Starting phenix.real_space_refine on Sun Mar 17 21:17:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usf_26737/03_2024/7usf_26737.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usf_26737/03_2024/7usf_26737.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usf_26737/03_2024/7usf_26737.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usf_26737/03_2024/7usf_26737.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usf_26737/03_2024/7usf_26737.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usf_26737/03_2024/7usf_26737.pdb" } resolution = 3.5 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= 0.002 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 8 6.06 5 P 150 5.49 5 S 64 5.16 5 C 11632 2.51 5 N 3472 2.21 5 O 3660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 7": "OE1" <-> "OE2" Residue "A GLU 32": "OE1" <-> "OE2" Residue "A TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 158": "OE1" <-> "OE2" Residue "A TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 249": "OD1" <-> "OD2" Residue "B GLU 28": "OE1" <-> "OE2" Residue "B ASP 122": "OD1" <-> "OD2" Residue "B GLU 134": "OE1" <-> "OE2" Residue "B GLU 158": "OE1" <-> "OE2" Residue "B TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 251": "OE1" <-> "OE2" Residue "C TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 71": "OE1" <-> "OE2" Residue "D TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 97": "OE1" <-> "OE2" Residue "D TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 258": "OD1" <-> "OD2" Residue "E GLU 7": "OE1" <-> "OE2" Residue "E GLU 32": "OE1" <-> "OE2" Residue "E TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 158": "OE1" <-> "OE2" Residue "E TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 249": "OD1" <-> "OD2" Residue "F GLU 28": "OE1" <-> "OE2" Residue "F ASP 122": "OD1" <-> "OD2" Residue "F GLU 134": "OE1" <-> "OE2" Residue "F GLU 158": "OE1" <-> "OE2" Residue "F TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 251": "OE1" <-> "OE2" Residue "G TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 71": "OE1" <-> "OE2" Residue "H TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 97": "OE1" <-> "OE2" Residue "H TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 258": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18988 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2121 Classifications: {'peptide': 265} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 246} Chain: "B" Number of atoms: 2019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2019 Classifications: {'peptide': 252} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 235} Chain breaks: 1 Chain: "C" Number of atoms: 1922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1922 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 226} Chain breaks: 3 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 1871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1871 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 222} Chain breaks: 4 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 27 Chain: "I" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 447 Classifications: {'DNA': 22} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 21} Chain: "J" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 813 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Chain: "K" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 296 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2121 Classifications: {'peptide': 265} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 246} Chain: "F" Number of atoms: 2019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2019 Classifications: {'peptide': 252} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 235} Chain breaks: 1 Chain: "G" Number of atoms: 1922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1922 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 226} Chain breaks: 3 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 1871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1871 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 222} Chain breaks: 4 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 27 Chain: "L" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 447 Classifications: {'DNA': 22} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 21} Chain: "M" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 813 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Chain: "N" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 296 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 299 SG CYS A 37 79.129 110.276 55.058 1.00101.43 S ATOM 320 SG CYS A 40 78.963 106.675 56.185 1.00103.87 S ATOM 2420 SG CYS B 37 14.537 81.224 45.444 1.00121.13 S ATOM 2441 SG CYS B 40 14.038 77.220 46.958 1.00123.63 S ATOM 4435 SG CYS C 37 40.874 151.914 71.798 1.00204.27 S ATOM 4456 SG CYS C 40 38.126 149.786 70.059 1.00204.91 S ATOM 6325 SG CYS D 37 50.304 127.400 26.565 1.00181.93 S ATOM 6346 SG CYS D 40 52.486 127.361 29.823 1.00187.21 S ATOM 9793 SG CYS E 37 59.731 57.404 55.058 1.00101.43 S ATOM 9814 SG CYS E 40 59.897 61.005 56.185 1.00103.87 S ATOM 11914 SG CYS F 37 124.323 86.456 45.444 1.00121.13 S ATOM 11935 SG CYS F 40 124.822 90.460 46.958 1.00123.63 S ATOM 13929 SG CYS G 37 97.986 15.766 71.798 1.00204.27 S ATOM 13950 SG CYS G 40 100.734 17.894 70.059 1.00204.91 S ATOM 15819 SG CYS H 37 88.556 40.280 26.565 1.00181.93 S ATOM 15840 SG CYS H 40 86.374 40.319 29.823 1.00187.21 S Time building chain proxies: 9.85, per 1000 atoms: 0.52 Number of scatterers: 18988 At special positions: 0 Unit cell: (140.17, 168.99, 115.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 Ca 2 19.99 S 64 16.00 P 150 15.00 O 3660 8.00 N 3472 7.00 C 11632 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.63 Conformation dependent library (CDL) restraints added in 2.