Starting phenix.real_space_refine (version: dev) on Fri Dec 16 06:42:42 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7asm_11900/12_2022/7asm_11900_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7asm_11900/12_2022/7asm_11900.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7asm_11900/12_2022/7asm_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_11900/12_2022/7asm_11900_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7asm_11900/12_2022/7asm_11900_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7asm_11900/12_2022/7asm_11900.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7asm_11900/12_2022/7asm_11900.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7asm_11900/12_2022/7asm_11900_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7asm_11900/12_2022/7asm_11900_updated.pdb" } resolution = 2.48 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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 Convert atoms to be neutral 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-4807/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: 11 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: 35.21, per 1000 atoms: 0.41 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: 36.62 Conformation dependent library (CDL) restraints added in 3.3 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: 33.81 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: 156.10 Time building geometry restraints manager: 39.68 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 1.150 1.442 -0.292 2.00e-02 2.50e+03 2.13e+02 bond pdb=" C5 5MU A 792 " pdb=" C6 5MU A 792 " ideal model delta sigma weight residual 1.150 1.438 -0.288 2.00e-02 2.50e+03 2.08e+02 bond pdb=" C4 5MU A 792 " pdb=" C5 5MU A 792 " ideal model delta sigma weight residual 1.805 1.594 0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C4 5MU A1966 " pdb=" C5 5MU A1966 " ideal model delta sigma weight residual 1.805 1.602 0.203 2.00e-02 2.50e+03 1.03e+02 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=" C4 2MA A2530 " ideal model delta sigma weight residual 103.49 136.21 -32.72 3.00e+00 1.11e-01 1.19e+02 angle pdb=" C1' 2MA A2530 " pdb=" N9 2MA A2530 " pdb=" C8 2MA A2530 " ideal model delta sigma weight residual 144.94 112.62 32.32 3.00e+00 1.11e-01 1.16e+02 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=" 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: 47980 35.79 - 71.58: 1638 71.58 - 107.38: 117 107.38 - 143.17: 9 143.17 - 178.96: 22 Dihedral angle restraints: 49766 sinusoidal: 41162 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 49763 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 16688 0.085 - 0.170: 1452 0.170 - 0.254: 115 0.254 - 0.339: 19 0.339 - 0.424: 5 Chirality restraints: 18279 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 18276 not shown) Planarity restraints: 6954 Sorted by residual: 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 delta sigma weight rms_deltas residual plane pdb=" C1' G A 557 " 0.066 2.00e-02 2.50e+03 2.72e-02 2.22e+01 pdb=" N9 G A 557 " -0.058 2.00e-02 2.50e+03 pdb=" C8 G A 557 " -0.006 2.00e-02 2.50e+03 pdb=" N7 G A 557 " -0.009 2.00e-02 2.50e+03 pdb=" C5 G A 557 " 0.004 2.00e-02 2.50e+03 pdb=" C6 G A 557 " 0.014 2.00e-02 2.50e+03 pdb=" O6 G A 557 " 0.017 2.00e-02 2.50e+03 pdb=" N1 G A 557 " 0.005 2.00e-02 2.50e+03 pdb=" C2 G A 557 " -0.003 2.00e-02 2.50e+03 pdb=" N2 G A 557 " -0.004 2.00e-02 2.50e+03 pdb=" N3 G A 557 " -0.016 2.00e-02 2.50e+03 pdb=" C4 G A 557 " -0.011 2.00e-02 2.50e+03 ... (remaining 6951 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 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. 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: 2.960 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: 0.050 Extract box with map and model: 14.920 Check model and map are aligned: 0.950 Convert atoms to be neutral: 0.560 Process input model: 312.940 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Set scattering table: 0.030 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:10.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 345.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9149 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 0.292 94000 Z= 0.629 Angle : 0.843 32.723 141521 Z= 0.449 Chirality : 0.050 0.424 18279 Planarity : 0.010 0.506 6954 Dihedral : 14.776 178.961 44221 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.40 % Allowed : 7.32 % Favored : 92.28 % Rotamer Outliers : 0.65 % 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 *********************** 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 : 3.661 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. outliers start: 15 outliers final: 7 residues processed: 699 average time/residue: 1.8273 time to fit residues: 1684.0989 Evaluate side-chains 566 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 559 time to evaluate : 3.531 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 0 time to fit residues: 3.6186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 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: 7.3992 ------------------------------------------------------------------------------- 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 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: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9129 moved from start: 