Starting phenix.real_space_refine on Tue Feb 20 10:50:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hma_0243/02_2024/6hma_0243_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hma_0243/02_2024/6hma_0243.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hma_0243/02_2024/6hma_0243_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hma_0243/02_2024/6hma_0243_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hma_0243/02_2024/6hma_0243_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hma_0243/02_2024/6hma_0243.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hma_0243/02_2024/6hma_0243.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hma_0243/02_2024/6hma_0243_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hma_0243/02_2024/6hma_0243_updated.pdb" } resolution = 2.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 2949 5.49 5 Mg 237 5.21 5 S 55 5.16 5 C 42561 2.51 5 N 15980 2.21 5 O 24619 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 43": "NH1" <-> "NH2" Residue "C ARG 69": "NH1" <-> "NH2" Residue "C ARG 243": "NH1" <-> "NH2" Residue "D ARG 89": "NH1" <-> "NH2" Residue "E ARG 45": "NH1" <-> "NH2" Residue "E ARG 54": "NH1" <-> "NH2" Residue "E ARG 106": "NH1" <-> "NH2" Residue "E ARG 107": "NH1" <-> "NH2" Residue "E ARG 168": "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 ARG 100": "NH1" <-> "NH2" Residue "I ARG 17": "NH1" <-> "NH2" Residue "I ARG 88": "NH1" <-> "NH2" Residue "J ARG 21": "NH1" <-> "NH2" 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 ARG 82": "NH1" <-> "NH2" Residue "K ARG 115": "NH1" <-> "NH2" Residue "L ARG 110": "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 "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 ARG 90": "NH1" <-> "NH2" Residue "N ARG 91": "NH1" <-> "NH2" Residue "O ARG 48": "NH1" <-> "NH2" Residue "P ARG 67": "NH1" <-> "NH2" Residue "P ARG 84": "NH1" <-> "NH2" Residue "Q ARG 8": "NH1" <-> "NH2" Residue "Q ARG 11": "NH1" <-> "NH2" Residue "Q ARG 86": "NH1" <-> "NH2" Residue "Q ARG 88": "NH1" <-> "NH2" 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 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 "V ARG 37": "NH1" <-> "NH2" 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 ARG 60": "NH1" <-> "NH2" Residue "X ARG 10": "NH1" <-> "NH2" Residue "Z ARG 6": "NH1" <-> "NH2" Residue "Z ARG 7": "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 "3 ARG 24": "NH1" <-> "NH2" Residue "3 ARG 42": "NH1" <-> "NH2" Residue "3 ARG 57": "NH1" <-> "NH2" Residue "4 ARG 19": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 86401 Number of models: 1 Model: "" Number of chains: 36 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': 297, 'rna2p_pyr': 152, 'rna3p': 1, 'rna3p_pur': 1327, 'rna3p_pyr': 1054} Link IDs: {'rna2p': 451, 'rna3p': 2382} Chain breaks: 10 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' C:plan': 1, ' C:plan2': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 2448 Classifications: {'RNA': 115} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 8, 'rna3p_pur': 53, 'rna3p_pyr': 48} Link IDs: {'rna2p': 14, 'rna3p': 100} Chain: "C" Number of atoms: 2094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2094 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 17, 'TRANS': 256} Chain: "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: "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: "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: "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: 128 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 11, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 68 Chain: "H" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1143 Classifications: {'peptide': 145} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 138} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 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: "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: "L" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 932 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 118} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 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: "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: "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: {'PCIS': 1, 'PTRANS': 1, '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: "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: "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: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 770 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 97} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 14 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: "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: "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: "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: "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: "3" Number of atoms: 521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 521 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} 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: "A" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 229 Unusual residues: {' MG': 229} Classifications: {'undetermined': 229} Link IDs: {None: 228} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 33.04, per 1000 atoms: 0.38 Number of scatterers: 86401 At special positions: 0 Unit cell: (233.376, 231.66, 201.63, 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 237 11.99 O 24619 8.00 N 15980 7.00 C 42561 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS 1 9 " - pdb=" SG CYS 1 12 " distance=2.02 Simple disulfide: pdb=" SG CYS 1 12 " - pdb=" SG CYS 1 36 " distance=2.04 Simple disulfide: pdb=" SG CYS 4 14 " - pdb=" SG CYS 4 27 " distance=2.05 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: 34.64 Conformation dependent library (CDL) restraints added in 4.0 seconds 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5536 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 77 helices and 45 sheets defined 22.9% alpha, 16.7% beta 935 base pairs and 1522 stacking pairs defined. Time for finding SS restraints: 40.31 Creating SS restraints... 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: 4.477A pdb=" N GLU C 201 " --> pdb=" O LEU C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 213 removed outlier: 3.664A pdb=" N ARG C 212 " --> pdb=" O ALA C 208 " (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 268 removed outlier: 3.843A pdb=" N LYS C 268 " --> pdb=" O SER C 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 265 through 268' Processing helix chain 'D' and resid 18 through 20 No H-bonds generated for 'chain 'D' and resid 18 through 20' Processing helix chain 'D' and resid 71 through 79 removed outlier: 3.515A pdb=" N LYS D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 109 No H-bonds generated for 'chain 'D' and resid 107 through 109' Processing helix chain 'D' and resid 130 through 133 No H-bonds generated for 'chain 'D' and resid 130 through 133' Processing helix chain 'E' and resid 30 through 43 removed outlier: 3.530A pdb=" N GLU E 35 " --> pdb=" O SER E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 120 removed outlier: 3.592A pdb=" N ARG E 107 " --> pdb=" O LYS E 103 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA E 109 " --> pdb=" O MET E 105 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU E 110 " --> pdb=" O ARG E 106 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU E 114 " --> pdb=" O LEU E 110 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE E 116 " --> pdb=" O SER E 112 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS E 117 " --> pdb=" O ALA E 113 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA E 118 " --> pdb=" O LEU E 114 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU E 120 " --> pdb=" O PHE E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 145 removed outlier: 3.612A pdb=" N ASN E 141 " --> pdb=" O LYS E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 166 Processing helix chain 'E' and resid 178 through 180 No H-bonds generated for 'chain 'E' and resid 178 through 180' Processing helix chain 'E' and resid 183 through 188 Processing helix chain 'E' and resid 196 through 206 Processing helix chain 'F' and resid 47 through 60 Processing helix chain 'F' and resid 94 through 105 removed outlier: 3.904A pdb=" N ASP F 101 " --> pdb=" O TYR F 97 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS F 102 " --> pdb=" O GLU F 98 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER F 105 " --> pdb=" O ASP F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 111 No H-bonds generated for 'chain 'F' and resid 108 through 111' Processing helix chain 'F' and resid 163 through 171 removed outlier: 3.772A pdb=" N GLU F 168 " --> pdb=" O GLU F 164 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU F 169 " --> pdb=" O GLU F 165 " (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: 3.637A pdb=" N GLY G 66 " --> pdb=" O ARG G 62 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG G 69 " --> pdb=" O HIS G 65 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA G 70 " --> pdb=" O GLY G 66 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL G 79 " --> pdb=" O MET G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 149 removed outlier: 3.606A pdb=" N ARG G 149 " --> pdb=" O ALA G 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 38 removed outlier: 3.845A pdb=" N GLU H 32 " --> pdb=" O ARG H 28 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER H 35 " --> pdb=" O SER H 31 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE H 36 " --> pdb=" O GLU H 32 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG H 38 " --> pdb=" O ALA H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 95 Processing helix chain 'H' and resid 98 through 109 removed outlier: 3.541A pdb=" N ILE H 102 " --> pdb=" O PRO H 98 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET H 109 " --> pdb=" O SER H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 122 removed outlier: 3.656A pdb=" N LYS H 121 " --> pdb=" O GLU H 117 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LYS H 122 " --> pdb=" O LYS H 118 " (cutoff:3.500A) Processing helix chain 'I' and resid 104 through 107 Processing helix chain 'I' and resid 112 through 116 Processing helix chain 'J' and resid 23 through 25 No H-bonds generated for 'chain 'J' and resid 23 through 25' 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 80 through 82 No H-bonds generated for 'chain 'J' and resid 80 through 82' Processing helix chain 'J' and resid 93 through 98 Processing helix chain 'J' and resid 130 through 139 removed outlier: 3.552A pdb=" N GLU J 134 " --> pdb=" O ALA J 130 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP J 137 " --> pdb=" O ALA J 133 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS J 139 " --> pdb=" O ALA J 135 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 58 removed outlier: 3.526A pdb=" N ARG K 51 " --> pdb=" O ILE K 47 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR K 57 " --> pdb=" O ALA K 53 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET K 58 " --> pdb=" O MET K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 124 removed outlier: 3.629A pdb=" N HIS K 123 " --> pdb=" O ARG K 119 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LYS K 124 " --> pdb=" O LEU K 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 26 removed outlier: 3.562A pdb=" N SER L 23 " --> pdb=" O ASP L 19 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU L 24 " --> pdb=" O LEU L 20 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE L 25 " --> pdb=" O ALA L 21 " (cutoff:3.500A) Processing helix chain 'L' and resid 34 through 53 removed outlier: 3.653A pdb=" N GLU L 39 " --> pdb=" O ALA L 35 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N SER L 42 " --> pdb=" O LYS L 38 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL L 43 " --> pdb=" O GLU L 39 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU L 45 " --> pdb=" O ARG L 41 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU L 50 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 64 removed outlier: 3.840A pdb=" N LYS L 64 " --> pdb=" O ARG L 60 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 87 Processing helix chain 'L' and resid 89 through 92 No H-bonds generated for 'chain 'L' and resid 89 through 92' Processing helix chain 'M' and resid 7 through 18 removed outlier: 3.724A pdb=" N LYS M 13 " --> pdb=" O LYS M 9 " (cutoff:3.500A) Processing helix chain 'M' and resid 71 through 86 removed outlier: 3.674A pdb=" N ALA M 81 " --> pdb=" O GLY M 77 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS M 82 " --> pdb=" O GLU M 78 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS M 83 " --> pdb=" O ALA M 79 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 115 removed outlier: 3.684A pdb=" N SER M 115 " --> pdb=" O ALA M 111 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 14 removed outlier: 5.456A pdb=" N SER N 13 " --> pdb=" O ALA N 9 " (cutoff:3.500A) removed outlier: 5.501A 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 104 removed outlier: 3.706A pdb=" N SER N 104 " --> pdb=" O TYR N 101 " (cutoff:3.500A) Processing helix chain 'N' and resid 107 through 109 No H-bonds generated for 'chain 'N' and resid 107 through 109' Processing helix chain 'O' and resid 9 through 21 removed outlier: 3.534A pdb=" N ARG O 13 " --> pdb=" O VAL O 9 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS O 16 " --> pdb=" O ALA O 12 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR O 17 " --> pdb=" O ARG O 13 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU O 20 " --> pdb=" O LYS O 16 " (cutoff:3.500A) Processing helix chain 'O' and resid 26 through 29 removed outlier: 3.574A pdb=" N HIS O 29 " --> pdb=" O GLY O 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 26 through 29' Processing helix chain 'O' and resid 32 through 69 removed outlier: 3.600A pdb=" N GLN O 37 " --> pdb=" O LYS O 33 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS O 41 " --> pdb=" O GLN O 37 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG O 51 " --> pdb=" O PHE O 47 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LYS O 54 " --> pdb=" O ARG O 50 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG O 55 " --> pdb=" O ARG O 51 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ARG O 58 " --> pdb=" O LYS O 54 " (cutoff:3.500A) Processing helix chain 'O' and resid 76 through 86 removed outlier: 3.599A pdb=" N LYS O 84 " --> pdb=" O MET O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 93 through 101 removed outlier: 3.603A pdb=" N ALA O 99 " --> pdb=" O LEU O 95 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE O 100 " --> pdb=" O SER O 96 " (cutoff:3.500A) Processing helix chain 'O' and resid 103 through 114 removed outlier: 3.653A pdb=" N GLN O 108 " --> pdb=" O LYS O 104 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU O 109 " --> pdb=" O ALA O 105 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR O 111 " --> pdb=" O ALA O 107 " (cutoff:3.500A) Processing helix chain 'Q' and resid 14 through 22 removed outlier: 3.957A pdb=" N LEU Q 19 " --> pdb=" O ARG Q 15 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL Q 20 " --> pdb=" O LYS Q 16 " (cutoff:3.500A) Processing helix chain 'Q' and resid 29 through 36 removed outlier: 3.551A pdb=" N ALA Q 34 " --> pdb=" O ALA Q 30 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 60 removed outlier: 3.500A pdb=" N SER Q 53 " --> pdb=" O LYS Q 49 " (cutoff:3.500A) Processing helix chain 'R' and resid 14 through 21 removed outlier: 3.716A pdb=" N ALA R 19 " --> pdb=" O LYS R 15 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA R 21 " --> pdb=" O SER R 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 35 through 45 removed outlier: 3.602A pdb=" N GLU R 43 " --> pdb=" O LYS R 39 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU R 44 " --> pdb=" O MET R 40 " (cutoff:3.500A) 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 'T' and resid 82 through 84 No H-bonds generated for 'chain 'T' and resid 82 through 84' Processing