57 " --> pdb=" O ALA K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 124 removed outlier: 3.674A pdb=" N HIS K 123 " --> pdb=" O ARG K 119 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LYS K 124 " --> pdb=" O LEU K 120 " (cutoff:3.500A) Processing helix chain 'M' and resid 7 through 18 removed outlier: 3.547A pdb=" N LYS M 13 " --> pdb=" O LYS M 9 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG M 14 " --> pdb=" O VAL M 10 " (cutoff:3.500A) Processing helix chain 'M' and resid 70 through 85 removed outlier: 3.523A pdb=" N LYS M 82 " --> pdb=" O GLU M 78 " (cutoff:3.500A) Processing helix chain 'M' and resid 103 through 115 Processing helix chain 'O' and resid 9 through 21 removed outlier: 3.680A pdb=" N THR O 17 " --> pdb=" O ARG O 13 " (cutoff:3.500A) Processing helix chain 'O' and resid 26 through 29 Processing helix chain 'O' and resid 32 through 72 removed outlier: 4.055A pdb=" N ARG O 51 " --> pdb=" O PHE O 47 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN O 52 " --> pdb=" O ARG O 48 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LYS O 54 " --> pdb=" O ARG O 50 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG O 55 " --> pdb=" O ARG O 51 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG O 58 " --> pdb=" O LYS O 54 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLN O 71 " --> pdb=" O ALA O 67 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N HIS O 72 " --> pdb=" O ALA O 68 " (cutoff:3.500A) Processing helix chain 'O' and resid 76 through 86 Processing helix chain 'O' and resid 92 through 101 Processing helix chain 'O' and resid 103 through 115 Processing helix chain 'R' and resid 3 through 6 No H-bonds generated for 'chain 'R' and resid 3 through 6' Processing helix chain 'R' and resid 14 through 21 Processing helix chain 'R' and resid 35 through 46 Processing helix chain 'S' and resid 65 through 67 No H-bonds generated for 'chain 'S' and resid 65 through 67' Processing helix chain 'T' and resid 15 through 23 Processing helix chain 'T' and resid 45 through 55 Processing helix chain 'W' and resid 3 through 8 removed outlier: 3.960A pdb=" N ASP W 8 " --> pdb=" O LYS W 4 " (cutoff:3.500A) Processing helix chain 'W' and resid 11 through 34 removed outlier: 3.605A pdb=" N GLU W 15 " --> pdb=" O THR W 11 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU W 23 " --> pdb=" O LYS W 19 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 65 removed outlier: 3.608A pdb=" N ILE W 43 " --> pdb=" O THR W 40 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG W 44 " --> pdb=" O ALA W 41 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL W 46 " --> pdb=" O ILE W 43 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG W 60 " --> pdb=" O ALA W 57 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN W 64 " --> pdb=" O GLU W 61 " (cutoff:3.500A) Processing helix chain '3' and resid 8 through 11 No H-bonds generated for 'chain '3' and resid 8 through 11' Processing helix chain '3' and resid 33 through 35 No H-bonds generated for 'chain '3' and resid 33 through 35' Processing helix chain '3' and resid 38 through 45 removed outlier: 3.933A pdb=" N ARG 3 45 " --> pdb=" O LYS 3 41 " (cutoff:3.500A) Processing helix chain '3' and resid 52 through 57 removed outlier: 3.999A pdb=" N ARG 3 57 " --> pdb=" O SER 3 53 " (cutoff:3.500A) Processing helix chain '3' and resid 60 through 62 No H-bonds generated for 'chain '3' and resid 60 through 62' Processing helix chain '2' and resid 10 through 16 Processing helix chain '2' and resid 19 through 24 Processing helix chain '2' and resid 26 through 38 Processing helix chain 'D' and resid 71 through 79 Processing helix chain 'D' and resid 107 through 109 No H-bonds generated for 'chain 'D' and resid 107 through 109' Processing helix chain 'F' and resid 47 through 60 Processing helix chain 'F' and resid 94 through 111 Proline residue: F 109 - end of helix Processing helix chain 'F' and resid 163 through 171 Processing helix chain 'I' and resid 107 through 109 No H-bonds generated for 'chain 'I' and resid 107 through 109' Processing helix chain 'I' and resid 112 through 117 Processing helix chain 'Q' and resid 14 through 23 removed outlier: 3.836A pdb=" N LEU Q 19 " --> pdb=" O ARG Q 15 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL Q 20 " --> pdb=" O LYS Q 16 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU Q 23 " --> pdb=" O LEU Q 19 " (cutoff:3.500A) Processing helix chain 'Q' and resid 29 through 38 Processing helix chain 'Q' and resid 44 through 60 Processing helix chain 'Q' and resid 89 through 91 No H-bonds generated for 'chain 'Q' and resid 89 through 91' Processing helix chain 'V' and resid 51 through 56 Processing helix chain 'X' and resid 17 through 26 Processing helix chain 'X' and resid 41 through 50 removed outlier: 3.727A pdb=" N VAL X 50 " --> pdb=" O GLN X 46 " (cutoff:3.500A) Processing helix chain 'Z' and resid 10 through 16 Processing helix chain 'L' and resid 10 through 27 Processing helix chain 'L' and resid 34 through 53 removed outlier: 4.727A pdb=" N SER L 42 " --> pdb=" O LYS L 38 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL L 43 " --> pdb=" O GLU L 39 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS L 46 " --> pdb=" O SER L 42 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 62 Processing helix chain 'L' and resid 74 through 76 No H-bonds generated for 'chain 'L' and resid 74 through 76' Processing helix chain 'L' and resid 81 through 92 removed outlier: 4.969A pdb=" N ALA L 90 " --> pdb=" O PHE L 86 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU L 91 " --> pdb=" O GLY L 87 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'N' and resid 85 through 90 removed outlier: 3.783A pdb=" N LYS N 85 " --> pdb=" O HIS N 31 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N THR N 27 " --> pdb=" O LYS N 89 " (cutoff:3.500A) removed outlier: 8.970A pdb=" N GLU N 46 " --> pdb=" O ILE N 66 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ILE N 66 " --> pdb=" O GLU N 46 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR N 62 " --> pdb=" O ILE N 50 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ARG N 52 " --> pdb=" O THR N 60 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR N 60 " --> pdb=" O ARG N 52 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'E' and resid 123 through 126 removed outlier: 6.260A pdb=" N LEU E 192 " --> pdb=" O THR E 124 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N VAL E 126 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE E 194 " --> pdb=" O VAL E 126 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 3 through 7 removed outlier: 4.414A pdb=" N GLY E 15 " --> pdb=" O VAL E 6 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 3 through 5 Processing sheet with id= E, first strand: chain 'C' and resid 34 through 36 Processing sheet with id= F, first strand: chain 'C' and resid 101 through 105 removed outlier: 3.742A pdb=" N SER C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL C 95 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N VAL C 78 " --> pdb=" O VAL C 95 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 129 through 131 Processing sheet with id= H, first strand: chain 'C' and resid 181 through 185 removed outlier: 3.794A pdb=" N GLY C 166 " --> pdb=" O LEU C 173 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ARG C 175 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N VAL C 164 " --> pdb=" O ARG C 175 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'G' and