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 500 " pdb="ZN ZN A 500 " - pdb=" NE2 HIS A 9 " pdb="ZN ZN A 500 " - pdb=" ND1 HIS A 13 " pdb="ZN ZN A 500 " - pdb=" SG CYS A 37 " pdb="ZN ZN A 500 " - pdb=" SG CYS A 40 " pdb=" ZN B 500 " pdb="ZN ZN B 500 " - pdb=" ND1 HIS B 13 " pdb="ZN ZN B 500 " - pdb=" NE2 HIS B 9 " pdb="ZN ZN B 500 " - pdb=" SG CYS B 40 " pdb="ZN ZN B 500 " - pdb=" SG CYS B 37 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" ND1 HIS C 13 " pdb="ZN ZN C 401 " - pdb=" NE2 HIS C 9 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 40 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 37 " pdb=" ZN D 401 " pdb="ZN ZN D 401 " - pdb=" ND1 HIS D 13 " pdb="ZN ZN D 401 " - pdb=" NE2 HIS D 9 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 40 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 37 " pdb=" ZN E 500 " pdb="ZN ZN E 500 " - pdb=" NE2 HIS E 9 " pdb="ZN ZN E 500 " - pdb=" ND1 HIS E 13 " pdb="ZN ZN E 500 " - pdb=" SG CYS E 37 " pdb="ZN ZN E 500 " - pdb=" SG CYS E 40 " pdb=" ZN F 500 " pdb="ZN ZN F 500 " - pdb=" ND1 HIS F 13 " pdb="ZN ZN F 500 " - pdb=" NE2 HIS F 9 " pdb="ZN ZN F 500 " - pdb=" SG CYS F 40 " pdb="ZN ZN F 500 " - pdb=" SG CYS F 37 " pdb=" ZN G 401 " pdb="ZN ZN G 401 " - pdb=" ND1 HIS G 13 " pdb="ZN ZN G 401 " - pdb=" NE2 HIS G 9 " pdb="ZN ZN G 401 " - pdb=" SG CYS G 40 " pdb="ZN ZN G 401 " - pdb=" SG CYS G 37 " pdb=" ZN H 401 " pdb="ZN ZN H 401 " - pdb=" ND1 HIS H 13 " pdb="ZN ZN H 401 " - pdb=" NE2 HIS H 9 " pdb="ZN ZN H 401 " - pdb=" SG CYS H 40 " pdb="ZN ZN H 401 " - pdb=" SG CYS H 37 " Number of angles added : 14 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3776 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 16 sheets defined 45.9% alpha, 16.8% beta 72 base pairs and 124 stacking pairs defined. Time for finding SS restraints: 7.21 Creating SS restraints... Processing helix chain 'A' and resid 1 through 13 Processing helix chain 'A' and resid 15 through 24 Processing helix chain 'A' and resid 26 through 37 removed outlier: 3.578A pdb=" N CYS A 37 " --> pdb=" O ILE A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 75 removed outlier: 6.761A pdb=" N LYS A 74 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 75 " --> pdb=" O PHE A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 113 Processing helix chain 'A' and resid 124 through 128 Processing helix chain 'A' and resid 129 through 139 Processing helix chain 'A' and resid 150 through 153 Processing helix chain 'A' and resid 154 through 175 Processing helix chain 'A' and resid 179 through 194 Processing helix chain 'A' and resid 202 through 208 Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'B' and resid 2 through 12 Processing helix chain 'B' and resid 15 through 24 removed outlier: 3.538A pdb=" N LEU B 19 " --> pdb=" O ASN B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 37 removed outlier: 3.706A pdb=" N CYS B 37 " --> pdb=" O ILE B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 113 Processing helix chain 'B' and resid 124 through 129 Processing helix chain 'B' and resid 129 through 139 Processing helix chain 'B' and resid 152 through 172 Processing helix chain 'B' and resid 179 through 194 Processing helix chain 'B' and resid 202 through 209 Processing helix chain 'C' and resid 2 through 13 Processing helix chain 'C' and resid 15 through 24 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 70 through 75 removed outlier: 6.606A pdb=" N LYS C 74 " --> pdb=" O GLU C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 114 Processing helix chain 'C' and resid 129 through 139 Processing helix chain 'C' and resid 155 through 175 removed outlier: 4.581A pdb=" N LYS C 173 " --> pdb=" O ASN C 169 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA C 174 " --> pdb=" O LYS C 170 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY C 175 " --> pdb=" O LEU C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 194 Processing helix chain 'C' and resid 202 through 208 Processing helix chain 'D' and resid 3 through 13 removed outlier: 3.503A pdb=" N GLU D 7 " --> pdb=" O GLU D 3 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 24 Processing helix chain 'D' and resid 26 through 37 Processing helix chain 'D' and resid 70 through 75 removed outlier: 6.714A pdb=" N LYS D 74 " --> pdb=" O GLU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 114 Processing helix chain 'D' and resid 129 through 139 Processing helix chain 'D' and resid 155 through 171 Processing helix chain 'D' and resid 179 through 194 Processing helix chain 'D' and resid 202 through 208 Processing helix chain 'E' and resid 1 through 13 Processing helix chain 'E' and resid 15 through 24 Processing helix chain 'E' and resid 26 through 37 removed outlier: 3.578A pdb=" N CYS E 37 " --> pdb=" O ILE E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 75 removed outlier: 6.761A pdb=" N LYS E 74 " --> pdb=" O GLU E 71 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU E 75 " --> pdb=" O PHE E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 113 Processing helix chain 'E' and resid 124 through 128 Processing helix chain 'E' and resid 129 through 139 Processing helix chain 'E' and resid 150 through 153 Processing helix chain 'E' and resid 154 through 175 Processing helix chain 'E' and resid 179 through 194 Processing helix chain 'E' and resid 202 through 208 Processing helix chain 'E' and resid 257 through 259 No H-bonds generated for 'chain 'E' and resid 257 through 259' Processing helix chain 'F' and resid 2 through 12 Processing helix chain 'F' and resid 15 through 24 removed outlier: 3.538A pdb=" N LEU F 19 " --> pdb=" O ASN F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 37 removed outlier: 3.706A pdb=" N CYS F 37 " --> pdb=" O ILE F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 113 Processing helix chain 'F' and resid 124 through 129 Processing helix chain 'F' and resid 129 through 139 Processing helix chain 'F' and resid 152 through 172 Processing helix chain 'F' and resid 179 through 194 Processing helix chain 'F' and resid 202 through 209 Processing helix chain 'G' and resid 2 through 13 Processing helix chain 'G' and resid 15 through 24 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 70 through 75 removed outlier: 6.606A pdb=" N LYS G 74 " --> pdb=" O GLU G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 114 Processing helix chain 'G' and resid 129 through 139 Processing helix chain 'G' and resid 155 through 175 removed outlier: 4.581A pdb=" N LYS G 173 " --> pdb=" O ASN G 169 