helix chain 'V' and resid 53 through 56 No H-bonds generated for 'chain 'V' and resid 53 through 56' Processing helix chain 'W' and resid 13 through 33 removed outlier: 3.547A pdb=" N LYS W 19 " --> pdb=" O GLU W 15 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU W 23 " --> pdb=" O LYS W 19 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N LEU W 32 " --> pdb=" O LEU W 28 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA W 33 " --> pdb=" O ARG W 29 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 65 removed outlier: 3.515A pdb=" N ILE W 43 " --> pdb=" O THR W 40 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG W 44 " --> pdb=" O ALA W 41 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR W 45 " --> pdb=" O ARG W 42 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LYS W 48 " --> pdb=" O THR W 45 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE W 50 " --> pdb=" O ARG W 47 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS W 54 " --> pdb=" O ALA W 51 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL W 56 " --> pdb=" O LEU W 53 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU W 59 " --> pdb=" O VAL W 56 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE W 62 " --> pdb=" O GLU W 59 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER W 65 " --> pdb=" O ILE W 62 " (cutoff:3.500A) Processing helix chain 'X' and resid 17 through 26 removed outlier: 3.745A pdb=" N THR X 22 " --> pdb=" O THR X 18 " (cutoff:3.500A) Processing helix chain 'X' and resid 41 through 49 removed outlier: 3.644A pdb=" N GLY X 45 " --> pdb=" O PRO X 41 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN X 46 " --> pdb=" O ALA X 42 " (cutoff:3.500A) Processing helix chain 'Z' and resid 10 through 18 removed outlier: 3.523A pdb=" N ARG Z 17 " --> pdb=" O LYS Z 13 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N THR Z 18 " --> pdb=" O ASN Z 14 " (cutoff:3.500A) Processing helix chain '2' and resid 10 through 16 removed outlier: 3.577A pdb=" N SER 2 14 " --> pdb=" O LYS 2 10 " (cutoff:3.500A) Processing helix chain '2' and resid 19 through 24 Processing helix chain '2' and resid 26 through 37 removed outlier: 3.655A pdb=" N VAL 2 31 " --> pdb=" O ASN 2 27 " (cutoff:3.500A) 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 43 Processing helix chain '3' and resid 52 through 58 removed outlier: 3.559A pdb=" N LYS 3 56 " --> pdb=" O LYS 3 52 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG 3 57 " --> pdb=" O SER 3 53 " (cutoff:3.500A) Processing helix chain '4' and resid 30 through 32 No H-bonds generated for 'chain '4' and resid 30 through 32' Processing sheet with id= A, first strand: chain 'C' and resid 34 through 36 Processing sheet with id= B, first strand: chain 'C' and resid 101 through 105 removed outlier: 3.803A pdb=" N SER C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL C 95 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N VAL C 78 " --> pdb=" O VAL C 95 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 129 through 131 Processing sheet with id= D, first strand: chain 'C' and resid 181 through 185 removed outlier: 3.723A pdb=" N GLY C 166 " --> pdb=" O LEU C 173 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ARG C 175 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N VAL C 164 " --> pdb=" O ARG C 175 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 5 through 7 Processing sheet with id= F, first strand: chain 'D' and resid 8 through 16 removed outlier: 7.063A pdb=" N VAL D 27 " --> pdb=" O ILE D 10 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N MET D 12 " --> pdb=" O VAL D 25 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL D 25 " --> pdb=" O MET D 12 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N GLN D 14 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE D 23 " --> pdb=" O GLN D 14 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN D 187 " --> pdb=" O LEU D 196 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LYS D 198 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL D 185 " --> pdb=" O LYS D 198 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 88 through 91 removed outlier: 3.680A pdb=" N GLN D 37 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N GLY D 52 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N VAL D 35 " --> pdb=" O GLY D 52 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 123 through 125 removed outlier: 6.051A pdb=" N LEU E 192 " --> pdb=" O THR E 124 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 31 through 35 removed outlier: 6.720A pdb=" N VAL F 157 " --> pdb=" O ASP F 32 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ILE F 34 " --> pdb=" O VAL F 155 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL F 155 " --> pdb=" O ILE F 34 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 16 through 19 Processing sheet with id= K, first strand: chain 'G' and resid 42 through 45 Processing sheet with id= L, first strand: chain 'G' and resid 161 through 164 Processing sheet with id= M, first strand: chain 'G' and resid 95 through 99 removed outlier: 3.837A pdb=" N ASP G 102 " --> pdb=" O GLN G 99 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'H' and resid 16 through 19 removed outlier: 6.678A pdb=" N TYR H 54 " --> pdb=" O TYR H 17 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ILE H 19 " --> pdb=" O TYR H 54 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ILE H 56 " --> pdb=" O ILE H 19 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 74 through 78 Processing sheet with id= P, first strand: chain 'I' and resid 7 through 9 removed outlier: 6.832A pdb=" N VAL I 40 " --> pdb=" O ILE I 22 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N VAL I 24 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N VAL I 38 " --> pdb=" O VAL I 24 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL I 63 " --> pdb=" O ALA I 83 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'J' and resid 75 through 77 Processing sheet with id= R, first strand: chain 'K' and resid 129 through 132 removed outlier: 4.118A pdb=" N PHE K 104 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ALA K 36 " --> pdb=" O ILE K 102 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE K 102 " --> pdb=" O ALA K 36 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'K' and resid 40 through 42 Processing sheet with id= T, first strand: chain 'K' and resid 72 through 75 removed outlier: 3.607A pdb=" N GLY K 92 " --> pdb=" O TYR K 74 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'L' and resid 29 through 33 Processing sheet with id= V, first strand: chain 'L' and resid 70 through 72 Processing sheet with id= W, first strand: chain 'M' and resid 30 through 35 removed outlier: 3.563A pdb=" N GLN M 43 " --> pdb=" O ASN M 32 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ALA M 54 " --> pdb=" O ILE M 44 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ASP M 46 " --> pdb=" O THR M 52 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N THR M 52 " --> pdb=" O ASP M 46 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'N' and resid 85 through 90 removed outlier: 3.611A pdb=" N LYS N 85 " --> pdb=" O HIS N 31 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N THR N 27 " --> pdb=" O LYS N 89 " (cutoff:3.500A) removed outlier: 9.128A pdb=" N GLU N 46 " --> pdb=" O ILE N 66 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ILE N 66 " --> pdb=" O GLU N 46 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR N 62 " --> pdb=" O ILE N 50 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ARG N 52 " --> pdb=" O THR N 60 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N THR N 60 " --> pdb=" O ARG N 52 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'P' and resid 10 through 14 removed outlier: 3.871A pdb=" N PHE P 40 " --> pdb=" O ILE P 4 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N GLU P 6 " --> pdb=" O VAL P 38 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL P 38 " --> pdb=" O GLU P 6 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'P' and resid 19 through 22 Processing sheet with id= AA, first strand: chain 'P' and resid 32 through 35 removed outlier: 3.801A pdb=" N LYS P 99 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N THR P 61 " --> pdb=" O ILE P 97 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ILE P 97 " --> pdb=" O THR P 61 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ASN P 63 " --> pdb=" O LEU P 95 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LEU P 95 " --> pdb=" O ASN P 63 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'P' and resid 71 through 77 removed outlier: 4.832A pdb=" N SER P 82 " --> pdb=" O LYS P 77 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'Q' and resid 2 through 7 removed outlier: 3.683A pdb=" N GLU Q 73 " --> pdb=" O VAL Q 106 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N SER Q 108 " --> pdb=" O VAL Q 71 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N VAL Q 71 " --> pdb=" O SER Q 108 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'Q' and resid 82 through 87 Processing sheet with id= AE, first strand: chain 'R' and resid 53 through 58 removed outlier: 3.547A pdb=" N ARG R 75 " --> pdb=" O TYR R 58 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ARG R 76 " --> pdb=" O VAL R 29 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'R' and resid 62 through 64 Processing sheet with id= AG, first strand: chain 'S' and resid 20 through 22 removed outlier: 3.607A pdb=" N GLY S 21 " --> pdb=" O VAL S 9 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'S' and resid 82 through 86 removed outlier: 3.514A pdb=" N LYS S 84 " --> pdb=" O VAL S 91 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'T' and resid 39 through 44 removed outlier: 7.048A pdb=" N ILE T 89 " --> pdb=" O VAL T 30 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N TYR T 32 " --> pdb=" O ILE T 89 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N PHE T 91 " --> pdb=" O TYR T 32 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASP T 76 " --> pdb=" O ASP T 90 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LEU T 92 " --> pdb=" O VAL T 74 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N VAL T 74 " --> pdb=" O LEU T 92 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS T 68 " --> pdb=" O VAL T 65 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'U' and resid 59 through 61 Processing sheet with id= AK, first strand: chain 'U' and resid 74 through 79 Processing sheet with id= AL, first strand: chain 'V' and resid 14 through 17 Processing sheet with id= AM, first strand: chain 'V' and resid 33 through 38 Processing sheet with id= AN, first strand: chain 'X' and resid 34 through 38 Processing sheet with id= AO, first strand: chain '1' and resid 3 through 6 Processing sheet with id= AP, first strand: chain '1' and resid 7 through 9 removed outlier: 4.103A pdb=" N LYS 1 41 " --> pdb=" O CYS 1 36 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N CYS 1 36 " --> pdb=" O LYS 1 41 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain '3' and resid 14 through 16 removed outlier: 3.606A pdb=" N LYS 3 15 " --> pdb=" O LYS 3 23 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain '4' and resid 2 through 4 removed outlier: 3.724A pdb=" N ARG 4 4 " --> pdb=" O ARG 4 35 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain '4' and resid 15 through 19 589 hydrogen bonds defined for protein. 1611 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2325 hydrogen bonds 3730 hydrogen bond angles 0 basepair planarities 935 basepair parallelities 1522 stacking parallelities Total time for adding SS restraints: 150.27 Time building geometry restraints manager: 37.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.52: 83626 1.52 - 1.88: 10388 1.88 - 2.23: 0 2.23 - 2.59: 0 2.59 - 2.95: 1 Bond restraints: 94015 Sorted by residual: bond pdb=" O3' G A1294 " pdb=" P C A1295 " ideal model delta sigma weight residual 1.607 2.945 -1.338 1.50e-02 4.44e+03 7.96e+03 bond pdb=" O3' 5MU A 792 " pdb=" P G A 793 " ideal model delta sigma weight residual 1.607 1.187 0.420 1.50e-02 4.44e+03 7.84e+02 bond pdb=" O3' G A 790 " pdb=" P U A 791 " ideal model delta sigma weight residual 1.607 1.340 0.267 1.50e-02 4.44e+03 3.17e+02 bond pdb=" C5 5MU A1966 " pdb=" C6 5MU A1966 " ideal model delta sigma weight residual 1.155 1.431 -0.276 2.00e-02 2.50e+03 1.90e+02 bond pdb=" C5 5MU A 792 " pdb=" C6 5MU A 792 " ideal model delta sigma weight residual 1.155 1.421 -0.266 2.00e-02 2.50e+03 1.77e+02 ... (remaining 94010 not shown) Histogram of bond angle deviations from ideal: 63.43 - 78.15: 4 78.15 - 92.88: 6 92.88 - 107.60: 23308 107.60 - 122.33: 98772 122.33 - 137.05: 19451 Bond angle restraints: 141541 Sorted by residual: angle pdb=" O3' G A1294 " pdb=" P C A1295 " pdb=" O5' C A1295 " ideal model delta sigma weight residual 104.00 63.92 40.08 1.50e+00 4.44e-01 7.14e+02 angle pdb=" O3' G A1294 " pdb=" P C A1295 " pdb=" OP1 C A1295 " ideal model delta sigma weight residual 108.00 63.43 44.57 3.00e+00 1.11e-01 2.21e+02 angle pdb=" OP1 G A2397 " pdb=" P G A2397 " pdb=" OP2 G A2397 " ideal model delta sigma weight residual 119.60 80.58 39.02 3.00e+00 1.11e-01 1.69e+02 angle pdb=" O3' G A2762 " pdb=" P G A2763 " pdb=" O5' G A2763 " ideal model delta sigma weight residual 104.00 86.17 17.83 1.50e+00 4.44e-01 1.41e+02 angle pdb=" OP1 G A2397 " pdb=" P G A2397 " pdb=" O5' G A2397 " ideal model delta sigma weight residual 108.00 74.06 33.94 3.00e+00 1.11e-01 1.28e+02 ... (remaining 141536 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.73: 53392 35.73 - 71.46: 6009 71.46 - 107.19: 661 107.19 - 142.92: 7 142.92 - 178.64: 18 Dihedral angle restraints: 60087 sinusoidal: 51473 harmonic: 8614 Sorted by residual: dihedral pdb=" O4' C A 882 " pdb=" C1' C A 882 " pdb=" N1 C A 882 " pdb=" C2 C A 882 " ideal model delta sinusoidal sigma weight residual 200.00 21.36 178.64 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 200.00 26.69 173.31 1 1.50e+01 4.44e-03 8.50e+01 dihedral pdb=" O4' U A1804 " pdb=" C1' U A1804 " pdb=" N1 U A1804 " pdb=" C2 U A1804 " ideal model delta sinusoidal sigma weight residual -160.00 10.77 -170.77 1 1.50e+01 4.44e-03 8.48e+01 ... (remaining 60084 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.181: 18150 0.181 - 0.363: 122 0.363 - 0.544: 4 0.544 - 0.726: 0 0.726 - 0.907: 2 Chirality restraints: 18278 Sorted by residual: chirality pdb=" C3' G A1957 " pdb=" C4' G A1957 " pdb=" O3' G A1957 " pdb=" C2' G A1957 " both_signs ideal model delta sigma weight residual False -2.74 -1.84 -0.91 2.00e-01 2.50e+01 2.06e+01 chirality pdb=" C3' A A1997 " pdb=" C4' A A1997 " pdb=" O3' A A1997 " pdb=" C2' A A1997 " both_signs ideal model delta sigma weight residual False -2.74 -1.96 -0.78 2.00e-01 2.50e+01 1.54e+01 chirality pdb=" C3' U A2003 " pdb=" C4' U A2003 " pdb=" O3' U A2003 " pdb=" C2' U A2003 " both_signs ideal model delta sigma weight residual False -2.48 -1.98 -0.49 2.00e-01 2.50e+01 6.09e+00 ... (remaining 18275 not shown) Planarity restraints: 6962 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MA A2530 " -0.793 2.00e-02 2.50e+03 5.67e-01 7.23e+03 pdb=" C4' 2MA A2530 " 0.231 2.00e-02 2.50e+03 pdb=" O4' 2MA A2530 " 0.635 2.00e-02 2.50e+03 pdb=" C3' 2MA A2530 " -0.236 2.00e-02 2.50e+03 pdb=" O3' 2MA A2530 " 0.939 2.00e-02 2.50e+03 pdb=" C2' 2MA A2530 " -0.640 2.00e-02 2.50e+03 pdb=" O2' 2MA A2530 " -0.535 2.00e-02 2.50e+03 pdb=" C1' 2MA A2530 " 0.414 2.00e-02 2.50e+03 pdb=" N9 2MA A2530 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MU A1966 " -0.682 2.00e-02 2.50e+03 5.03e-01 5.70e+03 pdb=" C4' 5MU A1966 " 0.246 2.00e-02 2.50e+03 pdb=" O4' 5MU A1966 " 0.472 2.00e-02 2.50e+03 pdb=" C3' 5MU A1966 " -0.236 2.00e-02 2.50e+03 pdb=" O3' 5MU A1966 " 0.848 2.00e-02 2.50e+03 pdb=" C2' 5MU A1966 " -0.601 2.00e-02 2.50e+03 pdb=" O2' 5MU A1966 " -0.479 2.00e-02 2.50e+03 pdb=" C1' 5MU A1966 " 0.403 2.00e-02 2.50e+03 pdb=" N1 5MU A1966 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MU A 792 " -0.043 2.00e-02 2.50e+03 4.79e-01 5.16e+03 pdb=" C4' 5MU A 792 " 0.402 2.00e-02 2.50e+03 pdb=" O4' 5MU A 792 " 0.555 2.00e-02 2.50e+03 pdb=" C3' 5MU A 792 " -0.572 2.00e-02 2.50e+03 pdb=" O3' 5MU A 792 " -0.343 2.00e-02 2.50e+03 pdb=" C2' 5MU A 792 " -0.297 2.00e-02 2.50e+03 pdb=" O2' 5MU A 792 " 0.720 2.00e-02 2.50e+03 pdb=" C1' 5MU A 792 " 0.264 2.00e-02 2.50e+03 pdb=" N1 5MU A 792 " -0.685 2.00e-02 2.50e+03 ... (remaining 6959 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.22: 165 2.22 - 2.89: 27782 2.89 - 3.56: 120788 3.56 - 4.23: 262125 4.23 - 4.90: 351089 Nonbonded interactions: 761949 Sorted by model distance: nonbonded pdb=" OP2 G A 208 " pdb="MG MG A3015 " model vdw 1.546 2.170 nonbonded pdb=" OP2 U A1715 " pdb="MG MG A3135 " model vdw 1.692 2.170 nonbonded pdb=" OP1 A A 796 " pdb="MG MG A3130 " model vdw 1.730 2.170 nonbonded pdb=" OP1 A A2296 " pdb="MG MG A3163 " model vdw 1.741 2.170 nonbonded pdb=" OP2 A A 952 " pdb="MG MG A3089 " model vdw 1.751 2.170 ... (remaining 761944 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.740 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: 10.940 Check model and map are aligned: 0.950 Set scattering table: 0.570 Process input model: 312.740 Find NCS groups from input model: 1.390 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:11.