resid 16 through 19 Processing sheet with id= J, first strand: chain 'G' and resid 42 through 45 removed outlier: 3.756A pdb=" N THR G 42 " --> pdb=" O VAL G 53 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 161 through 164 removed outlier: 3.516A pdb=" N VAL G 90 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER G 124 " --> pdb=" O LYS G 132 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 95 through 99 removed outlier: 3.576A pdb=" N GLN G 97 " --> pdb=" O ILE G 104 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE G 104 " --> pdb=" O GLN G 97 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP G 102 " --> pdb=" O GLN G 99 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'H' and resid 16 through 19 removed outlier: 6.710A pdb=" N TYR H 54 " --> pdb=" O TYR H 17 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ILE H 19 " --> pdb=" O TYR H 54 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ILE H 56 " --> pdb=" O ILE H 19 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'J' and resid 75 through 77 Processing sheet with id= O, first strand: chain 'K' and resid 32 through 36 Processing sheet with id= P, first strand: chain 'K' and resid 40 through 42 Processing sheet with id= Q, first strand: chain 'K' and resid 63 through 66 Processing sheet with id= R, first strand: chain 'K' and resid 72 through 76 removed outlier: 5.966A pdb=" N LYS K 76 " --> pdb=" O VAL K 90 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N VAL K 90 " --> pdb=" O LYS K 76 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'M' and resid 93 through 95 removed outlier: 3.743A pdb=" N VAL M 33 " --> pdb=" O ASP M 95 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA M 56 " --> pdb=" O ALA M 42 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA M 54 " --> pdb=" O ILE M 44 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ASP M 46 " --> pdb=" O THR M 52 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N THR M 52 " --> pdb=" O ASP M 46 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'P' and resid 10 through 14 removed outlier: 3.892A pdb=" N PHE P 40 " --> pdb=" O ILE P 4 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N GLU P 6 " --> pdb=" O VAL P 38 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL P 38 " --> pdb=" O GLU P 6 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'P' and resid 19 through 23 Processing sheet with id= V, first strand: chain 'P' and resid 32 through 35 removed outlier: 6.583A pdb=" N THR P 61 " --> pdb=" O ILE P 97 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE P 97 " --> pdb=" O THR P 61 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASN P 63 " --> pdb=" O LEU P 95 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LEU P 95 " --> pdb=" O ASN P 63 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'P' and resid 71 through 77 removed outlier: 4.596A pdb=" N SER P 82 " --> pdb=" O LYS P 77 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'R' and resid 52 through 58 removed outlier: 4.360A pdb=" N ARG R 76 " --> pdb=" O VAL R 29 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG R 9 " --> pdb=" O ASP R 28 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'R' and resid 62 through 64 Processing sheet with id= Z, first strand: chain 'S' and resid 9 through 11 Processing sheet with id= AA, first strand: chain 'S' and resid 40 through 45 Processing sheet with id= AB, first strand: chain 'S' and resid 82 through 86 Processing sheet with id= AC, first strand: chain 'T' and resid 3 through 5 removed outlier: 6.006A pdb=" N GLU T 62 " --> pdb=" O LEU T 4 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ASP T 90 " --> pdb=" O ALA T 75 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N TYR T 77 " --> pdb=" O HIS T 88 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N HIS T 88 " --> pdb=" O TYR T 77 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'U' and resid 59 through 61 Processing sheet with id= AE, first strand: chain 'U' and resid 74 through 79 Processing sheet with id= AF, first strand: chain '3' and resid 14 through 16 Processing sheet with id= AG, first strand: chain '1' and resid 17 through 21 removed outlier: 4.117A pdb=" N TYR 1 17 " --> pdb=" O LEU 1 7 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS 1 41 " --> pdb=" O CYS 1 36 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain '4' and resid 2 through 4 removed outlier: 3.521A pdb=" N ARG 4 4 " --> pdb=" O ARG 4 35 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain '4' and resid 15 through 19 Processing sheet with id= AJ, first strand: chain 'D' and resid 8 through 17 removed outlier: 6.776A pdb=" N VAL D 27 " --> pdb=" O ILE D 10 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N MET D 12 " --> pdb=" O VAL D 25 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL D 25 " --> pdb=" O MET D 12 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLN D 14 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE D 23 " --> pdb=" O GLN D 14 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N PHE D 16 " --> pdb=" O GLU D 21 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N GLU D 21 " --> pdb=" O PHE D 16 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN D 187 " --> pdb=" O LEU D 196 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LYS D 198 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL D 185 " --> pdb=" O LYS D 198 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'D' and resid 49 through 52 Processing sheet with id= AL, first strand: chain 'D' and resid 211 through 213 Processing sheet with id= AM, first strand: chain 'F' and resid 88 through 91 removed outlier: 6.419A pdb=" N VAL F 157 " --> pdb=" O ASP F 32 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ILE F 34 " --> pdb=" O VAL F 155 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL F 155 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N VAL F 36 " --> pdb=" O ASP F 153 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ASP F 153 " --> pdb=" O VAL F 36 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'I' and resid 83 through 86 removed outlier: 3.613A pdb=" N ALA I 83 " --> pdb=" O VAL I 63 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N THR I 42 " --> pdb=" O THR I 21 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N THR I 21 " --> pdb=" O THR I 42 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'Q' and resid 2 through 7 removed outlier: 6.650A pdb=" N SER Q 108 " --> pdb=" O VAL Q 71 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N VAL Q 71 " --> pdb=" O SER Q 108 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'Q' and resid 82 through 87 Processing sheet with id= AQ, first strand: chain 'V' and resid 14 through 18 Processing sheet with id= AR, first strand: chain 'V' and resid 33 through 39 Processing sheet with id= AS, first strand: chain 'X' and resid 34 through 38 Processing sheet with id= AT, first strand: chain 'L' and resid 29 through 33 Processing sheet with id= AU, first strand: chain 'L' and resid 70 through 73 removed outlier: 3.559A pdb=" N THR L 77 " --> pdb=" O ASN L 73 " (cutoff:3.500A) 675 hydrogen bonds defined for protein. 1863 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2212 hydrogen bonds 3524 hydrogen bond angles 0 basepair planarities 883 basepair parallelities 1504 stacking parallelities Total time for adding SS restraints: 131.63 Time building geometry restraints manager: 35.