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA G 174 " --> pdb=" O LYS G 170 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY G 175 " --> pdb=" O LEU G 171 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 194 Processing helix chain 'G' and resid 202 through 208 Processing helix chain 'H' and resid 3 through 13 removed outlier: 3.503A pdb=" N GLU H 7 " --> pdb=" O GLU H 3 " (cutoff:3.500A) Processing helix chain 'H' and resid 15 through 24 Processing helix chain 'H' and resid 26 through 37 Processing helix chain 'H' and resid 70 through 75 removed outlier: 6.714A pdb=" N LYS H 74 " --> pdb=" O GLU H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 114 Processing helix chain 'H' and resid 129 through 139 Processing helix chain 'H' and resid 155 through 171 Processing helix chain 'H' and resid 179 through 194 Processing helix chain 'H' and resid 202 through 208 Processing sheet with id= 1, first strand: chain 'A' and resid 89 through 93 removed outlier: 3.762A pdb=" N VAL A 78 " --> pdb=" O THR A 67 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N TRP A 62 " --> pdb=" O LYS A 120 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 254 through 256 removed outlier: 6.753A pdb=" N CYS A 244 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL A 234 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER A 228 " --> pdb=" O ASP A 223 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL A 219 " --> pdb=" O PRO A 232 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'B' and resid 89 through 94 removed outlier: 3.802A pdb=" N TYR B 77 " --> pdb=" O ARG B 94 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP B 65 " --> pdb=" O VAL B 80 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS B 120 " --> pdb=" O TRP B 62 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 144 " --> pdb=" O ILE B 119 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'B' and resid 254 through 257 removed outlier: 3.627A pdb=" N THR B 237 " --> pdb=" O CYS B 244 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE B 246 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N LEU B 235 " --> pdb=" O PHE B 246 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG B 262 " --> pdb=" O MET B 220 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'C' and resid 89 through 94 removed outlier: 6.522A pdb=" N TRP C 62 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ILE C 119 " --> pdb=" O VAL C 144 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'C' and resid 254 through 257 removed outlier: 3.786A pdb=" N THR C 237 " --> pdb=" O CYS C 244 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N PHE C 246 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N LEU C 235 " --> pdb=" O PHE C 246 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASP C 233 " --> pdb=" O VAL C 219 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL C 219 " --> pdb=" O ASP C 233 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'D' and resid 89 through 94 removed outlier: 3.608A pdb=" N TYR D 77 " --> pdb=" O ARG D 94 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE D 119 " --> pdb=" O VAL D 144 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'D' and resid 254 through 257 removed outlier: 6.728A pdb=" N PHE D 246 " --> pdb=" O LEU D 235 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LEU D 235 " --> pdb=" O PHE D 246 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL D 219 " --> pdb=" O PRO D 232 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'E' and resid 89 through 93 removed outlier: 3.762A pdb=" N VAL E 78 " --> pdb=" O THR E 67 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N TRP E 62 " --> pdb=" O LYS E 120 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'E' and resid 254 through 256 removed outlier: 6.753A pdb=" N CYS E 244 " --> pdb=" O ILE E 236 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL E 234 " --> pdb=" O PHE E 246 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER E 228 " --> pdb=" O ASP E 223 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL E 219 " --> pdb=" O PRO E 232 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'F' and resid 89 through 94 removed outlier: 3.802A pdb=" N TYR F 77 " --> pdb=" O ARG F 94 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP F 65 " --> pdb=" O VAL F 80 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS F 120 " --> pdb=" O TRP F 62 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL F 144 " --> pdb=" O ILE F 119 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'F' and resid 254 through 257 removed outlier: 3.627A pdb=" N THR F 237 " --> pdb=" O CYS F 244 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE F 246 " --> pdb=" O LEU F 235 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N LEU F 235 " --> pdb=" O PHE F 246 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG F 262 " --> pdb=" O MET F 220 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'G' and resid 89 through 94 removed outlier: 6.522A pdb=" N TRP G 62 " --> pdb=" O LYS G 120 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ILE G 119 " --> pdb=" O VAL G 144 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'G' and resid 254 through 257 removed outlier: 3.786A pdb=" N THR G 237 " --> pdb=" O CYS G 244 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N PHE G 246 " --> pdb=" O LEU G 235 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N LEU G 235 " --> pdb=" O PHE G 246 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASP G 233 " --> pdb=" O VAL G 219 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL G 219 " --> pdb=" O ASP G 233 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'H' and resid 89 through 94 removed outlier: 3.608A pdb=" N TYR H 77 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE H 119 " --> pdb=" O VAL H 144 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'H' and resid 254 through 257 removed outlier: 6.728A pdb=" N PHE H 246 " --> pdb=" O LEU H 235 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LEU H 235 " --> pdb=" O PHE H 246 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL H 219 " --> pdb=" O PRO H 232 " (cutoff:3.500A) 770 hydrogen bonds defined for protein. 