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 339.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 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 : 0.012 1.338 94015 Z= 0.728 Angle : 1.000 44.573 141541 Z= 0.505 Chirality : 0.058 0.907 18278 Planarity : 0.013 0.567 6962 Dihedral : 22.322 178.645 54542 Min Nonbonded Distance : 1.546 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.23 (0.12), residues: 2985 helix: -4.30 (0.09), residues: 722 sheet: -1.58 (0.20), residues: 589 loop : -2.62 (0.12), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.005 TRP H 16 HIS 0.024 0.003 HIS J 35 PHE 0.046 0.004 PHE L 86 TYR 0.045 0.004 TYR L 100 ARG 0.030 0.002 ARG E 45 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 738 time to evaluate : 3.378 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LYS G 175 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: C 39 LYS cc_start: 0.8022 (mttm) cc_final: 0.7322 (mttp) REVERT: C 111 GLU cc_start: 0.7293 (mt-10) cc_final: 0.6924 (mm-30) REVERT: C 115 ILE cc_start: 0.7672 (pt) cc_final: 0.7386 (mm) REVERT: C 168 GLU cc_start: 0.5960 (tp30) cc_final: 0.5234 (tt0) REVERT: C 177 ARG cc_start: 0.8141 (tpt90) cc_final: 0.7719 (tpt170) REVERT: C 183 MET cc_start: 0.8036 (mtt) cc_final: 0.7720 (mtp) REVERT: C 211 SER cc_start: 0.7837 (p) cc_final: 0.7635 (t) REVERT: C 236 GLU cc_start: 0.7375 (mm-30) cc_final: 0.6976 (mm-30) REVERT: C 252 LYS cc_start: 0.7279 (mptm) cc_final: 0.7016 (mptt) REVERT: C 268 LYS cc_start: 0.7472 (mmmt) cc_final: 0.6700 (ptmt) REVERT: D 64 LYS cc_start: 0.7436 (mtmm) cc_final: 0.6970 (mtpt) REVERT: D 184 GLU cc_start: 0.7290 (mt-10) cc_final: 0.6795 (tt0) REVERT: D 187 GLN cc_start: 0.7669 (tm-30) cc_final: 0.7344 (tt0) REVERT: D 193 LYS cc_start: 0.8087 (mttp) cc_final: 0.7857 (mttp) REVERT: E 100 LYS cc_start: 0.7423 (mttt) cc_final: 0.6291 (pttt) REVERT: E 107 ARG cc_start: 0.6687 (mtp85) cc_final: 0.6208 (mtt-85) REVERT: E 120 GLU cc_start: 0.7016 (mt-10) cc_final: 0.6770 (pt0) REVERT: E 147 GLU cc_start: 0.6956 (mp0) cc_final: 0.6128 (mm-30) REVERT: E 156 THR cc_start: 0.7715 (p) cc_final: 0.7433 (p) REVERT: E 157 GLU cc_start: 0.6906 (tt0) cc_final: 0.6632 (tt0) REVERT: E 164 GLU cc_start: 0.6800 (tm-30) cc_final: 0.6354 (tm-30) REVERT: E 177 THR cc_start: 0.8206 (m) cc_final: 0.7813 (t) REVERT: E 194 ILE cc_start: 0.7519 (pt) cc_final: 0.6803 (tt) REVERT: E 200 LYS cc_start: 0.6910 (mmpt) cc_final: 0.6392 (mtpt) REVERT: G 53 VAL cc_start: 0.4653 (t) cc_final: 0.4391 (p) REVERT: G 69 ARG cc_start: 0.5403 (tmt170) cc_final: 0.5172 (tmt170) REVERT: G 119 GLU cc_start: 0.6330 (mt-10) cc_final: 0.6018 (mp0) REVERT: G 132 LYS cc_start: 0.5490 (mtpp) cc_final: 0.4939 (ttpp) REVERT: H 15 LYS cc_start: 0.7322 (ptmt) cc_final: 0.6773 (ptpp) REVERT: H 22 GLU cc_start: 0.6873 (pt0) cc_final: 0.6664 (pt0) REVERT: H 32 GLU cc_start: 0.6996 (mm-30) cc_final: 0.6744 (mm-30) REVERT: H 62 LYS cc_start: 0.7824 (mptp) cc_final: 0.7620 (mmtp) REVERT: H 74 VAL cc_start: 0.7722 (m) cc_final: 0.7521 (p) REVERT: H 95 ARG cc_start: 0.6924 (ptp-110) cc_final: 0.6578 (ptt-90) REVERT: H 103 GLU cc_start: 0.7558 (pt0) cc_final: 0.7336 (pt0) REVERT: H 117 GLU cc_start: 0.7049 (mm-30) cc_final: 0.6725 (mm-30) REVERT: H 118 LYS cc_start: 0.7179 (tttt) cc_final: 0.6687 (ttpp) REVERT: H 130 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6879 (mm-30) REVERT: H 141 TYR cc_start: 0.7939 (t80) cc_final: 0.7625 (t80) REVERT: I 9 LYS cc_start: 0.7131 (ttmt) cc_final: 0.6506 (mmtt) REVERT: I 18 GLU cc_start: 0.7611 (tt0) cc_final: 0.7215 (tp30) REVERT: I 42 THR cc_start: 0.8026 (p) cc_final: 0.7724 (t) REVERT: I 104 ARG cc_start: 0.6534 (ttm-80) cc_final: 0.6013 (ttp-170) REVERT: J 59 ARG cc_start: 0.7403 (mmm-85) cc_final: 0.7193 (mmm160) REVERT: J 99 SER cc_start: 0.7048 (t) cc_final: 0.6752 (p) REVERT: J 120 LYS cc_start: 0.6631 (ttpm) cc_final: 0.6334 (tptt) REVERT: K 47 ILE cc_start: 0.7669 (pt) cc_final: 0.7446 (pt) REVERT: K 56 ARG cc_start: 0.7302 (ptp90) cc_final: 0.7012 (ptp90) REVERT: K 111 GLU cc_start: 0.7378 (tt0) cc_final: 0.7008 (tm-30) REVERT: K 116 GLU cc_start: 0.7539 (tp30) cc_final: 0.7139 (tp30) REVERT: K 130 LYS cc_start: 0.7642 (ttpp) cc_final: 0.7129 (ttmt) REVERT: L 31 GLU cc_start: 0.7556 (tt0) cc_final: 0.7255 (tt0) REVERT: L 34 GLU cc_start: 0.7713 (tt0) cc_final: 0.7090 (tp30) REVERT: L 42 SER cc_start: 0.8509 (p) cc_final: 0.8104 (t) REVERT: L 44 VAL cc_start: 0.7821 (p) cc_final: 0.7509 (m) REVERT: L 91 GLU cc_start: 0.7135 (mm-30) cc_final: 0.6849 (mm-30) REVERT: M 13 LYS cc_start: 0.6067 (mttm) cc_final: 0.5616 (mmtt) REVERT: M 38 LYS cc_start: 0.5978 (mttt) cc_final: 0.5587 (mmtp) REVERT: N 5 LYS cc_start: 0.7441 (tttt) cc_final: 0.6955 (tptp) REVERT: N 85 LYS cc_start: 0.6958 (tttt) cc_final: 0.6717 (ttmm) REVERT: N 93 LYS cc_start: 0.7447 (tttt) cc_final: 0.6844 (tmtt) REVERT: O 59 LYS cc_start: 0.7699 (ttpt) cc_final: 0.7398 (ttmt) REVERT: P 15 GLU cc_start: 0.7052 (mt-10) cc_final: 0.6245 (mp0) REVERT: P 24 LYS cc_start: 0.8242 (ttpp) cc_final: 0.7983 (ttmt) REVERT: P 37 LYS cc_start: 0.7891 (mppt) cc_final: 0.7371 (mmtt) REVERT: P 47 LYS cc_start: 0.8046 (mttt) cc_final: 0.7730 (mtpt) REVERT: Q 8 ARG cc_start: 0.7166 (mtp-110) cc_final: 0.6829 (mtt90) REVERT: Q 28 ASN cc_start: 0.7774 (p0) cc_final: 0.7559 (p0) REVERT: Q 31 GLU cc_start: 0.6081 (mt-10) cc_final: 0.5849 (mt-10) REVERT: Q 37 LYS cc_start: 0.7830 (mttm) cc_final: 0.7617 (mtmt) REVERT: Q 48 GLU cc_start: 0.7551 (tm-30) cc_final: 0.7348 (tm-30) REVERT: Q 59 GLU cc_start: 0.7399 (tt0) cc_final: 0.6827 (mt-10) REVERT: Q 105 ILE cc_start: 0.7303 (pp) cc_final: 0.6931 (mt) REVERT: R 20 MET cc_start: 0.6738 (mtp) cc_final: 0.6052 (mtt) REVERT: R 28 ASP cc_start: 0.7984 (t70) cc_final: 0.7651 (t0) REVERT: R 52 SER cc_start: 0.7993 (m) cc_final: 0.7758 (p) REVERT: S 19 LYS cc_start: 0.7538 (ttmp) cc_final: 0.7107 (ttmt) REVERT: S 63 ILE cc_start: 0.7186 (mt) cc_final: 0.6801 (mm) REVERT: S 84 LYS cc_start: 0.6507 (tmmt) cc_final: 0.6287 (ptmt) REVERT: T 26 LYS cc_start: 0.7255 (mptp) cc_final: 0.6827 (mttt) REVERT: U 19 LYS cc_start: 0.7420 (ptmm) cc_final: 0.7079 (ptpt) REVERT: U 25 GLU cc_start: 0.6399 (mt-10) cc_final: 0.6147 (mp0) REVERT: U 76 LYS cc_start: 0.7655 (mmtt) cc_final: 0.6958 (mmmt) REVERT: V 22 LEU cc_start: 0.7553 (mp) cc_final: 0.7283 (mm) REVERT: V 28 ARG cc_start: 0.7208 (mmm-85) cc_final: 0.7003 (mtp85) REVERT: W 17 GLN cc_start: 0.7188 (tp-100) cc_final: 0.6806 (tp-100) REVERT: W 23 GLU cc_start: 0.6557 (mt-10) cc_final: 0.5727 (mp0) REVERT: W 39 GLU cc_start: 0.7022 (mt-10) cc_final: 0.6596 (mt-10) REVERT: X 3 LYS cc_start: 0.7594 (mmtp) cc_final: 0.7338 (mmtp) REVERT: X 10 ARG cc_start: 0.7301 (mmm-85) cc_final: 0.7058 (mmm160) REVERT: X 57 GLU cc_start: 0.6758 (mt-10) cc_final: 0.6476 (tt0) REVERT: Z 37 LYS cc_start: 0.6444 (pttt) cc_final: 0.5837 (pttp) REVERT: 2 16 VAL cc_start: 0.7944 (m) cc_final: 0.7729 (t) REVERT: 2 31 VAL cc_start: 0.7539 (m) cc_final: 0.7082 (t) REVERT: 2 37 ARG cc_start: 0.6741 (ttp-110) cc_final: 0.6345 (ttt-90) REVERT: 3 55 MET cc_start: 0.7442 (mmm) cc_final: 0.7110 (tpp) REVERT: 4 1 MET cc_start: 0.7101 (tpp) cc_final: 0.6344 (tpp) REVERT: 4 2 LYS cc_start: 0.7351 (mtmt) cc_final: 0.6598 (mtmm) REVERT: 4 24 MET cc_start: 0.7848 (mtt) cc_final: 0.7438 (mtp) outliers start: 0 outliers final: 0 residues processed: 738 average time/residue: 1.9603 time to fit residues: 1870.1588 Evaluate side-chains 495 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 495 time to evaluate : 3.431 ------------------------------------------------------------------------------- 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: 20.0000 chunk 245 optimal weight: 3.9990 chunk 150 optimal weight: 40.0000 chunk 298 optimal weight: 0.8980 chunk 236 optimal weight: 8.9990 chunk 456 optimal weight: 0.0010 chunk 176 optimal weight: 0.9980 chunk 277 optimal weight: 7.9990 chunk 340 optimal weight: 5.9990 chunk 529 optimal weight: 6.9990 overall best weight: 2.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 90 ASN C 232 HIS D 33 ASN D 50 GLN D 134 HIS E 40 GLN E 162 ASN I 72 ASN J 4 HIS J 27 ASN J 54 GLN K 35 GLN N 3 ASN O 52 GLN R 54 ASN ** S 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 67 ASN ** T 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 23 ASN V 34 GLN 3 60 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 94015 Z= 0.154 Angle : 0.649 40.434 141541 Z= 0.330 Chirality : 0.035 0.286 18278 Planarity : 0.005 0.120 6962 Dihedral : 22.895 177.817 48983 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 4.66 % Allowed : 15.18 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.13), residues: 2985 helix: -2.52 (0.15), residues: 732 sheet: -1.01 (0.20), residues: 630 loop : -2.17 (0.13), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 250 HIS 0.008 0.001 HIS J 35 PHE 0.016 0.002 PHE C 67 TYR 0.018 0.001 TYR C 103 ARG 0.006 0.001 ARG D 172 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 523 time to evaluate : 3.401 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS G 175 " (corrupted residue). Skipping it. REVERT: C 30 GLU cc_start: 0.7341 (tt0) cc_final: 0.6859 (tp30) REVERT: C 39 LYS cc_start: 0.8075 (mttm) cc_final: 0.7384 (mttp) REVERT: C 105 ILE cc_start: 0.7321 (pt) cc_final: 0.7092 (mp) REVERT: C 111 GLU cc_start: 0.7444 (mt-10) cc_final: 0.6937 (mm-30) REVERT: C 168 GLU cc_start: 0.5843 (tp30) cc_final: 0.5093 (tt0) REVERT: C 175 ARG cc_start: 0.7384 (ttm110) cc_final: 0.7123 (ttm-80) REVERT: C 183 MET cc_start: 0.8086 (mtt) cc_final: 0.7882 (mtp) REVERT: C 236 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7073 (mm-30) REVERT: C 252 LYS cc_start: 0.7351 (mptm) cc_final: 0.7147 (mptt) REVERT: C 261 ARG cc_start: 0.6631 (OUTLIER) cc_final: 0.6279 (mtt180) REVERT: C 268 LYS cc_start: 0.7495 (mmmt) cc_final: 0.6859 (ptmt) REVERT: D 42 GLU cc_start: 0.6970 (OUTLIER) cc_final: 0.6626 (pm20) REVERT: D 64 LYS cc_start: 0.7494 (mtmm) cc_final: 0.6901 (mtpt) REVERT: D 100 GLU cc_start: 0.6903 (OUTLIER) cc_final: 0.6517 (pt0) REVERT: D 184 GLU cc_start: 0.7189 (mt-10) cc_final: 0.6897 (tt0) REVERT: E 100 LYS cc_start: 0.7419 (mttt) cc_final: 0.6341 (pttp) REVERT: E 107 ARG cc_start: 0.6709 (mtp85) cc_final: 0.6176 (mtt-85) REVERT: E 140 LYS cc_start: 0.6394 (OUTLIER) cc_final: 0.6149 (tptp) REVERT: E 147 GLU cc_start: 0.6799 (mp0) cc_final: 0.6055 (mm-30) REVERT: E 164 GLU cc_start: 0.6682 (tm-30) cc_final: 0.6423 (tm-30) REVERT: E 194 ILE cc_start: 0.7416 (pt) cc_final: 0.6863 (tt) REVERT: G 27 LYS cc_start: 0.5078 (ptpt) cc_final: 0.4443 (ptpt) REVERT: G 53 VAL cc_start: 0.4374 (t) cc_final: 0.4115 (p) REVERT: G 163 ARG cc_start: 0.5668 (OUTLIER) cc_final: 0.5368 (ptp-170) REVERT: H 1 MET cc_start: 0.7584 (OUTLIER) cc_final: 0.6794 (mtt) REVERT: H 22 GLU cc_start: 0.6888 (pt0) cc_final: 0.6661 (pt0) REVERT: H 32 GLU cc_start: 0.6865 (mm-30) cc_final: 0.6606 (mm-30) REVERT: H 95 ARG cc_start: 0.6740 (ptp-110) cc_final: 0.6386 (ptt-90) REVERT: H 117 GLU cc_start: 0.6845 (mm-30) cc_final: 0.6576 (mm-30) REVERT: H 118 LYS cc_start: 0.7218 (tttt) cc_final: 0.6765 (ttpp) REVERT: H 130 GLU cc_start: 0.7400 (mm-30) cc_final: 0.7070 (mm-30) REVERT: I 2 ILE cc_start: 0.7614 (mt) cc_final: 0.7308 (mm) REVERT: I 9 LYS cc_start: 0.7037 (ttmt) cc_final: 0.6534 (mmtt) REVERT: I 18 GLU cc_start: 0.7736 (tt0) cc_final: 0.7354 (tp30) REVERT: I 20 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7259 (tt) REVERT: I 34 ASN cc_start: 0.7892 (OUTLIER) cc_final: 0.7621 (t0) REVERT: I 66 LYS cc_start: 0.7537 (ttmp) cc_final: 0.7087 (ttmt) REVERT: I 104 ARG cc_start: 0.6308 (ttm-80) cc_final: 0.5807 (ttp-170) REVERT: J 6 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7455 (pp) REVERT: J 59 ARG cc_start: 0.7363 (mmm-85) cc_final: 0.7111 (mmm160) REVERT: J 99 SER cc_start: 0.7044 (t) cc_final: 0.6557 (p) REVERT: J 121 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7030 (pp) REVERT: K 116 GLU cc_start: 0.7574 (tp30) cc_final: 0.7278 (tp30) REVERT: K 130 LYS cc_start: 0.7468 (ttpp) cc_final: 0.6740 (ttmt) REVERT: L 31 GLU cc_start: 0.7356 (tt0) cc_final: 0.6527 (tp30) REVERT: L 34 GLU cc_start: 0.7436 (tt0) cc_final: 0.6828 (tp30) REVERT: L 44 VAL cc_start: 0.7669 (p) cc_final: 0.7394 (m) REVERT: L 91 GLU cc_start: 0.7316 (mm-30) cc_final: 0.7006 (mm-30) REVERT: M 13 LYS cc_start: 0.5674 (mttm) cc_final: 0.5348 (mmtt) REVERT: M 38 LYS cc_start: 0.6048 (mttt) cc_final: 0.5565 (mmtp) REVERT: N 5 LYS cc_start: 0.7381 (tttt) cc_final: 0.6763 (tptp) REVERT: N 93 LYS cc_start: 0.7394 (tttt) cc_final: 0.6777 (tmtt) REVERT: O 59 LYS cc_start: 0.7549 (ttpt) cc_final: 0.7164 (ttmt) REVERT: O 78 ARG cc_start: 0.7221 (OUTLIER) cc_final: 0.6818 (mtm110) REVERT: O 80 MET cc_start: 0.7742 (mmm) cc_final: 0.7407 (mmm) REVERT: P 15 GLU cc_start: 0.7078 (mt-10) cc_final: 0.6338 (mp0) REVERT: P 37 LYS cc_start: 0.7735 (mppt) cc_final: 0.7068 (mmtt) REVERT: P 47 LYS cc_start: 0.7978 (mttt) cc_final: 0.7667 (mtpt) REVERT: P 69 LYS cc_start: 0.7976 (tttt) cc_final: 0.7617 (tttm) REVERT: Q 8 ARG cc_start: 0.7229 (mtp-110) cc_final: 0.6820 (mtt90) REVERT: Q 28 ASN cc_start: 0.7651 (p0) cc_final: 0.7442 (p0) REVERT: Q 59 GLU cc_start: 0.6816 (tt0) cc_final: 0.6168 (mt-10) REVERT: Q 72 LYS cc_start: 0.7901 (mtpp) cc_final: 0.7467 (ttpt) REVERT: R 20 MET cc_start: 0.6540 (mtp) cc_final: 0.5954 (mtt) REVERT: R 28 ASP cc_start: 0.7731 (t70) cc_final: 0.7371 (t0) REVERT: S 19 LYS cc_start: 0.7403 (ttmp) cc_final: 0.7001 (ttmt) REVERT: S 29 LYS cc_start: 0.6403 (ptpt) cc_final: 0.5923 (ttmm) REVERT: T 26 LYS cc_start: 0.7116 (mptp) cc_final: 0.6754 (mttt) REVERT: U 19 LYS cc_start: 0.7187 (ptmm) cc_final: 0.6924 (ptpt) REVERT: U 25 GLU cc_start: 0.6461 (mt-10) cc_final: 0.6102 (mp0) REVERT: U 61 ARG cc_start: 0.7337 (ttt180) cc_final: 0.6753 (ttt180) REVERT: U 72 ASP cc_start: 0.7065 (p0) cc_final: 0.6630 (p0) REVERT: U 76 LYS cc_start: 0.7585 (mmtt) cc_final: 0.7051 (mmmt) REVERT: W 17 GLN cc_start: 0.7201 (tp-100) cc_final: 0.6806 (mm-40) REVERT: W 23 GLU cc_start: 0.6440 (mt-10) cc_final: 0.5782 (mp0) REVERT: W 39 GLU cc_start: 0.6717 (mt-10) cc_final: 0.6314 (mt-10) REVERT: X 3 LYS cc_start: 0.7393 (mmtp) cc_final: 0.7182 (mmtp) REVERT: Z 37 LYS cc_start: 0.6388 (pttt) cc_final: 0.5775 (pttp) REVERT: 2 10 LYS cc_start: 0.8351 (ttmt) cc_final: 0.8065 (mtmm) REVERT: 2 21 LYS cc_start: 0.8282 (tptt) cc_final: 0.8082 (tppt) REVERT: 2 37 ARG cc_start: 0.6896 (ttp-110) cc_final: 0.6456 (ttt-90) REVERT: 3 31 HIS cc_start: 0.5979 (OUTLIER) cc_final: 0.5518 (t-90) REVERT: 4 1 MET cc_start: 0.6911 (tpp) cc_final: 0.6125 (tpp) REVERT: 4 2 LYS cc_start: 0.7194 (mtmt) cc_final: 0.6727 (mtmm) REVERT: 4 24 MET cc_start: 0.7691 (mtt) cc_final: 0.7348 (mtp) outliers start: 108 outliers final: 32 residues processed: 584 average time/residue: 1.8818 time to fit residues: 1440.3648 Evaluate side-chains 487 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 443 time to evaluate : 3.