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 7204 1.29 - 1.43: 42964 1.43 - 1.56: 37842 1.56 - 1.69: 5890 1.69 - 1.82: 100 Bond restraints: 94000 Sorted by residual: bond pdb=" C5 5MU A1966 " pdb=" C6 5MU A1966 " ideal model delta sigma weight residual 1.155 1.442 -0.287 2.00e-02 2.50e+03 2.06e+02 bond pdb=" C5 5MU A 792 " pdb=" C6 5MU A 792 " ideal model delta sigma weight residual 1.155 1.438 -0.283 2.00e-02 2.50e+03 2.01e+02 bond pdb=" C4 5MU A 792 " pdb=" C5 5MU A 792 " ideal model delta sigma weight residual 1.802 1.594 0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C4 5MU A1966 " pdb=" C5 5MU A1966 " ideal model delta sigma weight residual 1.802 1.602 0.200 2.00e-02 2.50e+03 9.97e+01 bond pdb=" C TYR H 45 " pdb=" N THR H 46 " ideal model delta sigma weight residual 1.331 1.248 0.083 1.36e-02 5.41e+03 3.73e+01 ... (remaining 93995 not shown) Histogram of bond angle deviations from ideal: 96.53 - 104.47: 12012 104.47 - 112.40: 55698 112.40 - 120.34: 40176 120.34 - 128.28: 29269 128.28 - 136.21: 4366 Bond angle restraints: 141521 Sorted by residual: angle pdb=" C1' 2MA A2530 " pdb=" N9 2MA A2530 " pdb=" C8 2MA A2530 " ideal model delta sigma weight residual 135.36 112.62 22.74 3.00e+00 1.11e-01 5.74e+01 angle pdb=" N TYR H 76 " pdb=" CA TYR H 76 " pdb=" C TYR H 76 " ideal model delta sigma weight residual 110.80 126.88 -16.08 2.13e+00 2.20e-01 5.70e+01 angle pdb=" N THR D 109 " pdb=" CA THR D 109 " pdb=" C THR D 109 " ideal model delta sigma weight residual 112.54 104.28 8.26 1.22e+00 6.72e-01 4.58e+01 angle pdb=" C1' 2MA A2530 " pdb=" N9 2MA A2530 " pdb=" C4 2MA A2530 " ideal model delta sigma weight residual 116.52 136.21 -19.69 3.00e+00 1.11e-01 4.31e+01 angle pdb=" N ARG H 77 " pdb=" CA ARG H 77 " pdb=" C ARG H 77 " ideal model delta sigma weight residual 110.80 122.22 -11.42 2.13e+00 2.20e-01 2.88e+01 ... (remaining 141516 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.79: 53226 35.79 - 71.58: 6151 71.58 - 107.38: 682 107.38 - 143.17: 9 143.17 - 178.96: 22 Dihedral angle restraints: 60090 sinusoidal: 51486 harmonic: 8604 Sorted by residual: dihedral pdb=" CA ALA P 50 " pdb=" C ALA P 50 " pdb=" N PRO P 51 " pdb=" CA PRO P 51 " ideal model delta harmonic sigma weight residual 180.00 99.18 80.82 0 5.00e+00 4.00e-02 2.61e+02 dihedral pdb=" O4' U A2800 " pdb=" C1' U A2800 " pdb=" N1 U A2800 " pdb=" C2 U A2800 " ideal model delta sinusoidal sigma weight residual -160.00 18.96 -178.96 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C A1932 " pdb=" C1' C A1932 " pdb=" N1 C A1932 " pdb=" C2 C A1932 " ideal model delta sinusoidal sigma weight residual -160.00 18.88 -178.88 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 60087 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 16684 0.085 - 0.170: 1452 0.170 - 0.254: 115 0.254 - 0.339: 19 0.339 - 0.424: 5 Chirality restraints: 18275 Sorted by residual: chirality pdb=" C1' A A 125 " pdb=" O4' A A 125 " pdb=" C2' A A 125 " pdb=" N9 A A 125 " both_signs ideal model delta sigma weight residual False 2.46 2.03 0.42 2.00e-01 2.50e+01 4.50e+00 chirality pdb=" C3' A A2840 " pdb=" C4' A A2840 " pdb=" O3' A A2840 " pdb=" C2' A A2840 " both_signs ideal model delta sigma weight residual False -2.74 -2.33 -0.42 2.00e-01 2.50e+01 4.36e+00 chirality pdb=" C3' G A 808 " pdb=" C4' G A 808 " pdb=" O3' G A 808 " pdb=" C2' G A 808 " both_signs ideal model delta sigma weight residual False -2.48 -2.13 -0.35 2.00e-01 2.50e+01 3.10e+00 ... (remaining 18272 not shown) Planarity restraints: 6955 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MA A2530 " 0.837 2.00e-02 2.50e+03 5.71e-01 7.34e+03 pdb=" C4' 2MA A2530 " -0.223 2.00e-02 2.50e+03 pdb=" O4' 2MA A2530 " -0.656 2.00e-02 2.50e+03 pdb=" C3' 2MA A2530 " 0.216 2.00e-02 2.50e+03 pdb=" O3' 2MA A2530 " -0.901 2.00e-02 2.50e+03 pdb=" C2' 2MA A2530 " 0.604 2.00e-02 2.50e+03 pdb=" O2' 2MA A2530 " 0.576 2.00e-02 2.50e+03 pdb=" C1' 2MA A2530 " -0.447 2.00e-02 2.50e+03 pdb=" N9 2MA A2530 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MU A1966 " 0.696 2.00e-02 2.50e+03 5.06e-01 5.76e+03 pdb=" C4' 5MU A1966 " -0.246 2.00e-02 2.50e+03 pdb=" O4' 5MU A1966 " -0.500 2.00e-02 2.50e+03 pdb=" C3' 5MU A1966 " 0.242 2.00e-02 2.50e+03 pdb=" O3' 5MU A1966 " -0.837 2.00e-02 2.50e+03 pdb=" C2' 5MU A1966 " 0.600 2.00e-02 2.50e+03 pdb=" O2' 5MU A1966 " 0.473 2.00e-02 2.50e+03 pdb=" C1' 5MU A1966 " -0.408 2.00e-02 2.50e+03 pdb=" N1 5MU A1966 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MU A 792 " 0.031 2.00e-02 2.50e+03 4.86e-01 5.32e+03 pdb=" C4' 5MU A 792 " -0.407 2.00e-02 2.50e+03 pdb=" O4' 5MU A 792 " -0.549 2.00e-02 2.50e+03 pdb=" C3' 5MU A 792 " 0.567 2.00e-02 2.50e+03 pdb=" O3' 5MU A 792 " 0.376 2.00e-02 2.50e+03 pdb=" C2' 5MU A 792 " 0.281 2.00e-02 2.50e+03 pdb=" O2' 5MU A 792 " -0.746 2.00e-02 2.50e+03 pdb=" C1' 5MU A 792 " -0.257 2.00e-02 2.50e+03 pdb=" N1 5MU A 792 " 0.705 2.00e-02 2.50e+03 ... (remaining 6952 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 1168 2.59 - 3.17: 63323 3.17 - 3.74: 161223 3.74 - 4.32: 236508 4.32 - 4.90: 309848 Nonbonded interactions: 772070 Sorted by model distance: nonbonded pdb=" O2' A A1489 " pdb=" N7 G A1490 " model vdw 2.012 2.520 nonbonded pdb=" O2' C A1189 " pdb=" O5' A A1190 " model vdw 2.016 2.440 nonbonded pdb=" O2' G A2858 " pdb=" N7 G A2859 " model vdw 2.049 2.520 nonbonded pdb=" N1 A A1514 " pdb=" N2 G A1566 " model vdw 2.078 2.600 nonbonded pdb=" O2' U A2136 " pdb=" O2' G A2169 " model vdw 2.095 2.440 ... (remaining 772065 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: 2.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 12.560 Check model and map are aligned: 0.940 Set scattering table: 0.590 Process input model: 288.770 Find NCS groups from input model: 1.360 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:11.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 318.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 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 : 0.010 0.287 94000 Z= 0.628 Angle : 0.838 22.736 141521 Z= 0.447 Chirality : 0.050 0.424 18275 Planarity : 0.012 0.571 6955 Dihedral : 22.758 178.961 54545 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.40 % Allowed : 7.32 % Favored : 92.28 % Rotamer: Outliers : 0.65 % Allowed : 4.87 % Favored : 94.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.28 % 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: -3.05 (0.13), residues: 2980 helix: -1.53 (0.16), residues: 745 sheet: -1.60 (0.19), residues: 624 loop : -2.48 (0.12), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 83 HIS 0.014 0.002 HIS 2 17 PHE 0.036 0.003 PHE W 30 TYR 0.021 0.002 TYR H 126 ARG 0.019 0.001 ARG Q 11 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 686 time to evaluate : 3.378 Fit side-chains TARDY: cannot create tardy model for: "LYS G 175 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "VAL J 145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU X 58 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. REVERT: H 92 GLU cc_start: 0.7009 (mm-30) cc_final: 0.6358 (tp30) REVERT: T 80 ASP cc_start: 0.8586 (t0) cc_final: 0.8101 (t0) REVERT: W 11 THR cc_start: 0.9133 (m) cc_final: 0.8839 (m) REVERT: W 39 GLU cc_start: 0.7621 (mp0) cc_final: 0.7403 (mp0) REVERT: D 189 ASP cc_start: 0.8077 (t0) cc_final: 0.7531 (t0) REVERT: L 78 THR cc_start: 0.8720 (m) cc_final: 0.7807 (m) outliers start: 15 outliers final: 7 residues processed: 699 average time/residue: 1.8432 time to fit residues: 1689.0656 Evaluate side-chains 566 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 559 time to evaluate : 3.