2208 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 190 hydrogen bonds 380 hydrogen bond angles 0 basepair planarities 72 basepair parallelities 124 stacking parallelities Total time for adding SS restraints: 5.87 Time building geometry restraints manager: 9.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5270 1.34 - 1.45: 4410 1.45 - 1.57: 9746 1.57 - 1.69: 296 1.69 - 1.81: 104 Bond restraints: 19826 Sorted by residual: bond pdb=" C THR E 121 " pdb=" N ASP E 122 " ideal model delta sigma weight residual 1.330 1.307 0.023 1.60e-02 3.91e+03 1.99e+00 bond pdb=" C THR A 121 " pdb=" N ASP A 122 " ideal model delta sigma weight residual 1.330 1.307 0.023 1.60e-02 3.91e+03 1.99e+00 bond pdb=" C ILE B 147 " pdb=" N PRO B 148 " ideal model delta sigma weight residual 1.334 1.365 -0.031 2.34e-02 1.83e+03 1.78e+00 bond pdb=" C ILE F 147 " pdb=" N PRO F 148 " ideal model delta sigma weight residual 1.334 1.365 -0.031 2.34e-02 1.83e+03 1.78e+00 bond pdb=" CB ASN C 123 " pdb=" CG ASN C 123 " ideal model delta sigma weight residual 1.516 1.547 -0.031 2.50e-02 1.60e+03 1.52e+00 ... (remaining 19821 not shown) Histogram of bond angle deviations from ideal: 99.78 - 106.65: 1644 106.65 - 113.52: 10786 113.52 - 120.39: 7322 120.39 - 127.26: 7242 127.26 - 134.13: 590 Bond angle restraints: 27584 Sorted by residual: angle pdb=" N THR C 226 " pdb=" CA THR C 226 " pdb=" C THR C 226 " ideal model delta sigma weight residual 114.56 109.71 4.85 1.27e+00 6.20e-01 1.46e+01 angle pdb=" N THR G 226 " pdb=" CA THR G 226 " pdb=" C THR G 226 " ideal model delta sigma weight residual 114.56 109.71 4.85 1.27e+00 6.20e-01 1.46e+01 angle pdb=" N VAL H 194 " pdb=" CA VAL H 194 " pdb=" C VAL H 194 " ideal model delta sigma weight residual 111.62 109.10 2.52 7.90e-01 1.60e+00 1.02e+01 angle pdb=" N VAL D 194 " pdb=" CA VAL D 194 " pdb=" C VAL D 194 " ideal model delta sigma weight residual 111.62 109.10 2.52 7.90e-01 1.60e+00 1.02e+01 angle pdb=" N GLY F 209 " pdb=" CA GLY F 209 " pdb=" C GLY F 209 " ideal model delta sigma weight residual 112.34 118.68 -6.34 2.04e+00 2.40e-01 9.66e+00 ... (remaining 27579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 9380 17.97 - 35.93: 1096 35.93 - 53.90: 586 53.90 - 71.87: 160 71.87 - 89.83: 12 Dihedral angle restraints: 11234 sinusoidal: 5438 harmonic: 5796 Sorted by residual: dihedral pdb=" CA TRP H 139 " pdb=" C TRP H 139 " pdb=" N LYS H 140 " pdb=" CA LYS H 140 " ideal model delta harmonic sigma weight residual 180.00 160.97 19.03 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA TRP D 139 " pdb=" C TRP D 139 " pdb=" N LYS D 140 " pdb=" CA LYS D 140 " ideal model delta harmonic sigma weight residual 180.00 160.97 19.03 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA GLY B 209 " pdb=" C GLY B 209 " pdb=" N PRO B 210 " pdb=" CA PRO B 210 " ideal model delta harmonic sigma weight residual 180.00 161.11 18.89 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 11231 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2162 0.036 - 0.071: 622 0.071 - 0.107: 176 0.107 - 0.143: 36 0.143 - 0.178: 6 Chirality restraints: 3002 Sorted by residual: chirality pdb=" CB ILE A 211 " pdb=" CA ILE A 211 " pdb=" CG1 ILE A 211 " pdb=" CG2 ILE A 211 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.95e-01 chirality pdb=" CB ILE E 211 " pdb=" CA ILE E 211 " pdb=" CG1 ILE E 211 " pdb=" CG2 ILE E 211 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.95e-01 chirality pdb=" CA TRP D 139 " pdb=" N TRP D 139 " pdb=" C TRP D 139 " pdb=" CB TRP D 139 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.85e-01 ... (remaining 2999 not shown) Planarity restraints: 3000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN G 123 " 0.014 2.00e-02 2.50e+03 2.83e-02 7.98e+00 pdb=" C ASN G 123 " -0.049 2.00e-02 2.50e+03 pdb=" O ASN G 123 " 0.018 2.00e-02 2.50e+03 pdb=" N ALA G 124 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 123 " 0.014 2.00e-02 2.50e+03 2.83e-02 7.98e+00 pdb=" C ASN C 123 " -0.049 2.00e-02 2.50e+03 pdb=" O ASN C 123 " 0.018 2.00e-02 2.50e+03 pdb=" N ALA C 124 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 139 " 0.017 2.00e-02 2.50e+03 1.59e-02 6.29e+00 pdb=" CG TRP D 139 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP D 139 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP D 139 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 139 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 139 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 139 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 139 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 139 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP D 139 " -0.001 2.00e-02 2.50e+03 ... (remaining 2997 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 126 2.59 - 3.17: 15458 3.17 - 3.75: 32720 3.75 - 4.32: 43088 4.32 - 4.90: 68437 Nonbonded interactions: 159829 Sorted by model distance: nonbonded pdb=" OG1 THR H 202 " pdb=" OE1 GLU H 205 " model vdw 2.017 2.440 nonbonded pdb=" OG1 THR D 202 " pdb=" OE1 GLU D 205 " model vdw 2.017 2.440 nonbonded pdb=" OD1 ASP A 65 " pdb="CA CA A 501 " model vdw 2.209 2.510 nonbonded pdb=" OD1 ASP E 65 " pdb="CA CA E 501 " model vdw 2.209 2.510 nonbonded pdb=" OH TYR C 242 " pdb=" OP1 DG L 10 " model vdw 2.219 2.440 ... (remaining 159824 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 26 or (resid 27 through 28 and (name N or name CA \ or name C or name O or name CB )) or resid 29 through 30 or (resid 31 through 3 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 33 through 3 \ 4 or (resid 35 and (name N or name CA or name C or name O or name CB )) or resid \ 36 through 41 or resid 56 through 129 or (resid 130 and (name N or name CA or n \ ame C or name O or name CB )) or resid 131 through 143 or (resid 144 and (name N \ or name CA or name C or name O or name CB )) or resid 154 through 161 or (resid \ 162 and (name N or name CA or name C or name O or name CB )) or resid 163 throu \ gh 172 or (resid 173 and (name N or name CA or name C or name O or name CB )) or \ resid 177 through 210 or resid 218 through 264)) selection = (chain 'B' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 26 or (resid 27 through 28 and (name N or