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 261 ARG Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 163 ARG Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain L residue 9 THR Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain O residue 63 THR Chi-restraints excluded: chain O residue 78 ARG Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain W residue 11 THR Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 35 VAL Chi-restraints excluded: chain Z residue 18 THR Chi-restraints excluded: chain 2 residue 31 VAL Chi-restraints excluded: chain 3 residue 31 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 583 random chunks: chunk 294 optimal weight: 9.9990 chunk 164 optimal weight: 10.0000 chunk 440 optimal weight: 0.3980 chunk 360 optimal weight: 10.0000 chunk 146 optimal weight: 50.0000 chunk 530 optimal weight: 10.0000 chunk 572 optimal weight: 2.9990 chunk 472 optimal weight: 9.9990 chunk 525 optimal weight: 9.9990 chunk 180 optimal weight: 50.0000 chunk 425 optimal weight: 0.0470 overall best weight: 4.6884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 33 ASN D 47 ASN D 187 GLN E 38 ASN H 104 ASN ** J 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 35 GLN O 52 GLN O 91 ASN R 37 GLN S 39 ASN S 67 ASN T 85 GLN T 88 HIS U 20 ASN V 23 ASN 3 60 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 94015 Z= 0.228 Angle : 0.703 40.515 141541 Z= 0.359 Chirality : 0.038 0.329 18278 Planarity : 0.006 0.122 6962 Dihedral : 22.933 178.046 48983 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 6.21 % Allowed : 15.74 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.14), residues: 2985 helix: -1.47 (0.17), residues: 739 sheet: -0.74 (0.20), residues: 611 loop : -1.90 (0.13), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 250 HIS 0.014 0.002 HIS C 232 PHE 0.023 0.002 PHE U 77 TYR 0.026 0.002 TYR J 74 ARG 0.008 0.001 ARG D 172 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 466 time to evaluate : 3.482 Fit side-chains revert: symmetry clash REVERT: C 30 GLU cc_start: 0.7511 (tt0) cc_final: 0.7305 (tp30) REVERT: C 111 GLU cc_start: 0.7548 (mt-10) cc_final: 0.6881 (mm-30) REVERT: C 130 LEU cc_start: 0.7046 (OUTLIER) cc_final: 0.6611 (pt) REVERT: C 168 GLU cc_start: 0.5893 (tp30) cc_final: 0.5137 (tt0) REVERT: C 236 GLU cc_start: 0.7404 (mm-30) cc_final: 0.7038 (mm-30) REVERT: C 261 ARG cc_start: 0.6569 (OUTLIER) cc_final: 0.6192 (mtt180) REVERT: C 268 LYS cc_start: 0.7603 (mmmt) cc_final: 0.6905 (ptmt) REVERT: D 23 ILE cc_start: 0.7153 (OUTLIER) cc_final: 0.6254 (mt) REVERT: D 42 GLU cc_start: 0.6894 (OUTLIER) cc_final: 0.6667 (pt0) REVERT: D 64 LYS cc_start: 0.7340 (mtmm) cc_final: 0.6765 (mtpt) REVERT: D 184 GLU cc_start: 0.7206 (mt-10) cc_final: 0.6837 (tt0) REVERT: E 100 LYS cc_start: 0.7554 (mttt) cc_final: 0.6503 (pttp) REVERT: E 107 ARG cc_start: 0.6832 (mtp85) cc_final: 0.6365 (mtt-85) REVERT: E 147 GLU cc_start: 0.6890 (mp0) cc_final: 0.6196 (mm-30) REVERT: E 164 GLU cc_start: 0.6559 (tm-30) cc_final: 0.6338 (tm-30) REVERT: E 194 ILE cc_start: 0.7455 (pt) cc_final: 0.6955 (tt) REVERT: E 200 LYS cc_start: 0.6472 (mmpt) cc_final: 0.5969 (mttp) REVERT: G 53 VAL cc_start: 0.4397 (t) cc_final: 0.4156 (p) REVERT: G 163 ARG cc_start: 0.5828 (OUTLIER) cc_final: 0.5578 (ptp-170) REVERT: H 32 GLU cc_start: 0.6635 (mm-30) cc_final: 0.6326 (mm-30) REVERT: H 42 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.7850 (mttt) REVERT: H 95 ARG cc_start: 0.6783 (ptp-110) cc_final: 0.6288 (ptt90) REVERT: H 117 GLU cc_start: 0.6890 (mm-30) cc_final: 0.6544 (mm-30) REVERT: H 118 LYS cc_start: 0.7172 (tttt) cc_final: 0.6662 (ttpp) REVERT: H 130 GLU cc_start: 0.7302 (mm-30) cc_final: 0.6980 (mm-30) REVERT: I 9 LYS cc_start: 0.7127 (ttmt) cc_final: 0.6662 (mmtt) REVERT: I 18 GLU cc_start: 0.7761 (tt0) cc_final: 0.7551 (tt0) REVERT: I 20 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7609 (tt) REVERT: I 25 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.7018 (mt) REVERT: I 66 LYS cc_start: 0.7697 (ttmp) cc_final: 0.7280 (ttmt) REVERT: I 81 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7465 (pp20) REVERT: I 104 ARG cc_start: 0.6307 (ttm-80) cc_final: 0.5952 (ttp-170) REVERT: J 6 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7524 (pp) REVERT: J 16 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.6675 (ptt180) REVERT: J 59 ARG cc_start: 0.7205 (mmm-85) cc_final: 0.6467 (mtp-110) REVERT: J 69 ILE cc_start: 0.7094 (OUTLIER) cc_final: 0.6641 (mp) REVERT: J 84 LYS cc_start: 0.6623 (ptmt) cc_final: 0.6232 (pttp) REVERT: J 99 SER cc_start: 0.6909 (t) cc_final: 0.6541 (p) REVERT: J 121 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.6931 (pp) REVERT: K 5 LYS cc_start: 0.7653 (OUTLIER) cc_final: 0.7293 (mtpt) REVERT: K 42 ILE cc_start: 0.7695 (OUTLIER) cc_final: 0.7208 (mm) REVERT: K 47 ILE cc_start: 0.7215 (pt) cc_final: 0.6962 (pt) REVERT: K 116 GLU cc_start: 0.7552 (tp30) cc_final: 0.7174 (tp30) REVERT: K 130 LYS cc_start: 0.7560 (ttpp) cc_final: 0.6761 (ttmt) REVERT: L 31 GLU cc_start: 0.7406 (tt0) cc_final: 0.6507 (tp30) REVERT: M 13 LYS cc_start: 0.5674 (mttm) cc_final: 0.5267 (mmtt) REVERT: M 38 LYS cc_start: 0.6156 (mttt) cc_final: 0.5756 (mttm) REVERT: N 5 LYS cc_start: 0.7264 (tttt) cc_final: 0.6705 (tptp) REVERT: N 8 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6393 (mm-30) REVERT: N 13 SER cc_start: 0.8140 (p) cc_final: 0.7881 (p) REVERT: N 93 LYS cc_start: 0.7470 (tttt) cc_final: 0.6789 (tmtt) REVERT: N 96 ARG cc_start: 0.7321 (OUTLIER) cc_final: 0.6718 (mmt-90) REVERT: O 59 LYS cc_start: 0.7673 (ttpt) cc_final: 0.7230 (ttmt) REVERT: O 80 MET cc_start: 0.7701 (mmm) cc_final: 0.7236 (mmm) REVERT: P 15 GLU cc_start: 0.7160 (mt-10) cc_final: 0.6369 (mp0) REVERT: P 37 LYS cc_start: 0.7759 (mppt) cc_final: 0.7098 (mmtt) REVERT: P 47 LYS cc_start: 0.8059 (mttt) cc_final: 0.7736 (mtpt) REVERT: P 69 LYS cc_start: 0.7918 (tttt) cc_final: 0.7595 (tttm) REVERT: Q 8 ARG cc_start: 0.7070 (mtp-110) cc_final: 0.6651 (mtt90) REVERT: Q 28 ASN cc_start: 0.8006 (OUTLIER) cc_final: 0.7787 (p0) REVERT: Q 59 GLU cc_start: 0.7059 (tt0) cc_final: 0.6359 (mt-10) REVERT: Q 72 LYS cc_start: 0.7938 (mtpp) cc_final: 0.7445 (ttpt) REVERT: Q 106 VAL cc_start: 0.7621 (OUTLIER) cc_final: 0.7414 (t) REVERT: R 9 ARG cc_start: 0.6831 (OUTLIER) cc_final: 0.6571 (mtm-85) REVERT: R 28 ASP cc_start: 0.7707 (t70) cc_final: 0.7348 (m-30) REVERT: S 19 LYS cc_start: 0.7538 (ttmp) cc_final: 0.7094 (ttmt) REVERT: S 29 LYS cc_start: 0.6340 (ptpt) cc_final: 0.5917 (ttmm) REVERT: T 15 ARG cc_start: 0.7108 (OUTLIER) cc_final: 0.5076 (mpp80) REVERT: T 19 LYS cc_start: 0.6084 (ptpt) cc_final: 0.5132 (pttt) REVERT: T 83 LYS cc_start: 0.7155 (OUTLIER) cc_final: 0.6931 (ptmm) REVERT: U 19 LYS cc_start: 0.6896 (ptmm) cc_final: 0.6671 (ptpt) REVERT: U 25 GLU cc_start: 0.6391 (mt-10) cc_final: 0.5715 (mp0) REVERT: U 61 ARG cc_start: 0.7387 (ttt180) cc_final: 0.6855 (ttt180) REVERT: U 72 ASP cc_start: 0.7146 (p0) cc_final: 0.6756 (p0) REVERT: U 76 LYS cc_start: 0.7627 (mmtt) cc_final: 0.6852 (mmmt) REVERT: U 79 ARG cc_start: 0.7640 (ptp-170) cc_final: 0.7371 (ptp-170) REVERT: V 22 LEU cc_start: 0.7670 (mp) cc_final: 0.7316 (mm) REVERT: W 17 GLN cc_start: 0.7202 (tp-100) cc_final: 0.6876 (mm-40) REVERT: W 20 SER cc_start: 0.7448 (t) cc_final: 0.7073 (m) REVERT: W 23 GLU cc_start: 0.6689 (mt-10) cc_final: 0.5907 (mp0) REVERT: X 3 LYS cc_start: 0.7612 (mmtp) cc_final: 0.7251 (mmtp) REVERT: X 57 GLU cc_start: 0.6703 (mt-10) cc_final: 0.6425 (tm-30) REVERT: Z 37 LYS cc_start: 0.6394 (pttt) cc_final: 0.5754 (pttp) REVERT: 2 37 ARG cc_start: 0.6863 (ttp-110) cc_final: 0.6412 (ttt-90) REVERT: 4 2 LYS cc_start: 0.7227 (mtmt) cc_final: 0.6854 (mtmm) REVERT: 4 13 LYS cc_start: 0.6529 (mttt) cc_final: 0.6131 (mmtm) REVERT: 4 24 MET cc_start: 0.7771 (mtt) cc_final: 0.7443 (mtp) outliers start: 144 outliers final: 63 residues processed: 561 average time/residue: 1.9309 time to fit residues: 1415.3486 Evaluate side-chains 512 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 427 time to evaluate : 3.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 261 ARG Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 163 ARG Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 42 LYS Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 16 ARG Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 69 ILE Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 131 SER Chi-restraints excluded: chain K residue 5 LYS Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain L residue 9 THR Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 29 ARG Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 49 LYS Chi-restraints excluded: chain N residue 8 GLU Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 96 ARG Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain O residue 63 THR Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain Q residue 17 VAL Chi-restraints excluded: chain Q residue 28 ASN Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 9 ARG Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 27 LEU Chi-restraints excluded: chain S residue 63 ILE Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain T residue 15 ARG Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain T residue 83 LYS Chi-restraints excluded: chain U residue 75 VAL Chi-restraints excluded: chain U residue 87 VAL Chi-restraints excluded: chain V residue 27 ARG Chi-restraints excluded: chain W residue 11 THR Chi-restraints excluded: chain X residue 35 VAL Chi-restraints excluded: chain X residue 55 THR Chi-restraints excluded: chain Z residue 18 THR Chi-restraints excluded: chain 2 residue 2 VAL Chi-restraints excluded: chain 2 residue 31 VAL Chi-restraints excluded: chain 3 residue 15 LYS 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: 9.9990 chunk 356 optimal weight: 10.0000 chunk 532 optimal weight: 5.9990 chunk 563 optimal weight: 10.0000 chunk 278 optimal weight: 20.0000 chunk 504 optimal weight: 10.0000 chunk 151 optimal weight: 30.0000 overall best weight: 8.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 200 HIS D 50 GLN D 187 GLN E 40 GLN E 182 ASN G 111 HIS H 104 ASN O 91 ASN Q 60 HIS Q 61 ASN S 67 ASN T 85 GLN V 23 ASN 3 60 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.109 94015 Z= 0.380 Angle : 0.884 40.809 141541 Z= 0.446 Chirality : 0.047 0.376 18278 Planarity : 0.008 0.164 6962 Dihedral : 23.195 179.798 48983 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 7.55 % Allowed : 16.00 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.14), residues: 2985 helix: -1.06 (0.18), residues: 741 sheet: -0.63 (0.20), residues: 622 loop : -1.89 (0.13), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP C 250 HIS 0.026 0.003 HIS C 232 PHE 0.026 0.003 PHE E 90 TYR 0.039 0.003 TYR J 74 ARG 0.015 0.001 ARG J 33 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 444 time to evaluate : 3.423 Fit side-chains TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. REVERT: C 130 LEU cc_start: 0.7076 (OUTLIER) cc_final: 0.6609 (pt) REVERT: C 236 GLU cc_start: 0.7437 (mm-30) cc_final: 0.7109 (mm-30) REVERT: C 252 LYS cc_start: 0.7730 (OUTLIER) cc_final: 0.7197 (mptt) REVERT: D 23 ILE cc_start: 0.7235 (OUTLIER) cc_final: 0.6581 (tt) REVERT: D 42 GLU cc_start: 0.7069 (OUTLIER) cc_final: 0.6806 (pt0) REVERT: D 141 MET cc_start: 0.8378 (mmp) cc_final: 0.8169 (mmp) REVERT: D 184 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6722 (tt0) REVERT: E 100 LYS cc_start: 0.7667 (mttt) cc_final: 0.6558 (pttp) REVERT: E 107 ARG cc_start: 0.6820 (mtp85) cc_final: 0.6448 (mtt-85) REVERT: E 200 LYS cc_start: 0.6531 (mmpt) cc_final: 0.6013 (mtpt) REVERT: G 53 VAL cc_start: 0.4512 (t) cc_final: 0.4268 (p) REVERT: G 62 ARG cc_start: 0.5088 (ttp-110) cc_final: 0.4854 (mtm-85) REVERT: G 85 LYS cc_start: 0.4866 (OUTLIER) cc_final: 0.4060 (tppp) REVERT: G 98 MET cc_start: 0.5345 (mmt) cc_final: 0.4462 (mmm) REVERT: G 119 GLU cc_start: 0.6370 (mt-10) cc_final: 0.5976 (mp0) REVERT: G 163 ARG cc_start: 0.6007 (OUTLIER) cc_final: 0.5804 (ptp-170) REVERT: H 1 MET cc_start: 0.7739 (OUTLIER) cc_final: 0.6440 (mtt) REVERT: H 15 LYS cc_start: 0.7379 (ptmt) cc_final: 0.6978 (ptpt) REVERT: H 19 ILE cc_start: 0.8048 (OUTLIER) cc_final: 0.7657 (mm) REVERT: H 32 GLU cc_start: 0.6754 (mm-30) cc_final: 0.6308 (mm-30) REVERT: H 42 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.7899 (mttt) REVERT: H 65 PHE cc_start: 0.8283 (m-80) cc_final: 0.8051 (m-10) REVERT: H 117 GLU cc_start: 0.6862 (mm-30) cc_final: 0.6533 (tp30) REVERT: H 118 LYS cc_start: 0.7251 (tttt) cc_final: 0.6718 (ttpp) REVERT: H 130 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7073 (mm-30) REVERT: I 5 GLU cc_start: 0.7380 (mt-10) cc_final: 0.7046 (mm-30) REVERT: I 9 LYS cc_start: 0.7149 (ttmt) cc_final: 0.6638 (mmpt) REVERT: I 18 GLU cc_start: 0.7946 (tt0) cc_final: 0.7608 (tt0) REVERT: I 59 LYS cc_start: 0.8265 (mttp) cc_final: 0.8009 (mttp) REVERT: I 66 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7482 (ttmt) REVERT: I 104 ARG cc_start: 0.6374 (ttm-80) cc_final: 0.6004 (ttp80) REVERT: J 6 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7453 (pp) REVERT: J 16 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.6634 (ptt180) REVERT: J 84 LYS cc_start: 0.6897 (ptmt) cc_final: 0.6299 (pttp) REVERT: J 99 SER cc_start: 0.7040 (t) cc_final: 0.6697 (p) REVERT: K 5 LYS cc_start: 0.7557 (OUTLIER) cc_final: 0.7014 (mppt) REVERT: K 20 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.7002 (mpt180) REVERT: K 116 GLU cc_start: 0.7588 (tp30) cc_final: 0.7225 (tp30) REVERT: K 130 LYS cc_start: 0.7669 (ttpp) cc_final: 0.6808 (ttmt) REVERT: L 31 GLU cc_start: 0.7384 (tt0) cc_final: 0.6506 (tp30) REVERT: L 88 GLU cc_start: 0.7188 (mt-10) cc_final: 0.6836 (mt-10) REVERT: M 9 LYS cc_start: 0.6096 (mtmt) cc_final: 0.5531 (mtpt) REVERT: M 13 LYS cc_start: 0.5586 (mttm) cc_final: 0.5237 (mmtt) REVERT: M 38 LYS cc_start: 0.6185 (mttt) cc_final: 0.5920 (mtpt) REVERT: M 75 LYS cc_start: 0.7237 (mttm) cc_final: 0.6949 (mtpt) REVERT: N 93 LYS cc_start: 0.7565 (tttt) cc_final: 0.6847 (tptp) REVERT: N 96 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.6896 (mmt-90) REVERT: O 59 LYS cc_start: 0.7830 (ttpt) cc_final: 0.7316 (ttmt) REVERT: P 15 GLU cc_start: 0.7266 (mt-10) cc_final: 0.6434 (mp0) REVERT: P 37 LYS cc_start: 0.7703 (mppt) cc_final: 0.7226 (mptt) REVERT: P 47 LYS cc_start: 0.7964 (mttt) cc_final: 0.7648 (mtpt) REVERT: P 69 LYS cc_start: 0.8058 (tttt) cc_final: 0.7744 (tttm) REVERT: Q 8 ARG cc_start: 0.7181 (mtp-110) cc_final: 0.6705 (mtt90) REVERT: Q 19 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.8039 (mp) REVERT: Q 28 ASN cc_start: 0.7967 (OUTLIER) cc_final: 0.7694 (p0) REVERT: Q 52 MET cc_start: 0.8017 (OUTLIER) cc_final: 0.7569 (mmp) REVERT: Q 59 GLU cc_start: 0.7224 (tt0) cc_final: 0.6496 (mt-10) REVERT: Q 90 GLN cc_start: 0.7394 (OUTLIER) cc_final: 0.6647 (mt0) REVERT: R 9 ARG cc_start: 0.6809 (OUTLIER) cc_final: 0.6547 (mtm-85) REVERT: R 28 ASP cc_start: 0.7493 (t70) cc_final: 0.7243 (m-30) REVERT: S 19 LYS cc_start: 0.7570 (ttmp) cc_final: 0.7141 (ttmt) REVERT: S 29 LYS cc_start: 0.6502 (ptpt) cc_final: 0.6149 (ttmm) REVERT: T 13 GLN cc_start: 0.7082 (mp10) cc_final: 0.6809 (mp10) REVERT: T 15 ARG cc_start: 0.7236 (OUTLIER) cc_final: 0.5084 (mpp80) REVERT: T 63 LEU cc_start: 0.6880 (OUTLIER) cc_final: 0.6446 (tt) REVERT: U 19 LYS cc_start: 0.6922 (ptmm) cc_final: 0.6691 (ptpt) REVERT: U 25 GLU cc_start: 0.6366 (mt-10) cc_final: 0.5858 (mp0) REVERT: U 61 ARG cc_start: 0.7462 (ttt180) cc_final: 0.6920 (ttt180) REVERT: U 72 ASP cc_start: 0.6950 (p0) cc_final: 0.6602 (p0) REVERT: U 76 LYS cc_start: 0.7586 (mmtt) cc_final: 0.6791 (mmmt) REVERT: V 22 LEU cc_start: 0.7697 (mp) cc_final: 0.7320 (mm) REVERT: W 17 GLN cc_start: 0.7144 (tp-100) cc_final: 0.6616 (mm-40) REVERT: W 28 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6912 (mp) REVERT: X 3 LYS cc_start: 0.7539 (mmtp) cc_final: 0.7175 (mmtp) REVERT: Z 37 LYS cc_start: 0.6547 (pttt) cc_final: 0.6230 (pttp) REVERT: 2 37 ARG cc_start: 0.6992 (ttp-110) cc_final: 0.6479 (ttt-90) REVERT: 2 41 LYS cc_start: 0.8219 (tttt) cc_final: 0.8008 (tmtp) REVERT: 4 2 LYS cc_start: 0.7020 (mtmt) cc_final: 0.6818 (mtmm) REVERT: 4 13 LYS cc_start: 0.6203 (mttt) cc_final: 0.5797 (mmtm) REVERT: 4 24 MET cc_start: 0.7827 (mtt) cc_final: 0.7482 (mtp) REVERT: 4 33 LYS cc_start: 0.6934 (OUTLIER) cc_final: 0.6070 (mtmt) outliers start: 175 outliers final: 90 residues processed: 560 average time/residue: 1.9514 time to fit residues: 1428.2536 Evaluate side-chains 547 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 433 time to evaluate : 3.