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain L residue 122 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 583 random chunks: chunk 492 optimal weight: 4.9990 chunk 441 optimal weight: 5.9990 chunk 245 optimal weight: 10.0000 chunk 150 optimal weight: 8.9990 chunk 298 optimal weight: 10.0000 chunk 236 optimal weight: 60.0000 chunk 456 optimal weight: 7.9990 chunk 176 optimal weight: 50.0000 chunk 277 optimal weight: 10.0000 chunk 340 optimal weight: 6.9990 chunk 529 optimal weight: 50.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 4 HIS E 162 ASN C 90 ASN C 163 GLN C 199 GLN G 106 ASN H 11 ASN H 24 GLN H 59 ASN H 81 HIS J 54 GLN J 70 ASN J 81 GLN K 25 ASN M 8 ASN M 15 HIS O 71 GLN P 18 GLN ** T 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 20 ASN 3 60 GLN 1 16 ASN 2 7 GLN D 33 ASN D 37 GLN D 47 ASN D 143 HIS D 167 GLN I 4 GLN Q 28 ASN Q 60 HIS Q 65 ASN Q 90 GLN V 16 ASN X 5 GLN Z 19 HIS Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.0802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 94000 Z= 0.369 Angle : 0.690 13.750 141521 Z= 0.364 Chirality : 0.042 0.372 18275 Planarity : 0.006 0.125 6955 Dihedral : 22.969 178.619 48998 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.11 % Favored : 93.69 % Rotamer: Outliers : 3.67 % Allowed : 14.67 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.17 % 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: 2980 helix: -0.22 (0.18), residues: 751 sheet: -1.12 (0.19), residues: 649 loop : -2.05 (0.13), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 93 HIS 0.007 0.001 HIS M 39 PHE 0.021 0.002 PHE D 127 TYR 0.017 0.002 TYR 2 6 ARG 0.012 0.001 ARG Q 92 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 628 time to evaluate : 3.462 Fit side-chains TARDY: cannot create tardy model for: "LYS G 175 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "VAL J 145 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU X 58 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. REVERT: N 85 LYS cc_start: 0.8802 (ttpp) cc_final: 0.8390 (ttpp) REVERT: C 182 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.8594 (ttt180) REVERT: J 1 MET cc_start: 0.8247 (mtm) cc_final: 0.8018 (mtm) REVERT: M 22 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8828 (tt) REVERT: O 74 MET cc_start: 0.8287 (mtt) cc_final: 0.7948 (ttt) REVERT: U 76 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8201 (mptp) REVERT: I 81 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.6860 (pm20) REVERT: I 97 ARG cc_start: 0.8023 (mtp85) cc_final: 0.7806 (mtm110) REVERT: Q 2 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7467 (mt-10) REVERT: V 35 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8911 (tttp) REVERT: Z 27 MET cc_start: 0.7687 (ttp) cc_final: 0.7437 (ttp) outliers start: 85 outliers final: 43 residues processed: 672 average time/residue: 1.7556 time to fit residues: 1568.1837 Evaluate side-chains 633 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 585 time to evaluate : 3.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 84 GLU Chi-restraints excluded: chain N residue 93 LYS Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 182 ARG Chi-restraints excluded: chain G residue 150 SER Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain K residue 3 LEU Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 55 THR Chi-restraints excluded: chain K residue 91 GLU Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain O residue 77 SER Chi-restraints excluded: chain P residue 37 LYS Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain R residue 14 GLU Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain U residue 76 LYS Chi-restraints excluded: chain 3 residue 4 MET Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain Q residue 63 ASP Chi-restraints excluded: chain Q residue 94 SER Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain V residue 35 LYS Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain L residue 16 MET Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 122 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 583 random chunks: chunk 294 optimal weight: 10.0000 chunk 164 optimal weight: 10.0000 chunk 440 optimal weight: 4.9990 chunk 360 optimal weight: 20.0000 chunk 146 optimal weight: 10.0000 chunk 530 optimal weight: 50.0000 chunk 572 optimal weight: 0.9990 chunk 472 optimal weight: 1.9990 chunk 525 optimal weight: 40.0000 chunk 180 optimal weight: 50.0000 chunk 425 optimal weight: 2.9990 overall best weight: 4.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 GLN G 97 GLN J 27 ASN J 81 GLN K 25 ASN O 71 GLN T 20 GLN T 88 HIS D 50 GLN Q 65 ASN Q 90 GLN X 5 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 94000 Z= 0.235 Angle : 0.607 13.646 141521 Z= 0.325 Chirality : 0.037 0.332 18275 Planarity : 0.005 0.119 6955 Dihedral : 22.877 179.719 48998 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.91 % Favored : 93.93 % Rotamer: Outliers : 4.18 % Allowed : 16.82 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.21 % 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: -1.55 (0.14), residues: 2980 helix: 0.37 (0.19), residues: 747 sheet: -0.86 (0.19), residues: 642 loop : -1.83 (0.13), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP V 29 HIS 0.006 0.001 HIS J 35 PHE 0.015 0.001 PHE E 90 TYR 0.017 0.001 TYR 2 6 ARG 0.007 0.000 ARG 2 37 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 610 time to evaluate : 3.500 Fit side-chains TARDY: cannot create tardy model for: "LYS G 175 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "VAL J 145 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU X 58 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. REVERT: N 85 LYS cc_start: 0.8798 (ttpp) cc_final: 0.8401 (ttpp) REVERT: M 22 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8769 (tt) REVERT: O 74 MET cc_start: 0.8245 (mtt) cc_final: 0.7928 (ttt) REVERT: U 76 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8234 (mptp) REVERT: D 18 GLU cc_start: 0.7610 (pp20) cc_final: 0.7255 (pp20) REVERT: D 19 ASN cc_start: 0.8046 (p0) cc_final: 0.6004 (p0) REVERT: D 189 ASP cc_start: 0.7807 (t0) cc_final: 0.7514 (t0) REVERT: D 200 ASN cc_start: 0.8766 (OUTLIER) cc_final: 0.8431 (p0) REVERT: I 81 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.6860 (pm20) REVERT: X 51 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8517 (pttm) REVERT: Z 27 MET cc_start: 0.7521 (ttp) cc_final: 0.7196 (ttp) outliers start: 97 outliers final: 52 residues processed: 658 average time/residue: 1.6942 time to fit residues: 1497.1149 Evaluate side-chains 635 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 578 time to evaluate : 3.