0.0773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.070 94000 Z= 0.390 Angle : 0.690 13.894 141521 Z= 0.364 Chirality : 0.042 0.376 18279 Planarity : 0.006 0.126 6954 Dihedral : 14.264 179.652 38662 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.07 % Favored : 93.72 % Rotamer Outliers : 4.01 % 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: -2.06 (0.14), residues: 2980 helix: -0.23 (0.18), residues: 751 sheet: -1.20 (0.18), residues: 659 loop : -2.04 (0.13), residues: 1570 *********************** 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 719 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 626 time to evaluate : 3.930 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. revert: symmetry clash TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. outliers start: 93 outliers final: 44 residues processed: 672 average time/residue: 1.6639 time to fit residues: 1496.0343 Evaluate side-chains 630 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 586 time to evaluate : 3.523 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 22 residues processed: 23 average time/residue: 1.0744 time to fit residues: 41.0033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 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: 4.9990 chunk 525 optimal weight: 50.0000 chunk 180 optimal weight: 50.0000 chunk 425 optimal weight: 1.9990 overall best weight: 4.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 174 GLN C 163 GLN G 64 ASN J 27 ASN J 81 GLN K 25 ASN O 71 GLN Q 65 ASN Q 90 GLN X 5 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9104 moved from start: 0.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 94000 Z= 0.235 Angle : 0.630 13.819 141521 Z= 0.336 Chirality : 0.038 0.341 18279 Planarity : 0.005 0.120 6954 Dihedral : 14.235 179.928 38662 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.24 % Favored : 93.59 % Rotamer Outliers : 3.97 % 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: -1.64 (0.14), residues: 2980 helix: 0.29 (0.19), residues: 747 sheet: -0.94 (0.19), residues: 649 loop : -1.87 (0.13), residues: 1584 *********************** 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 697 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 605 time to evaluate : 3.508 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: "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. outliers start: 92 outliers final: 54 residues processed: 651 average time/residue: 1.6072 time to fit residues: 1418.3701 Evaluate side-chains 637 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 583 time to evaluate : 3.540 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 28 residues processed: 26 average time/residue: 1.0228 time to fit residues: 44.7205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 583 random chunks: chunk 524 optimal weight: 20.0000 chunk 398 optimal weight: 8.9990 chunk 275 optimal weight: 10.0000 chunk 58 optimal weight: 20.0000 chunk 253 optimal weight: 10.0000 chunk 356 optimal weight: 8.9990 chunk 532 optimal weight: 0.0770 chunk 563 optimal weight: 0.7980 chunk 278 optimal weight: 20.0000 chunk 504 optimal weight: 8.9990 chunk 151 optimal weight: 10.0000 overall best weight: 5.5744 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 GLN K 25 ASN O 71 GLN Q 90 GLN X 5 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9110 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 94000 Z= 0.300 Angle : 0.633 13.891 141521 Z= 0.335 Chirality : 0.039 0.346 18279 Planarity : 0.005 0.122 6954 Dihedral : 14.117 179.781 38662 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.41 % Favored : 93.46 % Rotamer Outliers : 4.40 % 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: -1.34 (0.14), residues: 2980 helix: 0.65 (0.19), residues: 752 sheet: -0.86 (0.19), residues: 646 loop : -1.69 (0.14), residues: 1582 *********************** 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 693 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 591 time to evaluate : 3.532 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. 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. outliers start: 102 outliers final: 58 residues processed: 651 average time/residue: 1.6103 time to fit residues: 1418.5513 Evaluate side-chains 649 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 591 time to evaluate : 3.630 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 33 residues processed: 28 average time/residue: 1.0288 time to fit residues: 48.1865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 419 optimal weight: 10.0000 chunk 232 optimal weight: 10.0000 chunk 480 optimal weight: 0.8980 chunk 389 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 287 optimal weight: 10.0000 chunk 505 optimal weight: 9.9990 chunk 142 optimal weight: 10.0000 overall best weight: 7.7790 ------------------------------------------------------------------------------- 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 G 97 GLN J 81 GLN O 71 GLN 3 40 GLN Q 65 ASN Q 90 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9134 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.069 94000 Z= 0.406 Angle : 0.699 14.283 141521 Z= 0.366 Chirality : 0.043 0.370 18279 Planarity : 0.006 0.126 6954 Dihedral : 14.206 179.657 38662 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.71 % Favored : 93.12 % Rotamer Outliers : 4.75 % 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: -1.25 (0.14), residues: 2980 helix: 0.67 (0.19), residues: 753 sheet: -0.71 (0.19), residues: 647 loop : -1.65 (0.14), residues: 1580 *********************** 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 695 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 585 time to evaluate : 4.377 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. 