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain G residue 85 LYS Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain G residue 163 ARG Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 42 LYS Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 66 LYS Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 16 ARG Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 131 SER Chi-restraints excluded: chain K residue 5 LYS Chi-restraints excluded: chain K residue 20 ARG Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain L residue 9 THR Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 49 LYS Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain N residue 7 ILE Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 96 ARG Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain O residue 63 THR Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 63 ASN Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain Q residue 17 VAL Chi-restraints excluded: chain Q residue 19 LEU Chi-restraints excluded: chain Q residue 28 ASN Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 90 GLN Chi-restraints excluded: chain Q residue 92 ARG Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 9 ARG Chi-restraints excluded: chain R residue 75 ARG Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 27 LEU Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain T residue 15 ARG Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain U residue 75 VAL Chi-restraints excluded: chain U residue 87 VAL Chi-restraints excluded: chain V residue 27 ARG Chi-restraints excluded: chain W residue 11 THR Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 45 THR Chi-restraints excluded: chain X residue 13 ILE Chi-restraints excluded: chain X residue 35 VAL Chi-restraints excluded: chain X residue 55 THR Chi-restraints excluded: chain Z residue 18 THR Chi-restraints excluded: chain 1 residue 44 LEU Chi-restraints excluded: chain 2 residue 2 VAL Chi-restraints excluded: chain 2 residue 31 VAL Chi-restraints excluded: chain 3 residue 15 LYS Chi-restraints excluded: chain 3 residue 35 ASN Chi-restraints excluded: chain 4 residue 33 LYS Chi-restraints excluded: chain 4 residue 35 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 583 random chunks: chunk 469 optimal weight: 10.0000 chunk 319 optimal weight: 8.9990 chunk 8 optimal weight: 20.0000 chunk 419 optimal weight: 9.9990 chunk 232 optimal weight: 10.0000 chunk 480 optimal weight: 5.9990 chunk 389 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 287 optimal weight: 40.0000 chunk 505 optimal weight: 0.9990 chunk 142 optimal weight: 20.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 50 GLN Q 61 ASN S 67 ASN ** T 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 23 ASN 3 60 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 94015 Z= 0.298 Angle : 0.776 40.552 141541 Z= 0.396 Chirality : 0.043 0.354 18278 Planarity : 0.007 0.136 6962 Dihedral : 23.066 176.647 48983 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 7.16 % Allowed : 17.25 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.14), residues: 2985 helix: -0.72 (0.19), residues: 741 sheet: -0.55 (0.20), residues: 620 loop : -1.80 (0.13), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 250 HIS 0.014 0.002 HIS J 35 PHE 0.023 0.002 PHE E 90 TYR 0.023 0.002 TYR J 74 ARG 0.010 0.001 ARG J 33 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 438 time to evaluate : 3.432 Fit side-chains TARDY: cannot create tardy model for: "LYS G 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. REVERT: C 30 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7026 (tp30) REVERT: C 130 LEU cc_start: 0.6975 (OUTLIER) cc_final: 0.6539 (pt) REVERT: C 236 GLU cc_start: 0.7529 (mm-30) cc_final: 0.7191 (mm-30) REVERT: C 252 LYS cc_start: 0.7679 (OUTLIER) cc_final: 0.7214 (mptt) REVERT: D 23 ILE cc_start: 0.7200 (OUTLIER) cc_final: 0.6298 (mt) REVERT: D 42 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.6808 (pm20) REVERT: D 184 GLU cc_start: 0.7160 (mt-10) cc_final: 0.6751 (tt0) REVERT: E 13 LYS cc_start: 0.6525 (OUTLIER) cc_final: 0.6206 (mtpt) REVERT: E 100 LYS cc_start: 0.7701 (mttt) cc_final: 0.6586 (pttp) REVERT: E 107 ARG cc_start: 0.6801 (mtp85) cc_final: 0.6432 (mtt-85) REVERT: E 200 LYS cc_start: 0.6480 (mmpt) cc_final: 0.5962 (mtpt) REVERT: G 53 VAL cc_start: 0.4828 (t) cc_final: 0.4569 (p) REVERT: G 85 LYS cc_start: 0.4802 (OUTLIER) cc_final: 0.3989 (tppp) REVERT: G 98 MET cc_start: 0.5382 (mmt) cc_final: 0.4541 (mmm) REVERT: G 119 GLU cc_start: 0.6597 (mt-10) cc_final: 0.6087 (mp0) REVERT: H 1 MET cc_start: 0.7737 (OUTLIER) cc_final: 0.6553 (mtt) REVERT: H 19 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7604 (mm) REVERT: H 32 GLU cc_start: 0.6840 (mm-30) cc_final: 0.6334 (mm-30) REVERT: H 42 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.7834 (mttt) REVERT: H 65 PHE cc_start: 0.8267 (m-80) cc_final: 0.8003 (m-10) REVERT: H 117 GLU cc_start: 0.6834 (mm-30) cc_final: 0.6466 (tp30) REVERT: H 118 LYS cc_start: 0.7222 (tttt) cc_final: 0.6697 (ttpp) REVERT: H 130 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7112 (mm-30) REVERT: I 5 GLU cc_start: 0.7355 (mt-10) cc_final: 0.7046 (mm-30) REVERT: I 9 LYS cc_start: 0.7085 (ttmt) cc_final: 0.6518 (mmtt) REVERT: I 18 GLU cc_start: 0.7887 (tt0) cc_final: 0.7686 (tt0) REVERT: I 59 LYS cc_start: 0.8306 (mttp) cc_final: 0.8010 (mttp) REVERT: I 66 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7458 (ttmt) REVERT: I 88 ARG cc_start: 0.6807 (OUTLIER) cc_final: 0.6239 (ttt90) REVERT: I 104 ARG cc_start: 0.6266 (ttm-80) cc_final: 0.6010 (ttp80) REVERT: J 6 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7414 (pp) REVERT: J 16 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.6719 (ptt180) REVERT: J 84 LYS cc_start: 0.6942 (ptmt) cc_final: 0.6318 (pttp) REVERT: J 99 SER cc_start: 0.7083 (t) cc_final: 0.6815 (p) REVERT: J 121 LEU cc_start: 0.7264 (OUTLIER) cc_final: 0.6742 (pp) REVERT: K 5 LYS cc_start: 0.7510 (OUTLIER) cc_final: 0.6973 (mppt) REVERT: K 6 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.7308 (ptm160) REVERT: K 20 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.7335 (mpt180) REVERT: K 42 ILE cc_start: 0.7764 (OUTLIER) cc_final: 0.7277 (mm) REVERT: K 116 GLU cc_start: 0.7608 (tp30) cc_final: 0.7241 (tp30) REVERT: K 130 LYS cc_start: 0.7660 (ttpp) cc_final: 0.6797 (ttmt) REVERT: L 31 GLU cc_start: 0.7358 (tt0) cc_final: 0.6494 (tp30) REVERT: L 53 LYS cc_start: 0.7135 (OUTLIER) cc_final: 0.6925 (mttt) REVERT: M 9 LYS cc_start: 0.6162 (mtmt) cc_final: 0.5576 (mtpt) REVERT: M 13 LYS cc_start: 0.5464 (mttm) cc_final: 0.5083 (mmtt) REVERT: N 93 LYS cc_start: 0.7579 (tttt) cc_final: 0.6816 (tmtt) REVERT: N 96 ARG cc_start: 0.7403 (OUTLIER) cc_final: 0.5408 (mtt180) REVERT: O 59 LYS cc_start: 0.7790 (ttpt) cc_final: 0.7320 (ttmm) REVERT: P 15 GLU cc_start: 0.7112 (mt-10) cc_final: 0.6828 (mt-10) REVERT: P 37 LYS cc_start: 0.7538 (mppt) cc_final: 0.7078 (mptt) REVERT: P 47 LYS cc_start: 0.8015 (mttt) cc_final: 0.7687 (mtpt) REVERT: P 69 LYS cc_start: 0.8026 (tttt) cc_final: 0.7711 (tttm) REVERT: Q 8 ARG cc_start: 0.7099 (mtp-110) cc_final: 0.6702 (mtt90) REVERT: Q 59 GLU cc_start: 0.7176 (tt0) cc_final: 0.6447 (mt-10) REVERT: R 9 ARG cc_start: 0.6875 (OUTLIER) cc_final: 0.6605 (mtm-85) REVERT: R 28 ASP cc_start: 0.7485 (t70) cc_final: 0.7244 (m-30) REVERT: R 65 MET cc_start: 0.5773 (OUTLIER) cc_final: 0.4646 (tmt) REVERT: S 19 LYS cc_start: 0.7610 (ttmp) cc_final: 0.7171 (ttmt) REVERT: S 29 LYS cc_start: 0.6514 (ptpt) cc_final: 0.6229 (ttmm) REVERT: S 30 LYS cc_start: 0.6427 (OUTLIER) cc_final: 0.5963 (mtmm) REVERT: T 13 GLN cc_start: 0.7055 (mp10) cc_final: 0.6791 (mp10) REVERT: T 15 ARG cc_start: 0.7035 (OUTLIER) cc_final: 0.4895 (mpp80) REVERT: T 63 LEU cc_start: 0.6780 (OUTLIER) cc_final: 0.6395 (tt) REVERT: U 19 LYS cc_start: 0.6897 (ptmm) cc_final: 0.6655 (ptpt) REVERT: U 25 GLU cc_start: 0.6258 (mt-10) cc_final: 0.5735 (mp0) REVERT: U 61 ARG cc_start: 0.7471 (ttt180) cc_final: 0.6983 (ttt180) REVERT: U 76 LYS cc_start: 0.7720 (mmtt) cc_final: 0.6946 (mmmt) REVERT: V 22 LEU cc_start: 0.7649 (mp) cc_final: 0.7291 (mm) REVERT: W 17 GLN cc_start: 0.7191 (tp-100) cc_final: 0.6633 (mm-40) REVERT: W 30 PHE cc_start: 0.7094 (OUTLIER) cc_final: 0.6115 (t80) REVERT: W 39 GLU cc_start: 0.6307 (OUTLIER) cc_final: 0.5842 (mp0) REVERT: X 3 LYS cc_start: 0.7555 (mmtp) cc_final: 0.7176 (mmtp) REVERT: X 10 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.7095 (mmt180) REVERT: Z 37 LYS cc_start: 0.6475 (pttt) cc_final: 0.6141 (pttp) REVERT: 2 37 ARG cc_start: 0.6992 (ttp-110) cc_final: 0.6480 (ttt-90) REVERT: 2 41 LYS cc_start: 0.8212 (tttt) cc_final: 0.7997 (tmtp) REVERT: 4 13 LYS cc_start: 0.6373 (mttt) cc_final: 0.5942 (mmtm) REVERT: 4 24 MET cc_start: 0.7825 (mtt) cc_final: 0.7485 (mtp) REVERT: 4 33 LYS cc_start: 0.6984 (OUTLIER) cc_final: 0.6109 (mtmt) outliers start: 166 outliers final: 97 residues processed: 539 average time/residue: 1.9238 time to fit residues: 1354.8033 Evaluate side-chains 555 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 428 time to evaluate : 3.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 13 LYS Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain G residue 85 LYS Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 42 LYS Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 4 GLN Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 66 LYS Chi-restraints excluded: chain I residue 88 ARG Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 16 ARG Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 131 SER Chi-restraints excluded: chain K residue 5 LYS Chi-restraints excluded: chain K residue 6 ARG Chi-restraints excluded: chain K residue 20 ARG Chi-restraints excluded: chain K residue 39 THR Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain L residue 9 THR Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 29 ARG Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 53 LYS Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 49 LYS Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 96 ARG Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain O residue 63 THR Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 63 ASN Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain Q residue 17 VAL Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 92 ARG Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 9 ARG Chi-restraints excluded: chain R residue 14 GLU Chi-restraints excluded: chain R residue 20 MET Chi-restraints excluded: chain R residue 65 MET Chi-restraints excluded: chain R residue 75 ARG Chi-restraints excluded: chain S residue 5 LYS Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 27 LEU Chi-restraints excluded: chain S residue 30 LYS Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain T residue 15 ARG Chi-restraints excluded: chain T residue 19 LYS Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain U residue 75 VAL Chi-restraints excluded: chain U residue 87 VAL Chi-restraints excluded: chain V residue 27 ARG Chi-restraints excluded: chain W residue 11 THR Chi-restraints excluded: chain W residue 30 PHE Chi-restraints excluded: chain W residue 39 GLU Chi-restraints excluded: chain W residue 45 THR Chi-restraints excluded: chain X residue 10 ARG Chi-restraints excluded: chain X residue 13 ILE Chi-restraints excluded: chain X residue 35 VAL Chi-restraints excluded: chain X residue 55 THR Chi-restraints excluded: chain Z residue 18 THR Chi-restraints excluded: chain 2 residue 2 VAL Chi-restraints excluded: chain 2 residue 31 VAL Chi-restraints excluded: chain 3 residue 15 LYS Chi-restraints excluded: chain 4 residue 33 LYS Chi-restraints excluded: chain 4 residue 35 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 583 random chunks: chunk 189 optimal weight: 20.0000 chunk 507 optimal weight: 2.9990 chunk 111 optimal weight: 10.0000 chunk 330 optimal weight: 0.3980 chunk 139 optimal weight: 30.0000 chunk 564 optimal weight: 20.0000 chunk 468 optimal weight: 9.9990 chunk 261 optimal weight: 10.0000 chunk 46 optimal weight: 20.0000 chunk 186 optimal weight: 50.0000 chunk 296 optimal weight: 9.9990 overall best weight: 6.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 199 GLN D 50 GLN I 72 ASN O 91 ASN Q 61 ASN R 37 GLN S 67 ASN ** T 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 23 ASN 3 60 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 94015 Z= 0.286 Angle : 0.767 40.547 141541 Z= 0.392 Chirality : 0.042 0.350 18278 Planarity : 0.007 0.132 6962 Dihedral : 23.074 176.501 48983 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 7.37 % Allowed : 17.34 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.14), residues: 2985 helix: -0.47 (0.19), residues: 736 sheet: -0.48 (0.20), residues: 637 loop : -1.72 (0.14), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 250 HIS 0.013 0.002 HIS J 35 PHE 0.022 0.002 PHE O 57 TYR 0.023 0.002 TYR J 74 ARG 0.010 0.001 ARG J 33 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 434 time to evaluate : 3.767 Fit side-chains TARDY: cannot create tardy model for: "LYS G 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. REVERT: C 130 LEU cc_start: 0.7055 (OUTLIER) cc_final: 0.6617 (pt) REVERT: C 236 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7123 (mm-30) REVERT: C 252 LYS cc_start: 0.7597 (OUTLIER) cc_final: 0.7066 (mptt) REVERT: D 23 ILE cc_start: 0.7211 (OUTLIER) cc_final: 0.6231 (mt) REVERT: D 42 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6799 (pm20) REVERT: D 141 MET cc_start: 0.8247 (mmp) cc_final: 0.8046 (mmp) REVERT: D 184 GLU cc_start: 0.7143 (mt-10) cc_final: 0.6742 (tt0) REVERT: E 13 LYS cc_start: 0.6517 (OUTLIER) cc_final: 0.6218 (mtpt) REVERT: E 62 ARG cc_start: 0.7470 (OUTLIER) cc_final: 0.7036 (ttm-80) REVERT: E 100 LYS cc_start: 0.7623 (mttt) cc_final: 0.6544 (pttp) REVERT: E 107 ARG cc_start: 0.6813 (mtp85) cc_final: 0.6492 (mtt-85) REVERT: E 200 LYS cc_start: 0.6480 (mmpt) cc_final: 0.5960 (mtpt) REVERT: G 53 VAL cc_start: 0.5012 (t) cc_final: 0.4759 (p) REVERT: G 85 LYS cc_start: 0.4835 (OUTLIER) cc_final: 0.4022 (tppp) REVERT: G 98 MET cc_start: 0.5346 (mmt) cc_final: 0.4527 (mmp) REVERT: G 119 GLU cc_start: 0.6505 (mt-10) cc_final: 0.5908 (mp0) REVERT: H 1 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.6536 (mtt) REVERT: H 19 ILE cc_start: 0.8074 (OUTLIER) cc_final: 0.7636 (mm) REVERT: H 32 GLU cc_start: 0.6812 (mm-30) cc_final: 0.6335 (mm-30) REVERT: H 42 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.7858 (mttt) REVERT: H 62 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7526 (mmtp) REVERT: H 117 GLU cc_start: 0.6811 (mm-30) cc_final: 0.6445 (tp30) REVERT: H 118 LYS cc_start: 0.7216 (tttt) cc_final: 0.6743 (ttpp) REVERT: H 130 GLU cc_start: 0.7390 (mm-30) cc_final: 0.7002 (mm-30) REVERT: I 5 GLU cc_start: 0.7374 (mt-10) cc_final: 0.7031 (mm-30) REVERT: I 9 LYS cc_start: 0.7095 (ttmt) cc_final: 0.6618 (mmtt) REVERT: I 18 GLU cc_start: 0.7958 (tt0) cc_final: 0.7745 (tt0) REVERT: I 66 LYS cc_start: 0.7815 (OUTLIER) cc_final: 0.7440 (ttmt) REVERT: I 104 ARG cc_start: 0.6253 (ttm-80) cc_final: 0.6011 (ttp80) REVERT: J 6 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7432 (pp) REVERT: J 16 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.6655 (ptt180) REVERT: J 84 LYS cc_start: 0.6950 (ptmt) cc_final: 0.6325 (pttp) REVERT: J 99 SER cc_start: 0.7128 (t) cc_final: 0.6923 (p) REVERT: J 120 LYS cc_start: 0.6131 (OUTLIER) cc_final: 0.5335 (tptt) REVERT: J 121 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.6667 (pp) REVERT: J 123 VAL cc_start: 0.7136 (m) cc_final: 0.6862 (t) REVERT: K 5 LYS cc_start: 0.7540 (OUTLIER) cc_final: 0.7250 (mtpt) REVERT: K 20 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.7264 (mpt180) REVERT: K 42 ILE cc_start: 