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 84 GLU Chi-restraints excluded: chain N residue 93 LYS Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 86 LYS Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 131 SER Chi-restraints excluded: chain K residue 3 LEU Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 91 GLU Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain O residue 77 SER Chi-restraints excluded: chain P residue 37 LYS Chi-restraints excluded: chain R residue 14 GLU Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain T residue 8 ILE Chi-restraints excluded: chain T residue 31 VAL Chi-restraints excluded: chain T residue 52 ILE Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain U residue 76 LYS Chi-restraints excluded: chain U residue 78 GLU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 164 PHE Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain Q residue 28 ASN Chi-restraints excluded: chain Q residue 63 ASP Chi-restraints excluded: chain Q residue 94 SER Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain V residue 55 LYS Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 51 LYS Chi-restraints excluded: chain X residue 57 GLU Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 122 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 583 random chunks: chunk 524 optimal weight: 0.1980 chunk 398 optimal weight: 2.9990 chunk 275 optimal weight: 10.0000 chunk 58 optimal weight: 20.0000 chunk 253 optimal weight: 10.0000 chunk 356 optimal weight: 50.0000 chunk 532 optimal weight: 30.0000 chunk 563 optimal weight: 8.9990 chunk 278 optimal weight: 20.0000 chunk 504 optimal weight: 8.9990 chunk 151 optimal weight: 10.0000 overall best weight: 6.2390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 174 GLN C 163 GLN C 199 GLN G 73 ASN J 81 GLN K 25 ASN O 71 GLN Q 90 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 94000 Z= 0.331 Angle : 0.662 14.061 141521 Z= 0.350 Chirality : 0.040 0.346 18275 Planarity : 0.005 0.123 6955 Dihedral : 22.877 179.302 48998 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.61 % Favored : 93.26 % Rotamer: Outliers : 4.40 % Allowed : 18.21 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.17 % 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: -1.33 (0.14), residues: 2980 helix: 0.58 (0.19), residues: 753 sheet: -0.80 (0.19), residues: 654 loop : -1.68 (0.14), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 93 HIS 0.006 0.001 HIS J 35 PHE 0.017 0.002 PHE E 90 TYR 0.018 0.002 TYR 2 6 ARG 0.006 0.001 ARG I 97 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 582 time to evaluate : 3.643 Fit side-chains TARDY: cannot create tardy model for: "LYS G 175 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "VAL J 145 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU X 58 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. REVERT: M 22 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8777 (tt) REVERT: O 74 MET cc_start: 0.8273 (mtt) cc_final: 0.7920 (ttt) REVERT: U 76 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8213 (mptp) REVERT: D 200 ASN cc_start: 0.8767 (OUTLIER) cc_final: 0.8474 (p0) REVERT: I 81 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.6926 (pm20) REVERT: V 35 LYS cc_start: 0.9152 (OUTLIER) cc_final: 0.8844 (tttp) REVERT: X 51 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8545 (pttm) REVERT: Z 27 MET cc_start: 0.7620 (ttp) cc_final: 0.7337 (ttp) outliers start: 102 outliers final: 62 residues processed: 636 average time/residue: 1.6468 time to fit residues: 1410.4039 Evaluate side-chains 651 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 583 time to evaluate : 3.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 84 GLU Chi-restraints excluded: chain N residue 93 LYS Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 150 SER Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 86 LYS Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain K residue 3 LEU Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 110 SER Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain O residue 77 SER Chi-restraints excluded: chain P residue 37 LYS Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain R residue 14 GLU Chi-restraints excluded: chain R residue 16 SER Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain T residue 8 ILE Chi-restraints excluded: chain T residue 31 VAL Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain U residue 76 LYS Chi-restraints excluded: chain U residue 78 GLU Chi-restraints excluded: chain U residue 87 VAL Chi-restraints excluded: chain 3 residue 25 SER Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 66 LYS Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 28 ASN Chi-restraints excluded: chain Q residue 63 ASP Chi-restraints excluded: chain Q residue 94 SER Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain V residue 24 SER Chi-restraints excluded: chain V residue 35 LYS Chi-restraints excluded: chain V residue 55 LYS Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 51 LYS Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 116 SER Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 122 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 583 random chunks: chunk 469 optimal weight: 9.9990 chunk 319 optimal weight: 40.0000 chunk 8 optimal weight: 6.9990 chunk 419 optimal weight: 3.9990 chunk 232 optimal weight: 10.0000 chunk 480 optimal weight: 0.8980 chunk 389 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 287 optimal weight: 10.0000 chunk 505 optimal weight: 0.9980 chunk 142 optimal weight: 10.0000 overall best weight: 4.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 174 GLN C 163 GLN C 199 GLN J 81 GLN O 71 GLN S 45 GLN 3 40 GLN D 19 ASN Q 65 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 94000 Z= 0.252 Angle : 0.631 13.902 141521 Z= 0.337 Chirality : 0.038 0.332 18275 Planarity : 0.005 0.121 6955 Dihedral : 22.882 179.679 48998 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.24 % Favored : 93.62 % Rotamer: Outliers : 4.27 % Allowed : 19.15 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.17 % 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: -1.24 (0.14), residues: 2980 helix: 0.73 (0.19), residues: 750 sheet: -0.80 (0.19), residues: 642 loop : -1.62 (0.14), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP V 29 HIS 0.006 0.001 HIS J 35 PHE 0.015 0.002 PHE E 90 TYR 0.019 0.001 TYR 2 6 ARG 0.006 0.000 ARG I 97 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 587 time to evaluate : 3.541 Fit side-chains TARDY: cannot create tardy model for: "LYS G 175 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "VAL J 145 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU X 58 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. REVERT: M 22 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8785 (tt) REVERT: O 74 MET cc_start: 0.8260 (mtt) cc_final: 0.7918 (ttt) REVERT: U 76 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8205 (mptp) REVERT: 4 18 LYS cc_start: 0.9237 (mtpt) cc_final: 0.9030 (tttt) REVERT: D 200 ASN cc_start: 0.8764 (OUTLIER) cc_final: 0.8468 (p0) REVERT: I 81 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.6825 (pm20) REVERT: X 51 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8507 (pttm) REVERT: Z 27 MET cc_start: 0.7588 (ttp) cc_final: 0.7299 (ttp) outliers start: 99 outliers final: 68 residues processed: 635 average time/residue: 1.6941 time to fit residues: 1445.0715 Evaluate side-chains 652 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 579 time to evaluate : 3.