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. outliers start: 110 outliers final: 65 residues processed: 643 average time/residue: 1.6270 time to fit residues: 1416.3825 Evaluate side-chains 642 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 577 time to evaluate : 3.562 Switching outliers to nearest non-outliers outliers start: 65 outliers final: 38 residues processed: 29 average time/residue: 0.8587 time to fit residues: 44.9695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 111 optimal weight: 10.0000 chunk 330 optimal weight: 9.9990 chunk 139 optimal weight: 50.0000 chunk 564 optimal weight: 7.9990 chunk 468 optimal weight: 8.9990 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: 8.7992 ------------------------------------------------------------------------------- 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 W 31 GLN 3 40 GLN Q 90 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9142 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.075 94000 Z= 0.456 Angle : 0.728 14.342 141521 Z= 0.379 Chirality : 0.044 0.393 18279 Planarity : 0.006 0.126 6954 Dihedral : 14.240 179.460 38662 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.64 % Favored : 93.19 % Rotamer Outliers : 4.40 % 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: 0.62 (0.19), residues: 757 sheet: -0.64 (0.19), residues: 650 loop : -1.63 (0.14), residues: 1573 *********************** 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 675 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 573 time to evaluate : 3.611 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. 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. outliers start: 102 outliers final: 62 residues processed: 630 average time/residue: 1.6610 time to fit residues: 1417.0045 Evaluate side-chains 624 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 562 time to evaluate : 3.525 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 40 residues processed: 24 average time/residue: 0.8791 time to fit residues: 38.5953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 319 optimal weight: 40.0000 chunk 474 optimal weight: 1.9990 chunk 314 optimal weight: 30.0000 chunk 561 optimal weight: 5.9990 chunk 351 optimal weight: 5.9990 chunk 342 optimal weight: 10.0000 chunk 259 optimal weight: 10.0000 overall best weight: 6.1992 ------------------------------------------------------------------------------- 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 T 20 GLN 3 40 GLN 4 34 GLN Q 65 ASN Q 90 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9119 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 94000 Z= 0.329 Angle : 0.646 13.891 141521 Z= 0.341 Chirality : 0.040 0.357 18279 Planarity : 0.005 0.122 6954 Dihedral : 14.092 179.826 38662 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.48 % Favored : 93.39 % Rotamer Outliers : 4.06 % 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: -1.09 (0.15), residues: 2980 helix: 0.78 (0.19), residues: 751 sheet: -0.55 (0.20), residues: 634 loop : -1.57 (0.14), residues: 1595 *********************** 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 666 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 572 time to evaluate : 3.633 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 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. outliers start: 94 outliers final: 63 residues processed: 624 average time/residue: 1.6347 time to fit residues: 1382.1045 Evaluate side-chains 626 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 563 time to evaluate : 3.581 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 41 residues processed: 24 average time/residue: 0.9222 time to fit residues: 39.3207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 335 optimal weight: 1.9990 chunk 169 optimal weight: 50.0000 chunk 110 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 chunk 357 optimal weight: 20.0000 chunk 382 optimal weight: 10.0000 chunk 277 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 441 optimal weight: 7.9990 overall best weight: 7.9996 ------------------------------------------------------------------------------- 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 M 43 GLN O 71 GLN S 45 GLN T 20 GLN W 31 GLN 3 40 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9138 moved from start: 0.1198 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= 0.417 Angle : 0.707 14.779 141521 Z= 0.370 Chirality : 0.043 0.378 18279 Planarity : 0.006 0.126 6954 Dihedral : 14.175 179.278 38662 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.91 % Favored : 92.95 % Rotamer Outliers : 3.49 % 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: -1.11 (0.15), residues: 2980 helix: 0.73 (0.19), residues: 754 sheet: -0.60 (0.19), residues: 654 loop : -1.55 (0.14), residues: 1572 *********************** 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 647 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 566 time to evaluate : 3.549 