0.7717 (OUTLIER) cc_final: 0.7241 (mm) REVERT: K 116 GLU cc_start: 0.7574 (tp30) cc_final: 0.7211 (tp30) REVERT: K 130 LYS cc_start: 0.7682 (ttpp) cc_final: 0.6785 (tttt) REVERT: L 31 GLU cc_start: 0.7350 (tt0) cc_final: 0.6481 (tp30) REVERT: L 53 LYS cc_start: 0.7134 (OUTLIER) cc_final: 0.6883 (mttt) REVERT: M 9 LYS cc_start: 0.6141 (mtmt) cc_final: 0.5611 (mtmt) REVERT: M 13 LYS cc_start: 0.5512 (mttm) cc_final: 0.5166 (mmtt) REVERT: N 93 LYS cc_start: 0.7621 (tttt) cc_final: 0.6867 (tmtt) REVERT: N 96 ARG cc_start: 0.7404 (OUTLIER) cc_final: 0.5386 (mtt180) REVERT: O 59 LYS cc_start: 0.7790 (ttpt) cc_final: 0.7284 (ttmt) REVERT: P 12 ILE cc_start: 0.7784 (OUTLIER) cc_final: 0.7351 (mm) REVERT: P 15 GLU cc_start: 0.7068 (mt-10) cc_final: 0.6706 (mt-10) REVERT: P 37 LYS cc_start: 0.7543 (mppt) cc_final: 0.7070 (mptt) REVERT: P 47 LYS cc_start: 0.7936 (mttt) cc_final: 0.7662 (mttm) REVERT: P 69 LYS cc_start: 0.8002 (tttt) cc_final: 0.7694 (tttm) REVERT: P 94 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7336 (tttt) REVERT: Q 8 ARG cc_start: 0.7142 (mtp-110) cc_final: 0.6748 (mtt90) REVERT: Q 52 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.7605 (mmp) REVERT: Q 59 GLU cc_start: 0.7188 (tt0) cc_final: 0.6378 (mt-10) REVERT: R 9 ARG cc_start: 0.6867 (OUTLIER) cc_final: 0.6581 (mtm-85) REVERT: R 28 ASP cc_start: 0.7487 (t70) cc_final: 0.7245 (m-30) REVERT: R 49 LYS cc_start: 0.7240 (mptm) cc_final: 0.6972 (mptm) REVERT: R 65 MET cc_start: 0.5639 (OUTLIER) cc_final: 0.4441 (tmt) REVERT: S 19 LYS cc_start: 0.7742 (ttmp) cc_final: 0.7316 (ttmt) REVERT: S 29 LYS cc_start: 0.6441 (ptpt) cc_final: 0.6223 (ttmm) REVERT: S 30 LYS cc_start: 0.6446 (OUTLIER) cc_final: 0.6005 (mtmm) REVERT: T 13 GLN cc_start: 0.7093 (mp10) cc_final: 0.6844 (mp10) REVERT: T 15 ARG cc_start: 0.7051 (OUTLIER) cc_final: 0.4943 (mpp80) REVERT: T 63 LEU cc_start: 0.6731 (OUTLIER) cc_final: 0.6331 (tt) REVERT: U 19 LYS cc_start: 0.6868 (ptmm) cc_final: 0.6644 (ptpt) REVERT: U 25 GLU cc_start: 0.6366 (mt-10) cc_final: 0.5873 (mp0) REVERT: U 61 ARG cc_start: 0.7448 (ttt180) cc_final: 0.6990 (ttt180) REVERT: U 76 LYS cc_start: 0.7658 (mmtt) cc_final: 0.6926 (mmmt) REVERT: V 22 LEU cc_start: 0.7701 (mp) cc_final: 0.7344 (mm) REVERT: W 17 GLN cc_start: 0.7203 (tp-100) cc_final: 0.6596 (mm-40) REVERT: W 30 PHE cc_start: 0.7340 (OUTLIER) cc_final: 0.6447 (t80) REVERT: W 52 ARG cc_start: 0.6547 (OUTLIER) cc_final: 0.5212 (mtm180) REVERT: X 3 LYS cc_start: 0.7574 (mmtp) cc_final: 0.7299 (mmtp) REVERT: Z 37 LYS cc_start: 0.6463 (pttt) cc_final: 0.6147 (pttp) REVERT: 2 12 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.6530 (tttt) REVERT: 2 37 ARG cc_start: 0.6972 (ttp-110) cc_final: 0.6462 (ttt-90) REVERT: 2 41 LYS cc_start: 0.8227 (tttt) cc_final: 0.8019 (tmtp) REVERT: 4 10 ILE cc_start: 0.7106 (OUTLIER) cc_final: 0.6898 (mm) REVERT: 4 13 LYS cc_start: 0.6321 (mttt) cc_final: 0.6007 (mttm) REVERT: 4 24 MET cc_start: 0.7765 (mtt) cc_final: 0.7429 (mtp) REVERT: 4 33 LYS cc_start: 0.7039 (OUTLIER) cc_final: 0.6227 (mtmt) outliers start: 171 outliers final: 106 residues processed: 546 average time/residue: 1.9767 time to fit residues: 1413.0552 Evaluate side-chains 565 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 425 time to evaluate : 3.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 13 LYS Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain G residue 30 LYS Chi-restraints excluded: chain G residue 85 LYS Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 42 LYS Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain H residue 70 GLU Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 4 GLN Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 66 LYS Chi-restraints excluded: chain I residue 72 ASN Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 16 ARG Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 120 LYS Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 131 SER Chi-restraints excluded: chain K residue 5 LYS Chi-restraints excluded: chain K residue 6 ARG Chi-restraints excluded: chain K residue 20 ARG Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain K residue 129 THR Chi-restraints excluded: chain L residue 9 THR Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 29 ARG Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 53 LYS Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 49 LYS Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain N residue 7 ILE Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 96 ARG Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain O residue 63 THR Chi-restraints excluded: chain P residue 12 ILE Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 63 ASN Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain P residue 94 LYS Chi-restraints excluded: chain Q residue 17 VAL Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 92 ARG Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 9 ARG Chi-restraints excluded: chain R residue 14 GLU Chi-restraints excluded: chain R residue 65 MET Chi-restraints excluded: chain R residue 75 ARG Chi-restraints excluded: chain S residue 5 LYS Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 27 LEU Chi-restraints excluded: chain S residue 30 LYS Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain T residue 15 ARG Chi-restraints excluded: chain T residue 19 LYS Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain U residue 74 VAL Chi-restraints excluded: chain U residue 75 VAL Chi-restraints excluded: chain U residue 87 VAL Chi-restraints excluded: chain V residue 27 ARG Chi-restraints excluded: chain W residue 11 THR Chi-restraints excluded: chain W residue 30 PHE Chi-restraints excluded: chain W residue 45 THR Chi-restraints excluded: chain W residue 52 ARG Chi-restraints excluded: chain X residue 13 ILE Chi-restraints excluded: chain X residue 35 VAL Chi-restraints excluded: chain X residue 55 THR Chi-restraints excluded: chain Z residue 18 THR Chi-restraints excluded: chain 1 residue 44 LEU Chi-restraints excluded: chain 2 residue 2 VAL Chi-restraints excluded: chain 2 residue 12 LYS Chi-restraints excluded: chain 2 residue 31 VAL Chi-restraints excluded: chain 3 residue 15 LYS Chi-restraints excluded: chain 3 residue 35 ASN Chi-restraints excluded: chain 4 residue 10 ILE Chi-restraints excluded: chain 4 residue 33 LYS Chi-restraints excluded: chain 4 residue 35 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 583 random chunks: chunk 543 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 321 optimal weight: 8.9990 chunk 411 optimal weight: 10.0000 chunk 319 optimal weight: 9.9990 chunk 474 optimal weight: 9.9990 chunk 314 optimal weight: 3.9990 chunk 561 optimal weight: 9.9990 chunk 351 optimal weight: 0.2980 chunk 342 optimal weight: 20.0000 chunk 259 optimal weight: 30.0000 overall best weight: 5.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 199 GLN ** D 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 GLN E 119 GLN I 72 ASN O 91 ASN Q 61 ASN S 67 ASN ** T 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 23 ASN 2 7 GLN 3 60 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 94015 Z= 0.253 Angle : 0.726 40.485 141541 Z= 0.373 Chirality : 0.040 0.337 18278 Planarity : 0.006 0.129 6962 Dihedral : 23.017 177.775 48983 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 6.90 % Allowed : 18.03 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.14), residues: 2985 helix: -0.33 (0.19), residues: 747 sheet: -0.33 (0.20), residues: 617 loop : -1.70 (0.14), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 250 HIS 0.012 0.001 HIS J 35 PHE 0.020 0.002 PHE O 57 TYR 0.018 0.002 TYR J 74 ARG 0.008 0.001 ARG J 33 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 422 time to evaluate : 3.531 Fit side-chains TARDY: cannot create tardy model for: "LYS G 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. REVERT: C 111 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.6739 (mm-30) REVERT: C 130 LEU cc_start: 0.7075 (OUTLIER) cc_final: 0.6650 (pt) REVERT: C 236 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7164 (mm-30) REVERT: C 252 LYS cc_start: 0.7536 (OUTLIER) cc_final: 0.7125 (mptt) REVERT: D 23 ILE cc_start: 0.7207 (OUTLIER) cc_final: 0.6230 (mt) REVERT: D 42 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6811 (pm20) REVERT: D 184 GLU cc_start: 0.7153 (mt-10) cc_final: 0.6761 (tt0) REVERT: E 13 LYS cc_start: 0.6552 (OUTLIER) cc_final: 0.6291 (mtpt) REVERT: E 100 LYS cc_start: 0.7594 (mttt) cc_final: 0.6541 (pttp) REVERT: E 107 ARG cc_start: 0.6825 (mtp85) cc_final: 0.6495 (mtt-85) REVERT: E 200 LYS cc_start: 0.6469 (mmpt) cc_final: 0.6083 (mttp) REVERT: G 53 VAL cc_start: 0.4993 (t) cc_final: 0.4732 (p) REVERT: G 85 LYS cc_start: 0.4815 (OUTLIER) cc_final: 0.3987 (tppp) REVERT: G 98 MET cc_start: 0.5292 (mmt) cc_final: 0.4506 (mmp) REVERT: G 119 GLU cc_start: 0.6562 (mt-10) cc_final: 0.5989 (mp0) REVERT: H 1 MET cc_start: 0.7743 (OUTLIER) cc_final: 0.6617 (mtt) REVERT: H 19 ILE cc_start: 0.8029 (OUTLIER) cc_final: 0.7594 (mm) REVERT: H 32 GLU cc_start: 0.6817 (mm-30) cc_final: 0.6346 (mm-30) REVERT: H 42 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.7838 (mttt) REVERT: H 117 GLU cc_start: 0.6809 (mm-30) cc_final: 0.6436 (mm-30) REVERT: H 118 LYS cc_start: 0.7086 (tttt) cc_final: 0.6637 (ttpp) REVERT: H 130 GLU cc_start: 0.7395 (mm-30) cc_final: 0.6988 (mm-30) REVERT: I 5 GLU cc_start: 0.7340 (mt-10) cc_final: 0.7066 (mm-30) REVERT: I 9 LYS cc_start: 0.7012 (ttmt) cc_final: 0.6576 (mmtt) REVERT: I 18 GLU cc_start: 0.7945 (tt0) cc_final: 0.7743 (tt0) REVERT: I 66 LYS cc_start: 0.7833 (ttmp) cc_final: 0.7354 (ttmt) REVERT: I 104 ARG cc_start: 0.6152 (ttm-80) cc_final: 0.5926 (ttp80) REVERT: I 112 MET cc_start: 0.6813 (OUTLIER) cc_final: 0.5490 (mpt) REVERT: J 6 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7448 (pp) REVERT: J 16 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.6729 (ptt180) REVERT: J 84 LYS cc_start: 0.6937 (ptmt) cc_final: 0.6304 (pttp) REVERT: J 90 GLU cc_start: 0.6150 (tt0) cc_final: 0.5768 (mt-10) REVERT: J 120 LYS cc_start: 0.6190 (OUTLIER) cc_final: 0.5353 (tptt) REVERT: J 121 LEU cc_start: 0.7272 (OUTLIER) cc_final: 0.6651 (pp) REVERT: J 123 VAL cc_start: 0.7114 (m) cc_final: 0.6849 (t) REVERT: K 5 LYS cc_start: 0.7510 (OUTLIER) cc_final: 0.7220 (mtpt) REVERT: K 6 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.7299 (ptm160) REVERT: K 20 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.7282 (mpt180) REVERT: K 42 ILE cc_start: 0.7702 (OUTLIER) cc_final: 0.7220 (mm) REVERT: K 116 GLU cc_start: 0.7597 (tp30) cc_final: 0.7233 (tp30) REVERT: K 130 LYS cc_start: 0.7659 (ttpp) cc_final: 0.6771 (tttt) REVERT: L 31 GLU cc_start: 0.7340 (tt0) cc_final: 0.6477 (tp30) REVERT: L 53 LYS cc_start: 0.7108 (OUTLIER) cc_final: 0.6849 (mttt) REVERT: M 9 LYS cc_start: 0.6112 (mtmt) cc_final: 0.5587 (mtmt) REVERT: M 13 LYS cc_start: 0.5469 (mttm) cc_final: 0.5108 (mmtt) REVERT: M 22 LEU cc_start: 0.7098 (OUTLIER) cc_final: 0.6729 (tt) REVERT: N 93 LYS cc_start: 0.7597 (tttt) cc_final: 0.6838 (tmtt) REVERT: N 96 ARG cc_start: 0.7411 (OUTLIER) cc_final: 0.5394 (mtt180) REVERT: O 59 LYS cc_start: 0.7776 (ttpt) cc_final: 0.7260 (ttmt) REVERT: P 15 GLU cc_start: 0.7043 (mt-10) cc_final: 0.6619 (mt-10) REVERT: P 37 LYS cc_start: 0.7546 (mppt) cc_final: 0.7075 (mptt) REVERT: P 47 LYS cc_start: 0.7917 (mttt) cc_final: 0.7647 (mttm) REVERT: P 69 LYS cc_start: 0.7999 (tttt) cc_final: 0.7693 (tttm) REVERT: P 94 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7286 (tttt) REVERT: Q 8 ARG cc_start: 0.7166 (mtp-110) cc_final: 0.6754 (mtt90) REVERT: Q 21 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7125 (mp) REVERT: Q 59 GLU cc_start: 0.7176 (tt0) cc_final: 0.6412 (mt-10) REVERT: Q 106 VAL cc_start: 0.7644 (OUTLIER) cc_final: 0.7428 (t) REVERT: R 9 ARG cc_start: 0.6868 (OUTLIER) cc_final: 0.6600 (mtm-85) REVERT: R 18 GLU cc_start: 0.6317 (OUTLIER) cc_final: 0.5970 (mt-10) REVERT: R 28 ASP cc_start: 0.7495 (t70) cc_final: 0.7234 (m-30) REVERT: R 49 LYS cc_start: 0.7121 (mptm) cc_final: 0.6889 (mptm) REVERT: R 65 MET cc_start: 0.5599 (OUTLIER) cc_final: 0.4404 (tmt) REVERT: S 12 ILE cc_start: 0.7449 (OUTLIER) cc_final: 0.7143 (pt) REVERT: S 19 LYS cc_start: 0.7736 (ttmp) cc_final: 0.7323 (ttmt) REVERT: S 30 LYS cc_start: 0.6396 (OUTLIER) cc_final: 0.5975 (mtmm) REVERT: T 13 GLN cc_start: 0.7071 (mp10) cc_final: 0.6800 (mp10) REVERT: T 15 ARG cc_start: 0.7039 (OUTLIER) cc_final: 0.4892 (mpp80) REVERT: T 63 LEU cc_start: 0.6736 (OUTLIER) cc_final: 0.6363 (tt) REVERT: U 19 LYS cc_start: 0.6859 (ptmm) cc_final: 0.6630 (ptpt) REVERT: U 25 GLU cc_start: 0.6448 (mt-10) cc_final: 0.5931 (mp0) REVERT: U 61 ARG cc_start: 0.7447 (ttt180) cc_final: 0.7000 (ttt180) REVERT: U 76 LYS cc_start: 0.7655 (mmtt) cc_final: 0.7064 (mmmt) REVERT: V 22 LEU cc_start: 0.7707 (mp) cc_final: 0.7315 (mm) REVERT: W 30 PHE cc_start: 0.7232 (OUTLIER) cc_final: 0.6297 (t80) REVERT: W 39 GLU cc_start: 0.6381 (OUTLIER) cc_final: 0.6060 (mt-10) REVERT: W 52 ARG cc_start: 0.6504 (OUTLIER) cc_final: 0.5221 (mtm180) REVERT: X 3 LYS cc_start: 0.7578 (mmtp) cc_final: 0.7304 (mmtp) REVERT: X 17 GLU cc_start: 0.6752 (OUTLIER) cc_final: 0.5972 (tp30) REVERT: Z 37 LYS cc_start: 0.6430 (pttt) cc_final: 0.6078 (pttp) REVERT: 2 37 ARG cc_start: 0.6963 (ttp-110) cc_final: 0.6174 (mtm110) REVERT: 2 41 LYS cc_start: 0.8227 (tttt) cc_final: 0.8014 (tmtp) REVERT: 4 13 LYS cc_start: 0.6391 (mttt) cc_final: 0.6036 (mttm) REVERT: 4 24 MET cc_start: 0.7759 (mtt) cc_final: 0.7433 (mtp) REVERT: 4 33 LYS cc_start: 0.6917 (OUTLIER) cc_final: 0.6040 (mtmt) outliers start: 160 outliers final: 103 residues processed: 522 average time/residue: 1.9447 time to fit residues: 1324.3200 Evaluate side-chains 556 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 416 time to evaluate : 3.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 13 LYS Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain G residue 85 LYS Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 42 LYS Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 4 GLN Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain I residue 112 MET Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 16 ARG Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 120 LYS Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 131 SER Chi-restraints excluded: chain K residue 5 LYS Chi-restraints excluded: chain K residue 6 ARG Chi-restraints excluded: chain K residue 20 ARG Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain K residue 129 THR Chi-restraints excluded: chain L residue 9 THR Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 29 ARG Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 53 LYS Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 49 LYS Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain N residue 7 ILE Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 96 ARG Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain O residue 63 THR Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 63 ASN Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain P residue 94 LYS Chi-restraints excluded: chain Q residue 17 VAL Chi-restraints excluded: chain Q residue 21 LEU Chi-restraints excluded: chain Q residue 28 ASN Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 92 ARG Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 9 ARG Chi-restraints excluded: chain R residue 14 GLU Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 20 MET Chi-restraints excluded: chain R residue 65 MET Chi-restraints excluded: chain R residue 75 ARG Chi-restraints excluded: chain S residue 5 LYS Chi-restraints excluded: chain S residue 12 ILE Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 27 LEU Chi-restraints excluded: chain S residue 30 LYS Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain T residue 15 ARG Chi-restraints excluded: chain T residue 19 LYS Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain U residue 75 VAL Chi-restraints excluded: chain U residue 78 GLU Chi-restraints excluded: chain U residue 87 VAL Chi-restraints excluded: chain V residue 27 ARG Chi-restraints excluded: chain W residue 30 PHE Chi-restraints excluded: chain W residue 39 GLU Chi-restraints excluded: chain W residue 45 THR Chi-restraints excluded: chain W residue 52 ARG Chi-restraints excluded: chain X residue 5 GLN Chi-restraints excluded: chain X residue 13 ILE Chi-restraints excluded: chain X residue 17 GLU Chi-restraints excluded: chain X residue 35 VAL Chi-restraints excluded: chain X residue 55 THR Chi-restraints excluded: chain Z residue 18 THR Chi-restraints excluded: chain 2 residue 2 VAL Chi-restraints excluded: chain 2 residue 31 VAL Chi-restraints excluded: chain 3 residue 15 LYS Chi-restraints excluded: chain 4 residue 10 ILE Chi-restraints excluded: chain 4 residue 33 LYS Chi-restraints excluded: chain 4 residue 35 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 583 random chunks: chunk 347 optimal weight: 3.9990 chunk 224 optimal weight: 50.0000 chunk 335 optimal weight: 10.0000 chunk 169 optimal weight: 30.0000 chunk 110 optimal weight: 10.0000 chunk 108 optimal weight: 50.0000 chunk 357 optimal weight: 6.9990 chunk 382 optimal weight: 30.0000 chunk 277 optimal weight: 10.0000 chunk 52 optimal weight: 20.0000 chunk 441 optimal weight: 20.0000 overall best weight: 8.