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 84 GLU Chi-restraints excluded: chain N residue 93 LYS Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 150 SER Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 86 LYS Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 107 SER Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain K residue 3 LEU Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 91 GLU Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain O residue 77 SER Chi-restraints excluded: chain P residue 37 LYS Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain P residue 93 THR Chi-restraints excluded: chain R residue 14 GLU Chi-restraints excluded: chain R residue 16 SER Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain T residue 8 ILE Chi-restraints excluded: chain T residue 31 VAL Chi-restraints excluded: chain T residue 52 ILE Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain U residue 76 LYS Chi-restraints excluded: chain U residue 78 GLU Chi-restraints excluded: chain U residue 87 VAL Chi-restraints excluded: chain 3 residue 25 SER Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 66 LYS Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 28 ASN Chi-restraints excluded: chain Q residue 63 ASP Chi-restraints excluded: chain Q residue 94 SER Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain V residue 24 SER Chi-restraints excluded: chain V residue 55 LYS Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 13 ILE Chi-restraints excluded: chain X residue 51 LYS Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 116 SER Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 122 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 583 random chunks: chunk 189 optimal weight: 10.0000 chunk 507 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 chunk 330 optimal weight: 10.0000 chunk 139 optimal weight: 50.0000 chunk 564 optimal weight: 6.9990 chunk 468 optimal weight: 10.0000 chunk 261 optimal weight: 10.0000 chunk 46 optimal weight: 20.0000 chunk 186 optimal weight: 30.0000 chunk 296 optimal weight: 10.0000 overall best weight: 8.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 174 GLN C 163 GLN C 199 GLN J 81 GLN M 8 ASN O 71 GLN ** D 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 94000 Z= 0.446 Angle : 0.733 14.582 141521 Z= 0.382 Chirality : 0.044 0.379 18275 Planarity : 0.006 0.127 6955 Dihedral : 22.913 178.305 48998 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.74 % Favored : 93.09 % Rotamer: Outliers : 4.87 % Allowed : 18.85 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.21 % 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: -1.22 (0.14), residues: 2980 helix: 0.67 (0.19), residues: 756 sheet: -0.69 (0.19), residues: 641 loop : -1.63 (0.14), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP E 83 HIS 0.006 0.001 HIS J 35 PHE 0.017 0.002 PHE D 127 TYR 0.020 0.002 TYR U 90 ARG 0.008 0.001 ARG I 97 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 572 time to evaluate : 3.464 Fit side-chains TARDY: cannot create tardy model for: "LYS G 175 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "VAL J 145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU X 58 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. REVERT: G 39 GLU cc_start: 0.7842 (mp0) cc_final: 0.7481 (mp0) REVERT: M 22 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8807 (tt) REVERT: M 104 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.7659 (mtm180) REVERT: O 74 MET cc_start: 0.8300 (mtt) cc_final: 0.7941 (ttt) REVERT: U 76 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8132 (mptp) REVERT: W 62 ILE cc_start: 0.9238 (OUTLIER) cc_final: 0.9019 (mp) REVERT: 3 56 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8340 (mtmt) REVERT: 4 18 LYS cc_start: 0.9240 (mtpt) cc_final: 0.9038 (tttt) REVERT: D 200 ASN cc_start: 0.8746 (OUTLIER) cc_final: 0.8458 (p0) REVERT: I 81 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.6907 (pm20) REVERT: Z 27 MET cc_start: 0.7721 (ttp) cc_final: 0.7510 (ttp) REVERT: L 105 LYS cc_start: 0.9266 (OUTLIER) cc_final: 0.9054 (mttp) outliers start: 113 outliers final: 74 residues processed: 627 average time/residue: 1.6691 time to fit residues: 1407.5906 Evaluate side-chains 644 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 562 time to evaluate : 3.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 84 GLU Chi-restraints excluded: chain N residue 93 LYS Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 150 SER Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 86 LYS Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 131 SER Chi-restraints excluded: chain K residue 3 LEU Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 55 THR Chi-restraints excluded: chain K residue 91 GLU Chi-restraints excluded: chain K residue 110 SER Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 104 ARG Chi-restraints excluded: chain O residue 77 SER Chi-restraints excluded: chain P residue 37 LYS Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain P residue 93 THR Chi-restraints excluded: chain R residue 14 GLU Chi-restraints excluded: chain R residue 16 SER Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain T residue 8 ILE Chi-restraints excluded: chain T residue 31 VAL Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain U residue 76 LYS Chi-restraints excluded: chain U residue 78 GLU Chi-restraints excluded: chain U residue 87 VAL Chi-restraints excluded: chain W residue 62 ILE Chi-restraints excluded: chain 3 residue 25 SER Chi-restraints excluded: chain 3 residue 56 LYS Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 66 LYS Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 63 ASP Chi-restraints excluded: chain Q residue 94 SER Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain V residue 24 SER Chi-restraints excluded: chain V residue 55 LYS Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 13 ILE Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 105 LYS Chi-restraints excluded: chain L residue 116 SER Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 122 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 583 random chunks: chunk 543 optimal weight: 6.9990 chunk 63 optimal weight: 20.0000 chunk 321 optimal weight: 10.0000 chunk 411 optimal weight: 8.9990 chunk 319 optimal weight: 40.0000 chunk 474 optimal weight: 3.9990 chunk 314 optimal weight: 30.0000 chunk 561 optimal weight: 9.9990 chunk 351 optimal weight: 9.9990 chunk 342 optimal weight: 9.9990 chunk 259 optimal weight: 10.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN C 163 GLN C 199 GLN J 81 GLN O 71 GLN S 45 GLN T 20 GLN W 31 GLN Q 65 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 94000 Z= 0.417 Angle : 0.707 14.113 141521 Z= 0.369 Chirality : 0.043 0.381 18275 Planarity : 0.006 0.125 6955 Dihedral : 22.876 178.309 48998 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.34 % Favored : 93.49 % Rotamer: Outliers : 4.27 % Allowed : 20.15 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.21 % 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: -1.18 (0.14), residues: 2980 helix: 0.71 (0.19), residues: 753 sheet: -0.69 (0.19), residues: 642 loop : -1.59 (0.14), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP E 83 HIS 0.005 0.001 HIS J 35 PHE 0.018 0.002 PHE D 127 TYR 0.017 0.002 TYR 2 6 ARG 0.011 0.001 ARG N 90 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 581 time to evaluate : 3.471 Fit side-chains TARDY: cannot create tardy model for: "LYS G 175 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "VAL J 145 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU X 58 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. REVERT: J 71 ARG cc_start: 0.9284 (OUTLIER) cc_final: 0.7722 (ttt90) REVERT: M 22 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8814 (tt) REVERT: M 104 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.7705 (mtm180) REVERT: O 74 MET cc_start: 0.8293 (mtt) cc_final: 0.7945 (ttt) REVERT: U 76 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8174 (mptp) REVERT: 3 56 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8343 (mtmt) REVERT: 2 41 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7874 (tppp) REVERT: 4 18 LYS cc_start: 0.9211 (mtpt) cc_final: 0.8990 (tttt) REVERT: D 200 ASN cc_start: 0.8775 (OUTLIER) cc_final: 0.8483 (p0) REVERT: I 81 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.6866 (pm20) REVERT: Z 27 MET cc_start: 0.7688 (ttp) cc_final: 0.7339 (ttp) REVERT: L 105 LYS cc_start: 0.9272 (OUTLIER) cc_final: 0.9071 (mttp) outliers start: 99 outliers final: 71 residues processed: 632 average time/residue: 1.6939 time to fit residues: 1441.9747 Evaluate side-chains 653 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 573 time to evaluate : 3.