name CA \ or name C or name O or name CB )) or resid 29 through 30 or (resid 31 through 3 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 33 through 3 \ 4 or (resid 35 and (name N or name CA or name C or name O or name CB )) or resid \ 36 through 41 or resid 56 through 129 or (resid 130 and (name N or name CA or n \ ame C or name O or name CB )) or resid 131 through 143 or (resid 144 and (name N \ or name CA or name C or name O or name CB )) or resid 154 through 161 or (resid \ 162 and (name N or name CA or name C or name O or name CB )) or resid 163 throu \ gh 172 or (resid 173 and (name N or name CA or name C or name O or name CB )) or \ resid 177 through 210 or resid 218 through 264)) selection = (chain 'C' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 26 or (resid 27 through 28 and (name N or name CA \ or name C or name O or name CB )) or resid 29 through 30 or (resid 31 through 3 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 33 through 3 \ 4 or (resid 35 and (name N or name CA or name C or name O or name CB )) or resid \ 36 through 41 or resid 56 through 129 or (resid 130 and (name N or name CA or n \ ame C or name O or name CB )) or resid 131 through 143 or (resid 144 and (name N \ or name CA or name C or name O or name CB )) or resid 154 through 172 or (resid \ 173 and (name N or name CA or name C or name O or name CB )) or resid 177 throu \ gh 264)) selection = (chain 'D' and (resid 2 through 161 or (resid 162 and (name N or name CA or name \ C or name O or name CB )) or resid 163 through 264)) selection = (chain 'E' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 26 or (resid 27 through 28 and (name N or name CA \ or name C or name O or name CB )) or resid 29 through 30 or (resid 31 through 3 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 33 through 3 \ 4 or (resid 35 and (name N or name CA or name C or name O or name CB )) or resid \ 36 through 41 or resid 56 through 129 or (resid 130 and (name N or name CA or n \ ame C or name O or name CB )) or resid 131 through 143 or (resid 144 and (name N \ or name CA or name C or name O or name CB )) or resid 154 through 161 or (resid \ 162 and (name N or name CA or name C or name O or name CB )) or resid 163 throu \ gh 172 or (resid 173 and (name N or name CA or name C or name O or name CB )) or \ resid 177 through 210 or resid 218 through 264)) selection = (chain 'F' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 26 or (resid 27 through 28 and (name N or name CA \ or name C or name O or name CB )) or resid 29 through 30 or (resid 31 through 3 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 33 through 3 \ 4 or (resid 35 and (name N or name CA or name C or name O or name CB )) or resid \ 36 through 41 or resid 56 through 129 or (resid 130 and (name N or name CA or n \ ame C or name O or name CB )) or resid 131 through 143 or (resid 144 and (name N \ or name CA or name C or name O or name CB )) or resid 154 through 161 or (resid \ 162 and (name N or name CA or name C or name O or name CB )) or resid 163 throu \ gh 172 or (resid 173 and (name N or name CA or name C or name O or name CB )) or \ resid 177 through 210 or resid 218 through 264)) selection = (chain 'G' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 26 or (resid 27 through 28 and (name N or name CA \ or name C or name O or name CB )) or resid 29 through 30 or (resid 31 through 3 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 33 through 3 \ 4 or (resid 35 and (name N or name CA or name C or name O or name CB )) or resid \ 36 through 41 or resid 56 through 129 or (resid 130 and (name N or name CA or n \ ame C or name O or name CB )) or resid 131 through 143 or (resid 144 and (name N \ or name CA or name C or name O or name CB )) or resid 154 through 172 or (resid \ 173 and (name N or name CA or name C or name O or name CB )) or resid 177 throu \ gh 264)) selection = (chain 'H' and (resid 2 through 161 or (resid 162 and (name N or name CA or name \ C or name O or name CB )) or resid 163 through 264)) } ncs_group { reference = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'K' selection = chain 'N' } 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 group one per residue 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: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.600 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 58.310 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19826 Z= 0.183 Angle : 0.553 10.252 27584 Z= 0.318 Chirality : 0.038 0.178 3002 Planarity : 0.004 0.052 3000 Dihedral : 19.616 89.833 7458 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.12 % Allowed : 0.00 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % 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: 0.79 (0.20), residues: 1936 helix: 1.58 (0.18), residues: 810 sheet: 0.37 (0.30), residues: 342 loop : -0.47 (0.24), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP D 139 HIS 0.012 0.001 HIS H 161 PHE 0.018 0.001 PHE G 88 TYR 0.015 0.001 TYR H 127 ARG 0.004 0.000 ARG E 130 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 314 time to evaluate : 1.808 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 MET cc_start: 0.8452 (mmm) cc_final: 0.8179 (mmm) REVERT: A 244 CYS cc_start: 0.8664 (t) cc_final: 0.8120 (t) REVERT: B 130 ARG cc_start: 0.7951 (mmp-170) cc_final: 0.7631 (mmp80) REVERT: B 201 HIS cc_start: 0.8146 (m-70) cc_final: 0.7891 (m-70) REVERT: B 220 MET cc_start: 0.7880 (tpt) cc_final: 0.6994 (tpt) REVERT: B 242 TYR cc_start: 0.8140 (m-10) cc_final: 0.7904 (m-10) REVERT: B 254 ILE cc_start: 0.8543 (mt) cc_final: 0.8316 (tt) REVERT: C 64 MET cc_start: 0.7830 (ttp) cc_final: 0.7601 (ttm) REVERT: C 65 ASP cc_start: 0.8305 (t0) cc_final: 0.8025 (t0) REVERT: C 85 TYR cc_start: 0.7379 (t80) cc_final: 0.7020 (t80) REVERT: C 110 PHE cc_start: 0.8497 (m-10) cc_final: 0.7893 (m-10) REVERT: C 196 MET cc_start: 0.7994 (ptp) cc_final: 0.6728 (ptp) REVERT: C 205 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8668 (mt-10) REVERT: D 7 GLU cc_start: 0.8884 (pt0) cc_final: 0.8365 (pp20) REVERT: D 62 TRP cc_start: 0.7266 (m-10) cc_final: 0.6954 (m-10) REVERT: D 134 GLU cc_start: 0.8224 (mp0) cc_final: 0.7979 (mp0) REVERT: D 138 ARG cc_start: 0.7332 (ttt180) cc_final: 0.7062 (tpt-90) REVERT: D 159 ARG cc_start: 0.9011 (tmt-80) cc_final: 0.8572 (tpt90) REVERT: D 161 HIS cc_start: 0.7013 (m-70) cc_final: 0.6615 (m90) REVERT: D 196 MET cc_start: 0.7355 (mmm) cc_final: 0.6792 (mmm) REVERT: D 205 GLU cc_start: 0.8167 (mp0) cc_final: 0.7170 (mp0) REVERT: E 64 MET cc_start: 0.8792 (ttm) cc_final: 0.8592 (ttm) REVERT: E 218 MET cc_start: 0.8460 (mmm) cc_final: 0.8186 (mmm) REVERT: E 244 CYS cc_start: 0.8671 (t) cc_final: 0.8128 (t) REVERT: F 130 ARG cc_start: 0.7952 (mmp-170) cc_final: 0.7632 (mmp80) REVERT: F 201 HIS cc_start: 0.8146 (m-70) cc_final: 0.7890 (m-70) REVERT: F 220 MET cc_start: 0.7880 (tpt) cc_final: 0.6992 (tpt) REVERT: F 242 TYR cc_start: 0.8139 (m-10) cc_final: 0.7899 (m-10) REVERT: F 254 ILE cc_start: 0.8547 (mt) cc_final: 0.8321 (tt) REVERT: G 64 MET cc_start: 0.7824 (ttp) cc_final: 0.7598 (ttm) REVERT: G 65 ASP cc_start: 0.8301 (t0) cc_final: 0.8016 (t0) REVERT: G 85 TYR cc_start: 0.7383 (t80) cc_final: 0.7019 (t80) REVERT: G 110 PHE cc_start: 0.8496 (m-10) cc_final: 0.7891 (m-10) REVERT: G 196 MET cc_start: 0.8001 (ptp) cc_final: 0.6738 (ptp) REVERT: G 205 GLU cc_start: 0.9029 (mt-10) cc_final: 0.8671 (mt-10) REVERT: H 7 GLU cc_start: 0.8882 (pt0) cc_final: 0.8364 (pp20) REVERT: H 62 TRP cc_start: 0.7268 (m-10) cc_final: 0.6955 (m-10) REVERT: H 134 GLU cc_start: 0.8223 (mp0) cc_final: 0.7977 (mp0) REVERT: H 138 ARG cc_start: 0.7335 (ttt180) cc_final: 0.7065 (tpt-90) REVERT: H 159 ARG cc_start: 0.9012 (tmt-80) cc_final: 0.8575 (tpt90) REVERT: H 161 HIS cc_start: 0.7012 (m-70) cc_final: 0.6617 (m90) REVERT: H 196 MET cc_start: 0.7356 (mmm) cc_final: 0.6794 (mmm) REVERT: H 205 GLU cc_start: 0.8172 (mp0) cc_final: 0.7173 (mp0) outliers start: 2 outliers final: 0 residues processed: 316 average time/residue: 0.2956 time to fit residues: 142.2814 Evaluate side-chains 208 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 1.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.9990 chunk 159 optimal weight: 6.9990 chunk 88 optimal weight: 7.9990 chunk 54 optimal weight: 8.9990 chunk 107 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 chunk 164 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 100 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 190 optimal weight: 6.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 HIS C 201 HIS ** D 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 HIS G 201 HIS ** H 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 19826 Z= 0.354 Angle : 0.606 6.719 27584 Z= 0.336 Chirality : 0.042 0.138 3002 Planarity : 0.004 0.034 3000 Dihedral : 22.072 87.763 3740 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.17 % Allowed : 8.32 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % 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: 0.69 (0.20), residues: 1936 helix: 1.31 (0.18), residues: 818 sheet: 0.59 (0.29), residues: 360 loop : -0.47 (0.24), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 208 HIS 0.008 0.002 HIS D 161 PHE 0.019 0.002 PHE C 23 TYR 0.017 0.002 TYR C 77 ARG 0.005 0.001 ARG E 130 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 250 time to evaluate : 2.032 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 MET cc_start: 0.8450 (mmm) cc_final: 0.8168 (mtt) REVERT: B 3 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7501 (mm-30) REVERT: B 7 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7467 (mt-10) REVERT: B 130 ARG cc_start: 0.7937 (mmp-170) cc_final: 0.7665 (mmp80) REVERT: B 134 GLU cc_start: 0.8355 (tm-30) cc_final: 0.8015 (tm-30) REVERT: B 220 MET cc_start: 0.7844 (tpt) cc_final: 0.7477 (mmm) REVERT: C 62 TRP cc_start: 0.6680 (m-10) cc_final: 0.5745 (m-10) REVERT: C 65 ASP cc_start: 0.8785 (t70) cc_final: 0.8369 (t0) REVERT: C 85 TYR cc_start: 0.7549 (t80) cc_final: 0.7150 (t80) REVERT: C 205 GLU cc_start: 0.8979 (mt-10) cc_final: 0.8606 (mt-10) REVERT: D 7 GLU cc_start: 0.8898 (pt0) cc_final: 0.8428 (pm20) REVERT: D 59 ARG cc_start: 0.7497 (mtm110) cc_final: 0.7008 (mpp80) REVERT: D 65 ASP cc_start: 0.8527 (t0) cc_final: 0.8268 (t70) REVERT: D 134 GLU cc_start: 0.8533 (mp0) cc_final: 0.8122 (tm-30) REVERT: D 161 HIS cc_start: 0.7263 (m-70) cc_final: 0.6478 (m90) REVERT: D 195 ASN cc_start: 0.8930 (m-40) cc_final: 0.8702 (t0) REVERT: D 196 MET cc_start: 0.7544 (mmm) cc_final: 0.7237 (mmt) REVERT: D 205 GLU cc_start: 0.8022 (mp0) cc_final: 0.6963 (mp0) REVERT: D 220 MET cc_start: 0.8936 (mmm) cc_final: 0.8013 (mmm) REVERT: D 251 GLU cc_start: 0.7976 (tp30) cc_final: 0.7763 (tp30) REVERT: D 265 THR cc_start: 0.8633 (m) cc_final: 0.8331 (p) REVERT: D 269 GLU cc_start: 0.5900 (pt0) cc_final: 0.5686 (pt0) REVERT: E 64 MET cc_start: 0.9033 (ttm) cc_final: 0.8815 (ttm) REVERT: E 218 MET cc_start: 0.8451 (mmm) cc_final: 0.8167 (mtt) REVERT: F 3 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7506 (mm-30) REVERT: F 7 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7469 (mt-10) REVERT: F 130 ARG cc_start: 0.7936 (mmp-170) cc_final: 0.7662 (mmp80) REVERT: F 134 GLU cc_start: 0.8356 (tm-30) cc_final: 0.8015 (tm-30) REVERT: F 220 MET cc_start: 0.7845 (tpt) cc_final: 0.7482 (mmm) REVERT: G 62 TRP cc_start: 0.6681 (m-10) cc_final: 0.5749 (m-10) REVERT: G 65 ASP cc_start: 0.8781 (t70) cc_final: 0.8362 (t0) REVERT: G 85 TYR cc_start: 0.7552 (t80) cc_final: 0.7148 (t80) REVERT: G 205 GLU cc_start: 0.8980 (mt-10) cc_final: 0.8607 (mt-10) REVERT: H 7 GLU cc_start: 0.8897 (pt0) cc_final: 0.8426 (pm20) REVERT: H 59 ARG cc_start: 0.7498 (mtm110) cc_final: 0.7009 (mpp80) REVERT: H 65 ASP cc_start: 0.8531 (t0) cc_final: 0.8272 (t70) REVERT: H 134 GLU cc_start: 0.8533 (mp0) cc_final: 0.8123 (tm-30) REVERT: H 161 HIS cc_start: 0.7252 (m-70) cc_final: 0.6465 (m90) REVERT: H 195 ASN cc_start: 0.8930 (m-40) cc_final: 0.8703 (t0) REVERT: H 196 MET cc_start: 0.7542 (mmm) cc_final: 0.7235 (mmt) REVERT: H 205 GLU cc_start: 0.8023 (mp0) cc_final: 0.6965 (mp0) REVERT: H 220 MET cc_start: 0.8937 (mmm) cc_final: 0.8012 (mmm) REVERT: H 251 GLU cc_start: 0.7973 (tp30) cc_final: 0.7764 (tp30) REVERT: H 265 THR cc_start: 0.8631 (m) cc_final: 0.8330 (p) REVERT: H 269 GLU cc_start: 0.5901 (pt0) cc_final: 0.5689 (pt0) outliers start: 36 outliers final: 24 residues processed: 266 average time/residue: 0.3047 time to fit residues: 123.3213 Evaluate side-chains 236 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 212 time to evaluate : 1.