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 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. outliers start: 81 outliers final: 55 residues processed: 614 average time/residue: 1.6284 time to fit residues: 1355.1206 Evaluate side-chains 615 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 560 time to evaluate : 3.552 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 40 residues processed: 16 average time/residue: 0.8887 time to fit residues: 26.9623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 583 random chunks: chunk 511 optimal weight: 0.7980 chunk 538 optimal weight: 5.9990 chunk 491 optimal weight: 4.9990 chunk 523 optimal weight: 9.9990 chunk 315 optimal weight: 30.0000 chunk 228 optimal weight: 7.9990 chunk 411 optimal weight: 2.9990 chunk 160 optimal weight: 10.0000 chunk 473 optimal weight: 0.9990 chunk 495 optimal weight: 1.9990 chunk 521 optimal weight: 7.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 T 20 GLN 3 40 GLN 4 34 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9091 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.077 94000 Z= 0.167 Angle : 0.622 13.883 141521 Z= 0.329 Chirality : 0.036 0.325 18279 Planarity : 0.005 0.118 6954 Dihedral : 14.154 179.992 38662 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.07 % Favored : 93.79 % Rotamer Outliers : 2.98 % 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: -0.92 (0.15), residues: 2980 helix: 0.93 (0.20), residues: 739 sheet: -0.45 (0.20), residues: 645 loop : -1.45 (0.14), residues: 1596 *********************** 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 641 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 572 time to evaluate : 3.525 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 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. outliers start: 69 outliers final: 51 residues processed: 621 average time/residue: 1.6267 time to fit residues: 1368.7117 Evaluate side-chains 621 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 570 time to evaluate : 3.557 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 40 residues processed: 13 average time/residue: 0.8355 time to fit residues: 21.7547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 337 optimal weight: 5.9990 chunk 262 optimal weight: 10.0000 chunk 384 optimal weight: 5.9990 chunk 580 optimal weight: 2.9990 chunk 534 optimal weight: 40.0000 chunk 462 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 357 optimal weight: 10.0000 chunk 283 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 T 20 GLN W 31 GLN 3 40 GLN Q 65 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9121 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.060 94000 Z= 0.328 Angle : 0.655 13.994 141521 Z= 0.345 Chirality : 0.040 0.354 18279 Planarity : 0.005 0.123 6954 Dihedral : 14.081 179.610 38662 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.64 % Favored : 93.26 % Rotamer Outliers : 2.37 % 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: -0.91 (0.15), residues: 2980 helix: 0.96 (0.20), residues: 740 sheet: -0.53 (0.20), residues: 654 loop : -1.42 (0.14), residues: 1586 ********************** 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 624 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 569 time to evaluate : 3.799 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 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. outliers start: 55 outliers final: 47 residues processed: 610 average time/residue: 1.6481 time to fit residues: 1360.6126 Evaluate side-chains 604 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 557 time to evaluate : 3.538 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 38 residues processed: 10 average time/residue: 1.0280 time to fit residues: 19.5519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 583 random chunks: chunk 367 optimal weight: 1.9990 chunk 492 optimal weight: 0.5980 chunk 141 optimal weight: 10.0000 chunk 426 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 128 optimal weight: 10.0000 chunk 463 optimal weight: 20.0000 chunk 193 optimal weight: 10.0000 chunk 475 optimal weight: 9.9990 chunk 58 optimal weight: 20.0000 chunk 85 optimal weight: 10.0000 overall best weight: 5.3190 ------------------------------------------------------------------------------- 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** C 163 GLN C 199 GLN H 24 GLN J 81 GLN O 71 GLN T 20 GLN W 31 GLN 3 40 GLN 4 34 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.121989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.072950 restraints weight = 127047.641| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 0.86 r_work: 0.2701 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9190 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.071 94000 Z= 0.290 Angle : 0.643 13.938 141521 Z= 0.340 Chirality : 0.039 0.343 18279 Planarity : 0.005 0.122 6954 Dihedral : 14.079 179.664 38662 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.71 % Favored : 93.19 % Rotamer Outliers : 2.37 % 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: -0.90 (0.15), residues: 2980 helix: 0.96 (0.20), residues: 740 sheet: -0.50 (0.20), residues: 654 loop : -1.42 (0.14), residues: 1586 =============================================================================== Job complete usr+sys time: 23073.94 seconds wall clock time: 403 minutes 36.66 seconds (24216.66 seconds total)