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 84 GLU Chi-restraints excluded: chain N residue 93 LYS Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 150 SER Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 86 LYS Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 71 ARG Chi-restraints excluded: chain J residue 107 SER Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 131 SER Chi-restraints excluded: chain K residue 3 LEU Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 55 THR Chi-restraints excluded: chain K residue 91 GLU Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 104 ARG Chi-restraints excluded: chain O residue 77 SER Chi-restraints excluded: chain P residue 37 LYS Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain R residue 14 GLU Chi-restraints excluded: chain R residue 16 SER Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain T residue 8 ILE Chi-restraints excluded: chain T residue 31 VAL Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain U residue 76 LYS Chi-restraints excluded: chain U residue 78 GLU Chi-restraints excluded: chain U residue 87 VAL Chi-restraints excluded: chain 3 residue 25 SER Chi-restraints excluded: chain 3 residue 56 LYS Chi-restraints excluded: chain 2 residue 41 LYS Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 66 LYS Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 63 ASP Chi-restraints excluded: chain Q residue 94 SER Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain V residue 24 SER Chi-restraints excluded: chain V residue 55 LYS Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 13 ILE Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 105 LYS Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 122 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 583 random chunks: chunk 347 optimal weight: 30.0000 chunk 224 optimal weight: 8.9990 chunk 335 optimal weight: 0.9990 chunk 169 optimal weight: 50.0000 chunk 110 optimal weight: 8.9990 chunk 108 optimal weight: 10.0000 chunk 357 optimal weight: 50.0000 chunk 382 optimal weight: 10.0000 chunk 277 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 441 optimal weight: 9.9990 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN C 163 GLN C 199 GLN H 24 GLN J 81 GLN M 43 GLN O 71 GLN S 45 GLN T 20 GLN T 85 GLN 3 40 GLN 4 34 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 94000 Z= 0.407 Angle : 0.708 14.544 141521 Z= 0.371 Chirality : 0.043 0.377 18275 Planarity : 0.006 0.125 6955 Dihedral : 22.876 178.278 48998 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.81 % Favored : 93.02 % Rotamer: Outliers : 4.44 % Allowed : 20.75 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.21 % 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: -1.12 (0.15), residues: 2980 helix: 0.73 (0.19), residues: 756 sheet: -0.61 (0.20), residues: 646 loop : -1.56 (0.14), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP E 83 HIS 0.006 0.001 HIS S 44 PHE 0.018 0.002 PHE D 127 TYR 0.018 0.002 TYR 2 6 ARG 0.010 0.001 ARG I 97 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 567 time to evaluate : 3.502 Fit side-chains TARDY: cannot create tardy model for: "LYS G 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL J 145 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU X 58 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. REVERT: J 71 ARG cc_start: 0.9281 (OUTLIER) cc_final: 0.7736 (ttt90) REVERT: J 89 THR cc_start: 0.8905 (p) cc_final: 0.7796 (m) REVERT: M 22 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8804 (tt) REVERT: M 104 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.7679 (mtm180) REVERT: O 74 MET cc_start: 0.8292 (mtt) cc_final: 0.7945 (ttt) REVERT: U 76 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8168 (mptp) REVERT: 3 56 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8340 (mtmt) REVERT: 2 41 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7871 (tppp) REVERT: D 200 ASN cc_start: 0.8763 (OUTLIER) cc_final: 0.8471 (p0) REVERT: I 81 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.6862 (pm20) REVERT: V 35 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8873 (tttp) REVERT: Z 27 MET cc_start: 0.7731 (ttp) cc_final: 0.7450 (ttp) REVERT: L 105 LYS cc_start: 0.9269 (OUTLIER) cc_final: 0.9059 (mttp) outliers start: 103 outliers final: 74 residues processed: 618 average time/residue: 1.7238 time to fit residues: 1430.1833 Evaluate side-chains 646 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 562 time to evaluate : 3.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain N residue 84 GLU Chi-restraints excluded: chain N residue 93 LYS Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 150 SER Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 86 LYS Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 71 ARG Chi-restraints excluded: chain J residue 107 SER Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain K residue 3 LEU Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 55 THR Chi-restraints excluded: chain K residue 91 GLU Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 104 ARG Chi-restraints excluded: chain O residue 77 SER Chi-restraints excluded: chain P residue 37 LYS Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain R residue 14 GLU Chi-restraints excluded: chain R residue 16 SER Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain T residue 8 ILE Chi-restraints excluded: chain T residue 31 VAL Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain U residue 76 LYS Chi-restraints excluded: chain U residue 78 GLU Chi-restraints excluded: chain U residue 87 VAL Chi-restraints excluded: chain 3 residue 25 SER Chi-restraints excluded: chain 3 residue 56 LYS Chi-restraints excluded: chain 2 residue 41 LYS Chi-restraints excluded: chain 4 residue 14 CYS Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 66 LYS Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 28 ASN Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 63 ASP Chi-restraints excluded: chain Q residue 94 SER Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain V residue 24 SER Chi-restraints excluded: chain V residue 35 LYS Chi-restraints excluded: chain V residue 55 LYS Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 13 ILE Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 105 LYS Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 122 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 583 random chunks: chunk 511 optimal weight: 0.6980 chunk 538 optimal weight: 2.9990 chunk 491 optimal weight: 10.0000 chunk 523 optimal weight: 9.9990 chunk 315 optimal weight: 30.0000 chunk 228 optimal weight: 7.9990 chunk 411 optimal weight: 3.9990 chunk 160 optimal weight: 10.0000 chunk 473 optimal weight: 0.9990 chunk 495 optimal weight: 4.9990 chunk 521 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 174 GLN C 163 GLN C 199 GLN H 3 GLN J 81 GLN O 71 GLN O 108 GLN S 45 GLN T 20 GLN W 31 GLN 3 40 GLN Q 65 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 94000 Z= 0.152 Angle : 0.562 13.546 141521 Z= 0.299 Chirality : 0.034 