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain B residue 39 ASN Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain E residue 52 ASN Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain F residue 39 ASN Chi-restraints excluded: chain F residue 132 ILE Chi-restraints excluded: chain F residue 249 ASP Chi-restraints excluded: chain G residue 39 ASN Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 131 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 5.9990 chunk 59 optimal weight: 20.0000 chunk 158 optimal weight: 0.8980 chunk 129 optimal weight: 4.9990 chunk 52 optimal weight: 30.0000 chunk 191 optimal weight: 4.9990 chunk 206 optimal weight: 4.9990 chunk 170 optimal weight: 6.9990 chunk 189 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 153 optimal weight: 4.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN ** B 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 192 ASN ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 12 HIS ** H 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.081 19826 Z= 0.521 Angle : 0.693 9.970 27584 Z= 0.378 Chirality : 0.045 0.143 3002 Planarity : 0.005 0.055 3000 Dihedral : 22.475 93.164 3740 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.50 % Allowed : 11.88 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % 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: 0.27 (0.20), residues: 1936 helix: 1.00 (0.18), residues: 820 sheet: 0.50 (0.31), residues: 358 loop : -0.83 (0.24), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 208 HIS 0.009 0.002 HIS A 9 PHE 0.021 0.002 PHE F 88 TYR 0.020 0.002 TYR C 77 ARG 0.006 0.001 ARG D 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 218 time to evaluate : 2.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 MET cc_start: 0.8565 (mmm) cc_final: 0.8159 (mtt) REVERT: B 134 GLU cc_start: 0.8516 (tm-30) cc_final: 0.8156 (tm-30) REVERT: B 220 MET cc_start: 0.7963 (tpt) cc_final: 0.7226 (mmm) REVERT: C 62 TRP cc_start: 0.6516 (m-10) cc_final: 0.4984 (m-10) REVERT: C 65 ASP cc_start: 0.8597 (t70) cc_final: 0.8313 (t0) REVERT: C 85 TYR cc_start: 0.7519 (t80) cc_final: 0.7201 (t80) REVERT: C 97 GLU cc_start: 0.7773 (mp0) cc_final: 0.7481 (mp0) REVERT: C 113 MET cc_start: 0.6538 (mtm) cc_final: 0.5800 (mtp) REVERT: C 205 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8491 (mt-10) REVERT: D 7 GLU cc_start: 0.8924 (pt0) cc_final: 0.8472 (pm20) REVERT: D 59 ARG cc_start: 0.7814 (mtm110) cc_final: 0.7613 (mpp80) REVERT: D 65 ASP cc_start: 0.8453 (t0) cc_final: 0.8142 (t70) REVERT: D 134 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8219 (tm-30) REVERT: D 161 HIS cc_start: 0.7448 (m-70) cc_final: 0.6636 (m90) REVERT: D 196 MET cc_start: 0.7548 (mmm) cc_final: 0.7301 (mmt) REVERT: D 205 GLU cc_start: 0.7946 (mp0) cc_final: 0.7046 (mp0) REVERT: D 220 MET cc_start: 0.8756 (mmm) cc_final: 0.7823 (mmm) REVERT: E 218 MET cc_start: 0.8567 (mmm) cc_final: 0.8155 (mtt) REVERT: F 134 GLU cc_start: 0.8513 (tm-30) cc_final: 0.8152 (tm-30) REVERT: F 220 MET cc_start: 0.7966 (tpt) cc_final: 0.7231 (mmm) REVERT: G 62 TRP cc_start: 0.6526 (m-10) cc_final: 0.4989 (m-10) REVERT: G 65 ASP cc_start: 0.8605 (t70) cc_final: 0.8318 (t0) REVERT: G 85 TYR cc_start: 0.7527 (t80) cc_final: 0.7200 (t80) REVERT: G 97 GLU cc_start: 0.7774 (mp0) cc_final: 0.7481 (mp0) REVERT: G 113 MET cc_start: 0.6539 (mtm) cc_final: 0.5795 (mtp) REVERT: G 205 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8491 (mt-10) REVERT: H 7 GLU cc_start: 0.8922 (pt0) cc_final: 0.8471 (pm20) REVERT: H 59 ARG cc_start: 0.7816 (mtm110) cc_final: 0.7614 (mpp80) REVERT: H 65 ASP cc_start: 0.8452 (t0) cc_final: 0.8145 (t70) REVERT: H 134 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8222 (tm-30) REVERT: H 161 HIS cc_start: 0.7445 (m-70) cc_final: 0.6631 (m90) REVERT: H 196 MET cc_start: 0.7549 (mmm) cc_final: 0.7298 (mmt) REVERT: H 205 GLU cc_start: 0.7946 (mp0) cc_final: 0.7046 (mp0) REVERT: H 220 MET cc_start: 0.8756 (mmm) cc_final: 0.7827 (mmm) outliers start: 58 outliers final: 39 residues processed: 258 average time/residue: 0.2971 time to fit residues: 117.7195 Evaluate side-chains 244 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 203 time to evaluate : 1.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain B residue 39 ASN Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 52 ASN Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain F residue 39 ASN Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 249 ASP Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain G residue 39 ASN Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain G residue 218 MET Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 134 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 191 optimal weight: 6.9990 chunk 202 optimal weight: 0.8980 chunk 100 optimal weight: 10.0000 chunk 181 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN ** B 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 ASN E 117 GLN ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 192 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 19826 Z= 0.386 Angle : 0.605 9.444 27584 Z= 0.333 Chirality : 0.041 0.132 3002 Planarity : 0.004 0.032 3000 Dihedral : 22.396 92.615 3740 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.68 % Allowed : 14.23 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % 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: 0.45 (0.20), residues: 1936 helix: 1.20 (0.18), residues: 822 sheet: 0.58 (0.31), residues: 344 loop : -0.78 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 208 HIS 0.007 0.001 HIS B 182 PHE 0.029 0.002 PHE C 21 TYR 0.021 0.002 TYR C 77 ARG 0.007 0.000 ARG D 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 213 time to evaluate : 2.