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 134 ASN C 199 GLN ** D 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 GLN E 119 GLN I 72 ASN O 91 ASN Q 61 ASN S 67 ASN 3 60 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 94015 Z= 0.341 Angle : 0.824 40.690 141541 Z= 0.418 Chirality : 0.045 0.367 18278 Planarity : 0.007 0.160 6962 Dihedral : 23.145 179.317 48983 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 7.76 % Allowed : 17.59 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.14), residues: 2985 helix: -0.42 (0.19), residues: 741 sheet: -0.38 (0.20), residues: 618 loop : -1.73 (0.13), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 250 HIS 0.014 0.002 HIS J 35 PHE 0.023 0.002 PHE O 57 TYR 0.022 0.002 TYR J 74 ARG 0.012 0.001 ARG J 33 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 427 time to evaluate : 3.610 Fit side-chains TARDY: cannot create tardy model for: "LYS G 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. REVERT: C 30 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7320 (mm-30) REVERT: C 130 LEU cc_start: 0.7119 (OUTLIER) cc_final: 0.6678 (pt) REVERT: C 236 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7123 (mm-30) REVERT: C 252 LYS cc_start: 0.7568 (OUTLIER) cc_final: 0.7088 (mptt) REVERT: D 23 ILE cc_start: 0.7215 (OUTLIER) cc_final: 0.6246 (mt) REVERT: D 42 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6798 (pm20) REVERT: D 184 GLU cc_start: 0.7153 (mt-10) cc_final: 0.6740 (tt0) REVERT: E 13 LYS cc_start: 0.6523 (OUTLIER) cc_final: 0.6232 (mtpt) REVERT: E 100 LYS cc_start: 0.7705 (mttt) cc_final: 0.6576 (pttp) REVERT: E 107 ARG cc_start: 0.6851 (mtp85) cc_final: 0.6493 (mtt-85) REVERT: E 200 LYS cc_start: 0.6489 (mmpt) cc_final: 0.5972 (mtpt) REVERT: G 85 LYS cc_start: 0.4888 (OUTLIER) cc_final: 0.4064 (tppp) REVERT: G 98 MET cc_start: 0.5412 (mmt) cc_final: 0.4496 (mmp) REVERT: G 119 GLU cc_start: 0.6600 (mt-10) cc_final: 0.6030 (mp0) REVERT: H 1 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.6541 (mtt) REVERT: H 15 LYS cc_start: 0.7417 (ptmt) cc_final: 0.7038 (ptpt) REVERT: H 19 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7735 (mm) REVERT: H 32 GLU cc_start: 0.6815 (mm-30) cc_final: 0.6347 (mm-30) REVERT: H 42 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.7899 (mttt) REVERT: H 62 LYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7493 (mmtp) REVERT: H 95 ARG cc_start: 0.7110 (OUTLIER) cc_final: 0.6696 (ttp80) REVERT: H 107 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7730 (mttt) REVERT: H 117 GLU cc_start: 0.6839 (mm-30) cc_final: 0.6454 (mm-30) REVERT: H 118 LYS cc_start: 0.7104 (tttt) cc_final: 0.6638 (ttpp) REVERT: H 130 GLU cc_start: 0.7448 (mm-30) cc_final: 0.7104 (mm-30) REVERT: I 5 GLU cc_start: 0.7324 (mt-10) cc_final: 0.7018 (mm-30) REVERT: I 9 LYS cc_start: 0.7088 (ttmt) cc_final: 0.6619 (mmtt) REVERT: I 18 GLU cc_start: 0.7956 (tt0) cc_final: 0.7746 (tt0) REVERT: I 66 LYS cc_start: 0.7930 (OUTLIER) cc_final: 0.7498 (ttmt) REVERT: I 104 ARG cc_start: 0.6259 (ttm-80) cc_final: 0.6004 (ttp80) REVERT: I 112 MET cc_start: 0.6773 (OUTLIER) cc_final: 0.5446 (mpt) REVERT: J 6 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7444 (pp) REVERT: J 16 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.6648 (ptt180) REVERT: J 84 LYS cc_start: 0.6984 (ptmt) cc_final: 0.6347 (pttp) REVERT: J 90 GLU cc_start: 0.6129 (tt0) cc_final: 0.5809 (mt-10) REVERT: J 120 LYS cc_start: 0.6267 (OUTLIER) cc_final: 0.5485 (tptt) REVERT: J 121 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.6601 (pp) REVERT: J 123 VAL cc_start: 0.7088 (m) cc_final: 0.6750 (t) REVERT: K 5 LYS cc_start: 0.7501 (OUTLIER) cc_final: 0.7228 (mtpt) REVERT: K 20 ARG cc_start: 0.7605 (OUTLIER) cc_final: 0.7282 (mpt180) REVERT: K 116 GLU cc_start: 0.7585 (tp30) cc_final: 0.7218 (tp30) REVERT: K 130 LYS cc_start: 0.7679 (ttpp) cc_final: 0.6787 (tttt) REVERT: L 31 GLU cc_start: 0.7353 (tt0) cc_final: 0.6478 (tp30) REVERT: L 53 LYS cc_start: 0.7121 (OUTLIER) cc_final: 0.6855 (mttt) REVERT: M 9 LYS cc_start: 0.6154 (mtmt) cc_final: 0.5640 (mtmt) REVERT: M 13 LYS cc_start: 0.5432 (mttm) cc_final: 0.5059 (mmtt) REVERT: M 22 LEU cc_start: 0.7095 (OUTLIER) cc_final: 0.6729 (tt) REVERT: N 93 LYS cc_start: 0.7671 (tttt) cc_final: 0.6871 (tptp) REVERT: N 96 ARG cc_start: 0.7475 (OUTLIER) cc_final: 0.5447 (mtt180) REVERT: O 59 LYS cc_start: 0.7822 (ttpt) cc_final: 0.7319 (ttmt) REVERT: P 12 ILE cc_start: 0.7801 (OUTLIER) cc_final: 0.7338 (mm) REVERT: P 15 GLU cc_start: 0.7198 (mt-10) cc_final: 0.6813 (mt-10) REVERT: P 37 LYS cc_start: 0.7594 (mppt) cc_final: 0.7138 (mptt) REVERT: P 47 LYS cc_start: 0.7922 (mttt) cc_final: 0.7655 (mttm) REVERT: P 69 LYS cc_start: 0.8031 (tttt) cc_final: 0.7722 (tttm) REVERT: P 94 LYS cc_start: 0.7726 (OUTLIER) cc_final: 0.7283 (tttt) REVERT: Q 8 ARG cc_start: 0.7188 (mtp-110) cc_final: 0.6761 (mtt90) REVERT: Q 21 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7215 (mp) REVERT: Q 59 GLU cc_start: 0.7219 (tt0) cc_final: 0.6415 (mt-10) REVERT: Q 90 GLN cc_start: 0.7714 (OUTLIER) cc_final: 0.7105 (mm-40) REVERT: R 9 ARG cc_start: 0.6902 (OUTLIER) cc_final: 0.6612 (mtm-85) REVERT: R 28 ASP cc_start: 0.7490 (OUTLIER) cc_final: 0.7237 (m-30) REVERT: R 49 LYS cc_start: 0.7142 (mptm) cc_final: 0.6913 (mptm) REVERT: R 65 MET cc_start: 0.5596 (OUTLIER) cc_final: 0.4363 (tmt) REVERT: S 12 ILE cc_start: 0.7491 (OUTLIER) cc_final: 0.7214 (pt) REVERT: S 19 LYS cc_start: 0.7723 (ttmp) cc_final: 0.7313 (ttmt) REVERT: S 30 LYS cc_start: 0.6410 (OUTLIER) cc_final: 0.5997 (mtmm) REVERT: T 13 GLN cc_start: 0.7098 (mp10) cc_final: 0.6842 (mp10) REVERT: T 15 ARG cc_start: 0.7109 (OUTLIER) cc_final: 0.5022 (mpp80) REVERT: T 63 LEU cc_start: 0.6740 (OUTLIER) cc_final: 0.6336 (tt) REVERT: U 19 LYS cc_start: 0.6825 (ptmm) cc_final: 0.6592 (ptpt) REVERT: U 25 GLU cc_start: 0.6315 (mt-10) cc_final: 0.5824 (mp0) REVERT: U 61 ARG cc_start: 0.7460 (ttt180) cc_final: 0.7008 (ttt180) REVERT: U 76 LYS cc_start: 0.7668 (mmtt) cc_final: 0.7063 (mmmt) REVERT: V 22 LEU cc_start: 0.7662 (mp) cc_final: 0.7353 (mm) REVERT: W 17 GLN cc_start: 0.7272 (tp-100) cc_final: 0.6625 (mm-40) REVERT: W 30 PHE cc_start: 0.7238 (OUTLIER) cc_final: 0.6297 (t80) REVERT: W 52 ARG cc_start: 0.6508 (OUTLIER) cc_final: 0.5320 (mtm180) REVERT: X 3 LYS cc_start: 0.7640 (mmtp) cc_final: 0.7327 (mmtp) REVERT: X 10 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.7101 (mmt180) REVERT: X 17 GLU cc_start: 0.6797 (OUTLIER) cc_final: 0.5980 (tp30) REVERT: Z 37 LYS cc_start: 0.6465 (pttt) cc_final: 0.6113 (pttp) REVERT: 2 37 ARG cc_start: 0.7005 (ttp-110) cc_final: 0.6211 (mtm110) REVERT: 2 41 LYS cc_start: 0.8246 (tttt) cc_final: 0.8038 (tmtp) REVERT: 4 24 MET cc_start: 0.7809 (mtt) cc_final: 0.7457 (mtp) REVERT: 4 33 LYS cc_start: 0.6959 (OUTLIER) cc_final: 0.6127 (mtmt) outliers start: 180 outliers final: 117 residues processed: 544 average time/residue: 1.9304 time to fit residues: 1372.9927 Evaluate side-chains 583 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 426 time to evaluate : 3.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 13 LYS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain G residue 85 LYS Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 22 GLU Chi-restraints excluded: chain H residue 42 LYS Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain H residue 95 ARG Chi-restraints excluded: chain H residue 107 LYS Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 4 GLN Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 66 LYS Chi-restraints excluded: chain I residue 72 ASN Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain I residue 112 MET Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 16 ARG Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 99 SER Chi-restraints excluded: chain J residue 120 LYS Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 131 SER Chi-restraints excluded: chain K residue 5 LYS Chi-restraints excluded: chain K residue 6 ARG Chi-restraints excluded: chain K residue 20 ARG Chi-restraints excluded: chain K residue 25 ASN Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain K residue 129 THR Chi-restraints excluded: chain L residue 9 THR Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 29 ARG Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 53 LYS Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 49 LYS Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain N residue 7 ILE Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 96 ARG Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain O residue 63 THR Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain P residue 12 ILE Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 63 ASN Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain P residue 94 LYS Chi-restraints excluded: chain Q residue 17 VAL Chi-restraints excluded: chain Q residue 21 LEU Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 90 GLN Chi-restraints excluded: chain Q residue 92 ARG Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 9 ARG Chi-restraints excluded: chain R residue 14 GLU Chi-restraints excluded: chain R residue 20 MET Chi-restraints excluded: chain R residue 28 ASP Chi-restraints excluded: chain R residue 65 MET Chi-restraints excluded: chain R residue 75 ARG Chi-restraints excluded: chain S residue 5 LYS Chi-restraints excluded: chain S residue 12 ILE Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 27 LEU Chi-restraints excluded: chain S residue 30 LYS Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain T residue 15 ARG Chi-restraints excluded: chain T residue 19 LYS Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain U residue 74 VAL Chi-restraints excluded: chain U residue 75 VAL Chi-restraints excluded: chain U residue 78 GLU Chi-restraints excluded: chain U residue 87 VAL Chi-restraints excluded: chain V residue 27 ARG Chi-restraints excluded: chain W residue 11 THR Chi-restraints excluded: chain W residue 30 PHE Chi-restraints excluded: chain W residue 45 THR Chi-restraints excluded: chain W residue 52 ARG Chi-restraints excluded: chain X residue 5 GLN Chi-restraints excluded: chain X residue 10 ARG Chi-restraints excluded: chain X residue 13 ILE Chi-restraints excluded: chain X residue 17 GLU Chi-restraints excluded: chain X residue 35 VAL Chi-restraints excluded: chain X residue 55 THR Chi-restraints excluded: chain Z residue 18 THR Chi-restraints excluded: chain 1 residue 44 LEU Chi-restraints excluded: chain 2 residue 2 VAL Chi-restraints excluded: chain 2 residue 31 VAL Chi-restraints excluded: chain 2 residue 43 LEU Chi-restraints excluded: chain 3 residue 15 LYS Chi-restraints excluded: chain 3 residue 35 ASN Chi-restraints excluded: chain 4 residue 10 ILE Chi-restraints excluded: chain 4 residue 33 LYS Chi-restraints excluded: chain 4 residue 35 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 583 random chunks: chunk 511 optimal weight: 20.0000 chunk 538 optimal weight: 20.0000 chunk 491 optimal weight: 2.9990 chunk 523 optimal weight: 2.9990 chunk 315 optimal weight: 0.6980 chunk 228 optimal weight: 20.0000 chunk 411 optimal weight: 9.9990 chunk 160 optimal weight: 10.0000 chunk 473 optimal weight: 20.0000 chunk 495 optimal weight: 2.9990 chunk 521 optimal weight: 6.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 199 GLN ** D 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 GLN E 119 GLN I 72 ASN O 91 ASN Q 61 ASN S 67 ASN ** T 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 60 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 94015 Z= 0.172 Angle : 0.681 40.885 141541 Z= 0.353 Chirality : 0.039 0.330 18278 Planarity : 0.006 0.119 6962 Dihedral : 23.078 176.523 48983 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 5.91 % Allowed : 19.58 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.14), residues: 2985 helix: -0.17 (0.19), residues: 740 sheet: -0.36 (0.20), residues: 618 loop : -1.65 (0.14), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 250 HIS 0.005 0.001 HIS J 35 PHE 0.018 0.002 PHE O 57 TYR 0.018 0.001 TYR 2 6 ARG 0.005 0.000 ARG J 16 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 422 time to evaluate : 3.578 Fit side-chains TARDY: cannot create tardy model for: "LYS G 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. REVERT: C 77 LYS cc_start: 0.7563 (ttmm) cc_final: 0.7038 (ttmm) REVERT: C 111 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.6742 (mm-30) REVERT: C 130 LEU cc_start: 0.7028 (OUTLIER) cc_final: 0.6600 (pt) REVERT: C 236 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7153 (mm-30) REVERT: C 252 LYS cc_start: 0.7482 (OUTLIER) cc_final: 0.7084 (mptt) REVERT: D 23 ILE cc_start: 0.7192 (OUTLIER) cc_final: 0.6194 (mt) REVERT: D 141 MET cc_start: 0.8323 (mmp) cc_final: 0.8090 (mmp) REVERT: D 184 GLU cc_start: 0.7133 (mt-10) cc_final: 0.6766 (tt0) REVERT: E 13 LYS cc_start: 0.6519 (OUTLIER) cc_final: 0.6261 (mtpt) REVERT: E 100 LYS cc_start: 0.7638 (mttt) cc_final: 0.6576 (pttp) REVERT: E 107 ARG cc_start: 0.6801 (mtp85) cc_final: 0.6470 (mtt-85) REVERT: E 200 LYS cc_start: 0.6469 (mmpt) cc_final: 0.5941 (mtpt) REVERT: G 98 MET cc_start: 0.5384 (mmt) cc_final: 0.4476 (mmp) REVERT: G 119 GLU cc_start: 0.6560 (mt-10) cc_final: 0.5982 (mp0) REVERT: H 19 ILE cc_start: 0.8006 (OUTLIER) cc_final: 0.7583 (mm) REVERT: H 32 GLU cc_start: 0.6788 (mm-30) cc_final: 0.6323 (mm-30) REVERT: H 42 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.7836 (mttt) REVERT: H 62 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7438 (mmtp) REVERT: H 95 ARG cc_start: 0.7125 (OUTLIER) cc_final: 0.6687 (ttp80) REVERT: H 107 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7636 (mttt) REVERT: H 117 GLU cc_start: 0.6788 (mm-30) cc_final: 0.6415 (mm-30) REVERT: H 118 LYS cc_start: 0.7093 (tttt) cc_final: 0.6631 (ttpp) REVERT: H 130 GLU cc_start: 0.7424 (mm-30) cc_final: 0.7171 (mp0) REVERT: I 5 GLU cc_start: 0.7326 (mt-10) cc_final: 0.6955 (mm-30) REVERT: I 9 LYS cc_start: 0.7083 (ttmt) cc_final: 0.6623 (mmtt) REVERT: I 18 GLU cc_start: 0.7935 (tt0) cc_final: 0.7730 (tt0) REVERT: I 66 LYS cc_start: 0.7796 (ttmp) cc_final: 0.7323 (ttmt) REVERT: I 104 ARG cc_start: 0.6202 (ttm-80) cc_final: 0.5924 (ptt90) REVERT: J 6 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7415 (pp) REVERT: J 84 LYS cc_start: 0.6918 (ptmt) cc_final: 0.6284 (pttp) REVERT: J 120 LYS cc_start: 0.6226 (OUTLIER) cc_final: 0.5437 (tptt) REVERT: J 121 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.6652 (pp) REVERT: J 123 VAL cc_start: 0.7105 (m) cc_final: 0.6807 (t) REVERT: K 5 LYS cc_start: 0.7524 (OUTLIER) cc_final: 0.7217 (mtpt) REVERT: K 42 ILE cc_start: 0.7768 (OUTLIER) cc_final: 0.7231 (mm) REVERT: K 116 GLU cc_start: 0.7606 (tp30) cc_final: 0.7223 (tp30) REVERT: K 130 LYS cc_start: 0.7686 (ttpp) cc_final: 0.6788 (tttt) REVERT: L 31 GLU cc_start: 0.7337 (tt0) cc_final: 0.6472 (tp30) REVERT: L 53 LYS cc_start: 0.7086 (OUTLIER) cc_final: 0.6836 (mttt) REVERT: M 9 LYS cc_start: 0.6118 (mtmt) cc_final: 0.5596 (mtmt) REVERT: M 13 LYS cc_start: 0.5379 (mttm) cc_final: 0.5025 (mmtt) REVERT: M 22 LEU cc_start: 0.7091 (OUTLIER) cc_final: 0.6725 (tt) REVERT: N 93 LYS cc_start: 0.7603 (tttt) cc_final: 0.6846 (tmtt) REVERT: N 96 ARG cc_start: 0.7325 (OUTLIER) cc_final: 0.5260 (mtt-85) REVERT: O 59 LYS cc_start: 0.7751 (ttpt) cc_final: 0.7258 (ttmt) REVERT: P 15 GLU cc_start: 0.7079 (mt-10) cc_final: 0.6713 (mt-10) REVERT: P 37 LYS cc_start: 0.7548 (mppt) cc_final: 0.7077 (mptt) REVERT: P 47 LYS cc_start: 0.7923 (mttt) cc_final: 0.7670 (mttm) REVERT: P 69 LYS cc_start: 0.7997 (tttt) cc_final: 0.7701 (tttm) REVERT: P 94 LYS cc_start: 0.7633 (OUTLIER) cc_final: 0.7208 (tttt) REVERT: Q 8 ARG cc_start: 0.7152 (mtp-110) cc_final: 0.6745 (mtt90) REVERT: Q 59 GLU cc_start: 0.7191 (tt0) cc_final: 0.6471 (mt-10) REVERT: R 18 GLU cc_start: 0.6297 (OUTLIER) cc_final: 0.5955 (mt-10) REVERT: R 28 ASP cc_start: 0.7449 (t70) cc_final: 0.7221 (m-30) REVERT: R 49 LYS cc_start: 0.7104 (mptm) cc_final: 0.6878 (mptm) REVERT: S 12 ILE cc_start: 0.7485 (OUTLIER) cc_final: 0.7217 (pt) REVERT: S 19 LYS cc_start: 0.7727 (ttmp) cc_final: 0.7326 (ttmt) REVERT: T 13 GLN cc_start: 0.7097 (mp10) cc_final: 0.6846 (mp10) REVERT: T 15 ARG cc_start: 0.6962 (OUTLIER) cc_final: 0.4904 (mpp80) REVERT: T 63 LEU cc_start: 0.6677 (OUTLIER) cc_final: 0.6303 (tt) REVERT: U 19 LYS cc_start: 0.6790 (ptmm) cc_final: 0.6563 (ptpt) REVERT: U 25 GLU cc_start: 0.6449 (mt-10) cc_final: 0.5928 (mp0) REVERT: U 61 ARG cc_start: 0.7419 (ttt180) cc_final: 0.6990 (ttt180) REVERT: U 76 LYS cc_start: 0.7675 (mmtt) cc_final: 0.6991 (mmmt) REVERT: U 87 VAL cc_start: 0.7603 (OUTLIER) cc_final: 0.7383 (p) REVERT: V 22 LEU cc_start: 0.7629 (mp) cc_final: 0.7342 (mm) REVERT: W 17 GLN cc_start: 0.7264 (tp-100) cc_final: 0.6616 (mm-40) REVERT: W 30 PHE cc_start: 0.7200 (OUTLIER) cc_final: 0.6288 (t80) REVERT: W 52 ARG cc_start: 0.6469 (OUTLIER) cc_final: 0.5199 (mtm180) REVERT: X 10 ARG cc_start: 0.7488 (OUTLIER) cc_final: 0.7104 (mmt180) REVERT: X 17 GLU cc_start: 0.6682 (OUTLIER) cc_final: 0.5886 (tp30) REVERT: Z 37 LYS cc_start: 0.6410 (pttt) cc_final: 0.6118 (pttp) REVERT: 2 37 ARG cc_start: 0.6944 (ttp-110) cc_final: 0.6139 (mtm110) REVERT: 2 41 LYS cc_start: 0.8236 (tttt) cc_final: 0.8032 (tmtp) REVERT: 4 13 LYS cc_start: 0.6278 (mttt) cc_final: 0.5937 (mttm) REVERT: 4 24 MET cc_start: 0.7754 (mtt) cc_final: 0.7411 (mtp) REVERT: 4 33 LYS cc_start: 0.7005 (OUTLIER) cc_final: 0.6181 (mtmt) outliers start: 137 outliers final: 86 residues processed: 505 average time/residue: 1.9685 time to fit residues: 1298.6316 Evaluate side-chains 534 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 419 time to evaluate : 3.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 13 LYS Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 42 LYS Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain H residue 95 ARG Chi-restraints excluded: chain H residue 107 LYS Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 120 LYS Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain K residue 5 LYS Chi-restraints excluded: chain K residue 6 ARG Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain K residue 129 THR Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 29 ARG Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 53 LYS Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 49 LYS Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain N residue 7 ILE Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 96 ARG Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain O residue 63 THR Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 63 ASN Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain P residue 94 LYS Chi-restraints excluded: chain Q residue 17 VAL Chi-restraints excluded: chain Q residue 28 ASN Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 92 ARG Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain R residue 14 GLU Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 75 ARG Chi-restraints excluded: chain S residue 5 LYS Chi-restraints excluded: chain S residue 12 ILE Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 27 LEU Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain T residue 15 ARG Chi-restraints excluded: chain T residue 19 LYS Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain U residue 75 VAL Chi-restraints excluded: chain U residue 78 GLU Chi-restraints excluded: chain U residue 87 VAL Chi-restraints excluded: chain W residue 11 THR Chi-restraints excluded: chain W residue 30 PHE Chi-restraints excluded: chain W residue 45 THR Chi-restraints excluded: chain W residue 52 ARG Chi-restraints excluded: chain X residue 5 GLN Chi-restraints excluded: chain X residue 10 ARG Chi-restraints excluded: chain X residue 17 GLU Chi-restraints excluded: chain X residue 35 VAL Chi-restraints excluded: chain X residue 55 THR Chi-restraints excluded: chain Z residue 18 THR Chi-restraints excluded: chain 1 residue 44 LEU Chi-restraints excluded: chain 2 residue 2 VAL Chi-restraints excluded: chain 2 residue 31 VAL Chi-restraints excluded: chain 2 residue 43 LEU Chi-restraints excluded: chain 3 residue 15 LYS Chi-restraints excluded: chain 4 residue 33 LYS Chi-restraints excluded: chain 4 residue 35 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 583 random chunks: chunk 343 optimal weight: 20.0000 chunk 553 optimal weight: 6.9990 chunk 337 optimal weight: 10.0000 chunk 262 optimal weight: 10.0000 chunk 384 optimal weight: 9.9990 chunk 580 optimal weight: 0.9980 chunk 534 optimal weight: 0.0170 chunk 462 optimal weight: 20.0000 chunk 48 optimal weight: 10.0000 chunk 357 optimal weight: 10.0000 chunk 283 optimal weight: 40.0000 overall best weight: 5.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 199 GLN ** D 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 GLN I 72 ASN O 91 ASN S 67 ASN ** T 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 60 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 94015 Z= 0.244 Angle : 0.721 40.583 141541 Z= 0.370 Chirality : 0.040 0.336 18278 Planarity : 0.006 0.128 6962 Dihedral : 23.027 177.754 48983 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 5.52 % Allowed : 20.01 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.14), residues: 2985 helix: -0.15 (0.19), residues: 739 sheet: -0.35 (0.20), residues: 617 loop : -1.64 (0.14), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 250 HIS 0.012 0.001 HIS J 35 PHE 0.020 0.002 PHE O 57 TYR 0.014 0.002 TYR 2 6 ARG 0.008 0.001 ARG J 33 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 413 time to evaluate : 3.407 Fit side-chains TARDY: cannot create tardy model for: "LYS G 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. REVERT: C 30 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7032 (tp30) REVERT: C 130 LEU cc_start: 0.7093 (OUTLIER) cc_final: 0.6756 (pt) REVERT: C 236 GLU cc_start: 0.7558 (mm-30) cc_final: 0.7184 (mm-30) REVERT: C 252 LYS cc_start: 0.7460 (OUTLIER) cc_final: 0.7014 (mptt) REVERT: D 184 GLU cc_start: 0.7146 (mt-10) cc_final: 0.6752 (tt0) REVERT: E 100 LYS cc_start: 0.7656 (mttt) cc_final: 0.6579 (pttp) REVERT: E 107 ARG cc_start: 0.6824 (mtp85) cc_final: 0.6500 (mtt-85) REVERT: E 200 LYS cc_start: 0.6472 (mmpt) cc_final: 0.5998 (mtpt) REVERT: G 98 MET cc_start: 0.5340 (mmt) cc_final: 0.4443 (mmp) REVERT: G 119 GLU cc_start: 0.6634 (mt-10) cc_final: 0.6064 (mp0) REVERT: H 1 MET cc_start: 0.7659 (OUTLIER) cc_final: 0.6625 (mtt) REVERT: H 19 ILE cc_start: 0.8039 (OUTLIER) cc_final: 0.7630 (mm) REVERT: H 32 GLU cc_start: 0.6809 (mm-30) cc_final: 0.6337 (mm-30) REVERT: H 42 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.7818 (mttt) REVERT: H 62 LYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7488 (mmtp) REVERT: H 107 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7664 (mttt) REVERT: H 117 GLU cc_start: 0.6794 (mm-30) cc_final: 0.6431 (mm-30) REVERT: H 118 LYS cc_start: 0.7105 (tttt) cc_final: 0.6638 (ttpp) REVERT: H 130 GLU cc_start: 0.7483 (mm-30) cc_final: 0.7244 (mp0) REVERT: I 5 GLU cc_start: 0.7323 (mt-10) cc_final: 0.6958 (mm-30) REVERT: I 9 LYS cc_start: 0.7047 (ttmt) cc_final: 0.6599 (mmtt) REVERT: I 66 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7314 (ttmt) REVERT: I 104 ARG cc_start: 0.6127 (ttm-80) cc_final: 0.5860 (ptt90) REVERT: J 6 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7421 (pp) REVERT: J 16 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.6727 (ptt180) REVERT: J 84 LYS cc_start: 0.6930 (ptmt) cc_final: 0.6302 (pttp) REVERT: J 90 GLU cc_start: 0.6118 (tt0) cc_final: 0.5729 (mt-10) REVERT: J 120 LYS cc_start: 0.6224 (OUTLIER) cc_final: 0.5410 (tptt) REVERT: J 121 LEU cc_start: 0.7298 (OUTLIER) cc_final: 0.6667 (pp) REVERT: J 123 VAL cc_start: 0.7098 (m) cc_final: 0.6803 (t) REVERT: K 5 LYS cc_start: 0.7519 (OUTLIER) cc_final: 0.7203 (mtpt) REVERT: K 6 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.7298 (ptm160) REVERT: K 116 GLU cc_start: 0.7591 (tp30) cc_final: 0.7225 (tp30) REVERT: K 130 LYS cc_start: 0.7686 (ttpp) cc_final: 0.6792 (tttt) REVERT: L 31 GLU cc_start: 0.7343 (tt0) cc_final: 0.6474 (tp30) REVERT: L 53 LYS cc_start: 0.7101 (OUTLIER) cc_final: 0.6839 (mttt) REVERT: M 9 LYS cc_start: 0.6141 (mtmt) cc_final: 0.5632 (mtmt) REVERT: M 13 LYS cc_start: 0.5451 (mttm) cc_final: 0.5082 (mmtt) REVERT: M 22 LEU cc_start: 0.7103 (OUTLIER) cc_final: 0.6731 (tt) REVERT: N 93 LYS cc_start: 0.7662 (tttt) cc_final: 0.6857 (tptp) REVERT: N 96 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.5383 (mtt-85) REVERT: O 59 LYS cc_start: 0.7788 (ttpt) cc_final: 0.7280 (ttmt) REVERT: P 15 GLU cc_start: 0.7064 (mt-10) cc_final: 0.6717 (mt-10) REVERT: P 37 LYS cc_start: 0.7566 (mppt) cc_final: 0.7111 (mptt) REVERT: P 47 LYS cc_start: 0.7911 (mttt) cc_final: 0.7645 (mttm) REVERT: P 69 LYS cc_start: 0.8002 (tttt) cc_final: 0.7698 (tttm) REVERT: P 94 LYS cc_start: 0.7644 (OUTLIER) cc_final: 0.7230 (tttt) REVERT: Q 8 ARG cc_start: 0.7185 (mtp-110) cc_final: 0.6766 (mtt90) REVERT: Q 21 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7077 (mp) REVERT: Q 59 GLU cc_start: 0.7228 (tt0) cc_final: 0.6424 (mt-10) REVERT: R 18 GLU cc_start: 0.6319 (OUTLIER) cc_final: 0.5978 (mt-10) REVERT: R 28 ASP cc_start: 0.7504 (t70) cc_final: 0.7267 (m-30) REVERT: R 49 LYS cc_start: 0.7129 (mptm) cc_final: 0.6905 (mptm) REVERT: S 12 ILE cc_start: 0.7504 (OUTLIER) cc_final: 0.7235 (pt) REVERT: S 19 LYS cc_start: 0.7727 (ttmp) cc_final: 0.7325 (ttmt) REVERT: T 13 GLN cc_start: 0.7077 (mp10) cc_final: 0.6814 (mp10) REVERT: T 15 ARG cc_start: 0.6992 (OUTLIER) cc_final: 0.4900 (mpp80) REVERT: T 63 LEU cc_start: 0.6666 (OUTLIER) cc_final: 0.6303 (tt) REVERT: U 19 LYS cc_start: 0.6811 (ptmm) cc_final: 0.6578 (ptpt) REVERT: U 25 GLU cc_start: 0.6363 (mt-10) cc_final: 0.5871 (mp0) REVERT: U 61 ARG cc_start: 0.7444 (ttt180) cc_final: 0.7007 (ttt180) REVERT: U 76 LYS cc_start: 0.7673 (mmtt) cc_final: 0.6987 (mmtt) REVERT: U 87 VAL cc_start: 0.7625 (OUTLIER) cc_final: 0.7412 (p) REVERT: V 22 LEU cc_start: 0.7691 (mp) cc_final: 0.7415 (mm) REVERT: W 17 GLN cc_start: 0.7267 (tp-100) cc_final: 0.6603 (mm-40) REVERT: W 30 PHE cc_start: 0.7226 (OUTLIER) cc_final: 0.6317 (t80) REVERT: W 52 ARG cc_start: 0.6493 (OUTLIER) cc_final: 0.5139 (mtm180) REVERT: X 3 LYS cc_start: 0.7789 (mmtm) cc_final: 0.7404 (mmtp) REVERT: X 10 ARG cc_start: 0.7509 (OUTLIER) cc_final: 0.7079 (mmt180) REVERT: X 17 GLU cc_start: 0.6758 (OUTLIER) cc_final: 0.5944 (tp30) REVERT: Z 37 LYS cc_start: 0.6426 (pttt) cc_final: 0.6054 (pttp) REVERT: 2 37 ARG cc_start: 0.6972 (ttp-110) cc_final: 0.6441 (ttt-90) REVERT: 4 24 MET cc_start: 0.7756 (mtt) cc_final: 0.7425 (mtp) REVERT: 4 33 LYS cc_start: 0.6878 (OUTLIER) cc_final: 0.6019 (mtmt) outliers start: 128 outliers final: 89 residues processed: 494 average time/residue: 1.9981 time to fit residues: 1287.2254 Evaluate side-chains 529 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 410 time to evaluate : 3.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 42 LYS Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain H residue 107 LYS Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 66 LYS Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 16 ARG Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 120 LYS Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain K residue 5 LYS Chi-restraints excluded: chain K residue 6 ARG Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain K residue 129 THR Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 29 ARG Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 53 LYS Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 49 LYS Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain N residue 7 ILE Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 96 ARG Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain O residue 63 THR Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 63 ASN Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain P residue 94 LYS Chi-restraints excluded: chain Q residue 17 VAL Chi-restraints excluded: chain Q residue 21 LEU Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 92 ARG Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain R residue 14 GLU Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 75 ARG Chi-restraints excluded: chain S residue 5 LYS Chi-restraints excluded: chain S residue 12 ILE Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 27 LEU Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain T residue 15 ARG Chi-restraints excluded: chain T residue 19 LYS Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain U residue 74 VAL Chi-restraints excluded: chain U residue 75 VAL Chi-restraints excluded: chain U residue 78 GLU Chi-restraints excluded: chain U residue 87 VAL Chi-restraints excluded: chain W residue 11 THR Chi-restraints excluded: chain W residue 30 PHE Chi-restraints excluded: chain W residue 45 THR Chi-restraints excluded: chain W residue 52 ARG Chi-restraints excluded: chain X residue 5 GLN Chi-restraints excluded: chain X residue 10 ARG Chi-restraints excluded: chain X residue 17 GLU Chi-restraints excluded: chain X residue 35 VAL Chi-restraints excluded: chain X residue 55 THR Chi-restraints excluded: chain Z residue 18 THR Chi-restraints excluded: chain 1 residue 44 LEU Chi-restraints excluded: chain 2 residue 2 VAL Chi-restraints excluded: chain 2 residue 31 VAL Chi-restraints excluded: chain 2 residue 43 LEU Chi-restraints excluded: chain 3 residue 15 LYS Chi-restraints excluded: chain 4 residue 33 LYS Chi-restraints excluded: chain 4 residue 35 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 583 random chunks: chunk 367 optimal weight: 0.0270 chunk 492 optimal weight: 4.9990 chunk 141 optimal weight: 20.0000 chunk 426 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 128 optimal weight: 10.0000 chunk 463 optimal weight: 30.0000 chunk 193 optimal weight: 10.0000 chunk 475 optimal weight: 10.0000 chunk 58 optimal weight: 20.0000 chunk 85 optimal weight: 10.0000 overall best weight: 6.2050 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 199 GLN ** D 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 GLN I 72 ASN O 91 ASN Q 61 ASN S 67 ASN ** T 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 60 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.183192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.144639 restraints weight = 774143.230| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 4.47 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 94015 Z= 0.266 Angle : 0.744 40.556 141541 Z= 0.382 Chirality : 0.041 0.342 18278 Planarity : 0.006 0.133 6962 Dihedral : 23.059 178.292 48983 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 5.99 % Allowed : 19.71 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.14), residues: 2985 helix: -0.18 (0.19), residues: 736 sheet: -0.34 (0.20), residues: 614 loop : -1.64 (0.14), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 250 HIS 0.011 0.001 HIS J 35 PHE 0.021 0.002 PHE O 57 TYR 0.015 0.002 TYR 2 6 ARG 0.009 0.001 ARG J 33 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19986.90 seconds wall clock time: 351 minutes 43.37 seconds (21103.37 seconds total)