0.298 18275 Planarity : 0.005 0.114 6955 Dihedral : 22.800 179.091 48998 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.34 % Favored : 94.60 % Rotamer: Outliers : 2.93 % Allowed : 22.48 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.15), residues: 2980 helix: 1.04 (0.20), residues: 747 sheet: -0.45 (0.20), residues: 647 loop : -1.44 (0.14), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 213 HIS 0.005 0.001 HIS J 35 PHE 0.011 0.001 PHE E 24 TYR 0.014 0.001 TYR H 75 ARG 0.015 0.000 ARG N 90 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 585 time to evaluate : 3.445 Fit side-chains TARDY: cannot create tardy model for: "LYS G 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL J 145 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU X 58 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: N 85 LYS cc_start: 0.8916 (ttpp) cc_final: 0.8656 (ttpp) REVERT: C 13 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.8235 (ttt180) REVERT: O 74 MET cc_start: 0.8178 (mtt) cc_final: 0.7923 (ttt) REVERT: R 65 MET cc_start: 0.7280 (ttm) cc_final: 0.7041 (ttt) REVERT: 4 18 LYS cc_start: 0.9157 (mtpt) cc_final: 0.8949 (tttt) REVERT: I 81 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.6849 (pm20) REVERT: Z 27 MET cc_start: 0.7334 (ttp) cc_final: 0.7007 (ttp) REVERT: L 105 LYS cc_start: 0.9253 (OUTLIER) cc_final: 0.9051 (mttp) outliers start: 68 outliers final: 40 residues processed: 622 average time/residue: 1.7392 time to fit residues: 1457.7105 Evaluate side-chains 601 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 558 time to evaluate : 3.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 84 GLU Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain K residue 3 LEU Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 91 GLU Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain O residue 77 SER Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain R residue 14 GLU Chi-restraints excluded: chain R residue 16 SER Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain T residue 8 ILE Chi-restraints excluded: chain T residue 31 VAL Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain U residue 78 GLU Chi-restraints excluded: chain U residue 87 VAL Chi-restraints excluded: chain 3 residue 25 SER Chi-restraints excluded: chain 4 residue 14 CYS Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain V residue 24 SER Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain L residue 105 LYS Chi-restraints excluded: chain L residue 116 SER Chi-restraints excluded: chain L residue 117 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 583 random chunks: chunk 343 optimal weight: 9.9990 chunk 553 optimal weight: 6.9990 chunk 337 optimal weight: 3.9990 chunk 262 optimal weight: 10.0000 chunk 384 optimal weight: 2.9990 chunk 580 optimal weight: 0.0970 chunk 534 optimal weight: 40.0000 chunk 462 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 357 optimal weight: 0.1980 chunk 283 optimal weight: 10.0000 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 174 GLN C 163 GLN H 3 GLN J 81 GLN K 25 ASN O 71 GLN O 108 GLN T 20 GLN U 48 GLN 3 40 GLN 4 34 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 94000 Z= 0.159 Angle : 0.559 13.389 141521 Z= 0.297 Chirality : 0.033 0.278 18275 Planarity : 0.005 0.116 6955 Dihedral : 22.738 179.199 48997 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.81 % Favored : 94.09 % Rotamer: Outliers : 2.37 % Allowed : 23.55 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.15), residues: 2980 helix: 1.10 (0.20), residues: 747 sheet: -0.34 (0.20), residues: 634 loop : -1.39 (0.14), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 213 HIS 0.005 0.001 HIS J 35 PHE 0.012 0.001 PHE E 90 TYR 0.029 0.001 TYR M 101 ARG 0.010 0.000 ARG C 261 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 568 time to evaluate : 3.424 Fit side-chains TARDY: cannot create tardy model for: "LYS G 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL J 145 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU X 58 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: C 13 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8242 (ttt180) REVERT: G 39 GLU cc_start: 0.7899 (pm20) cc_final: 0.7692 (mm-30) REVERT: M 22 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8776 (tt) REVERT: O 74 MET cc_start: 0.8213 (mtt) cc_final: 0.7932 (ttt) REVERT: R 65 MET cc_start: 0.7365 (ttm) cc_final: 0.7165 (ttt) REVERT: 4 18 LYS cc_start: 0.9132 (mtpt) cc_final: 0.8924 (tttt) REVERT: I 81 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.6897 (pm20) REVERT: Q 100 THR cc_start: 0.9127 (p) cc_final: 0.8916 (p) REVERT: Z 27 MET cc_start: 0.7275 (ttp) cc_final: 0.6993 (ttp) outliers start: 55 outliers final: 37 residues processed: 597 average time/residue: 1.7150 time to fit residues: 1379.8176 Evaluate side-chains 597 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 557 time to evaluate : 3.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 84 GLU Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 131 SER Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 91 GLU Chi-restraints excluded: chain K residue 110 SER Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain O residue 77 SER Chi-restraints excluded: chain R residue 14 GLU Chi-restraints excluded: chain R residue 16 SER Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain T residue 31 VAL Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain U residue 78 GLU Chi-restraints excluded: chain U residue 87 VAL Chi-restraints excluded: chain 3 residue 25 SER Chi-restraints excluded: chain 4 residue 14 CYS Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain V residue 24 SER Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain L residue 116 SER Chi-restraints excluded: chain L residue 117 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 583 random chunks: chunk 367 optimal weight: 20.0000 chunk 492 optimal weight: 8.9990 chunk 141 optimal weight: 10.0000 chunk 426 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 128 optimal weight: 10.0000 chunk 463 optimal weight: 7.9990 chunk 193 optimal weight: 10.0000 chunk 475 optimal weight: 10.0000 chunk 58 optimal weight: 30.0000 chunk 85 optimal weight: 10.0000 overall best weight: 9.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN C 163 GLN H 11 ASN J 81 GLN M 43 GLN O 71 GLN T 20 GLN W 17 GLN W 31 GLN 3 40 GLN Q 65 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.120386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.071059 restraints weight = 127220.555| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 0.95 r_work: 0.2668 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2578 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9054 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.079 94000 Z= 0.483 Angle : 0.745 15.348 141521 Z= 0.387 Chirality : 0.045 0.374 18275 Planarity : 0.006 0.127 6955 Dihedral : 22.836 178.021 48997 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.91 % Favored : 92.99 % Rotamer: Outliers : 2.59 % Allowed : 23.51 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.15), residues: 2980 helix: 0.85 (0.19), residues: 752 sheet: -0.53 (0.19), residues: 659 loop : -1.46 (0.14), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 213 HIS 0.008 0.001 HIS J 35 PHE 0.018 0.002 PHE D 127 TYR 0.030 0.002 TYR M 101 ARG 0.010 0.001 ARG C 261 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23720.69 seconds wall clock time: 415 minutes 38.45 seconds (24938.45 seconds total)