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 MET cc_start: 0.8536 (mmm) cc_final: 0.8145 (mtt) REVERT: B 3 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7546 (mm-30) REVERT: B 7 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7562 (mt-10) REVERT: B 12 HIS cc_start: 0.6437 (OUTLIER) cc_final: 0.6000 (m-70) REVERT: B 134 GLU cc_start: 0.8537 (tm-30) cc_final: 0.7793 (tm-30) REVERT: B 220 MET cc_start: 0.7994 (tpt) cc_final: 0.7252 (mmm) REVERT: C 62 TRP cc_start: 0.6515 (m-10) cc_final: 0.4802 (m-10) REVERT: C 65 ASP cc_start: 0.8587 (t0) cc_final: 0.8270 (t0) REVERT: C 85 TYR cc_start: 0.7531 (t80) cc_final: 0.7272 (t80) REVERT: C 113 MET cc_start: 0.6675 (mtm) cc_final: 0.5788 (mtp) REVERT: C 169 ASN cc_start: 0.7233 (m-40) cc_final: 0.6197 (t0) REVERT: C 205 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8437 (mt-10) REVERT: D 7 GLU cc_start: 0.8908 (pt0) cc_final: 0.8450 (pm20) REVERT: D 59 ARG cc_start: 0.7973 (mtm110) cc_final: 0.7655 (mpp80) REVERT: D 65 ASP cc_start: 0.8480 (t0) cc_final: 0.8217 (t70) REVERT: D 134 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8097 (tm-30) REVERT: D 161 HIS cc_start: 0.7381 (m-70) cc_final: 0.6481 (m90) REVERT: D 205 GLU cc_start: 0.7833 (mp0) cc_final: 0.7022 (mp0) REVERT: D 220 MET cc_start: 0.8655 (mmm) cc_final: 0.7542 (mmm) REVERT: D 251 GLU cc_start: 0.7684 (tp30) cc_final: 0.7316 (tp30) REVERT: E 218 MET cc_start: 0.8537 (mmm) cc_final: 0.8145 (mtt) REVERT: F 3 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7553 (mm-30) REVERT: F 7 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7561 (mt-10) REVERT: F 12 HIS cc_start: 0.6425 (OUTLIER) cc_final: 0.5989 (m-70) REVERT: F 134 GLU cc_start: 0.8533 (tm-30) cc_final: 0.7788 (tm-30) REVERT: F 220 MET cc_start: 0.7999 (tpt) cc_final: 0.7259 (mmm) REVERT: G 62 TRP cc_start: 0.6521 (m-10) cc_final: 0.4809 (m-10) REVERT: G 65 ASP cc_start: 0.8588 (t0) cc_final: 0.8268 (t0) REVERT: G 85 TYR cc_start: 0.7537 (t80) cc_final: 0.7270 (t80) REVERT: G 113 MET cc_start: 0.6669 (mtm) cc_final: 0.5775 (mtp) REVERT: G 169 ASN cc_start: 0.7237 (m-40) cc_final: 0.6199 (t0) REVERT: G 205 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8435 (mt-10) REVERT: H 7 GLU cc_start: 0.8908 (pt0) cc_final: 0.8448 (pm20) REVERT: H 59 ARG cc_start: 0.7974 (mtm110) cc_final: 0.7655 (mpp80) REVERT: H 65 ASP cc_start: 0.8481 (t0) cc_final: 0.8218 (t70) REVERT: H 134 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8099 (tm-30) REVERT: H 161 HIS cc_start: 0.7376 (m-70) cc_final: 0.6477 (m90) REVERT: H 205 GLU cc_start: 0.7833 (mp0) cc_final: 0.7023 (mp0) REVERT: H 220 MET cc_start: 0.8656 (mmm) cc_final: 0.7545 (mmm) REVERT: H 251 GLU cc_start: 0.7688 (tp30) cc_final: 0.7319 (tp30) outliers start: 61 outliers final: 41 residues processed: 250 average time/residue: 0.2942 time to fit residues: 112.9499 Evaluate side-chains 245 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 200 time to evaluate : 1.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 221 TRP Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 39 ASN Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 52 ASN Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 221 TRP Chi-restraints excluded: chain F residue 12 HIS Chi-restraints excluded: chain F residue 39 ASN Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 237 THR Chi-restraints excluded: chain F residue 249 ASP Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain G residue 39 ASN Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain G residue 218 MET Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 233 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 0.0970 chunk 115 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 173 optimal weight: 7.9990 chunk 140 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 103 optimal weight: 8.9990 chunk 182 optimal weight: 7.9990 chunk 51 optimal weight: 30.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 HIS G 161 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19826 Z= 0.192 Angle : 0.531 8.094 27584 Z= 0.289 Chirality : 0.038 0.131 3002 Planarity : 0.004 0.033 3000 Dihedral : 22.025 86.400 3740 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.08 % Allowed : 15.92 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % 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: 0.74 (0.20), residues: 1936 helix: 1.57 (0.19), residues: 824 sheet: 0.78 (0.30), residues: 348 loop : -0.83 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 208 HIS 0.005 0.001 HIS B 9 PHE 0.015 0.001 PHE C 21 TYR 0.012 0.001 TYR C 112 ARG 0.003 0.000 ARG D 159 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 225 time to evaluate : 2.011 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 3 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7473 (mm-30) REVERT: B 7 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7483 (mt-10) REVERT: B 12 HIS cc_start: 0.5881 (OUTLIER) cc_final: 0.5674 (m-70) REVERT: B 134 GLU cc_start: 0.8494 (tm-30) cc_final: 0.8083 (tm-30) REVERT: B 220 MET cc_start: 0.7996 (tpt) cc_final: 0.7290 (mmm) REVERT: C 62 TRP cc_start: 0.6483 (m-10) cc_final: 0.4881 (m-10) REVERT: C 65 ASP cc_start: 0.8694 (t0) cc_final: 0.8309 (t0) REVERT: C 85 TYR cc_start: 0.7481 (t80) cc_final: 0.7267 (t80) REVERT: C 92 THR cc_start: 0.2944 (OUTLIER) cc_final: 0.2586 (p) REVERT: C 113 MET cc_start: 0.6763 (mtm) cc_final: 0.5970 (mtm) REVERT: C 169 ASN cc_start: 0.6951 (m-40) cc_final: 0.6174 (t0) REVERT: C 205 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8321 (mt-10) REVERT: D 7 GLU cc_start: 0.8870 (pt0) cc_final: 0.8403 (pm20) REVERT: D 15 ASN cc_start: 0.7840 (m-40) cc_final: 0.7188 (p0) REVERT: D 59 ARG cc_start: 0.7881 (mtm110) cc_final: 0.7484 (mpp80) REVERT: D 134 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8038 (tm-30) REVERT: D 161 HIS cc_start: 0.7439 (m-70) cc_final: 0.6831 (m90) REVERT: D 195 ASN cc_start: 0.8496 (m-40) cc_final: 0.7837 (m-40) REVERT: D 196 MET cc_start: 0.6476 (mmt) cc_final: 0.5842 (mmm) REVERT: D 205 GLU cc_start: 0.8119 (mp0) cc_final: 0.7306 (mp0) REVERT: D 220 MET cc_start: 0.8635 (mmm) cc_final: 0.7232 (mmm) REVERT: F 3 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7477 (mm-30) REVERT: F 7 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7485 (mt-10) REVERT: F 12 HIS cc_start: 0.5885 (OUTLIER) cc_final: 0.5681 (m-70) REVERT: F 134 GLU cc_start: 0.8490 (tm-30) cc_final: 0.8077 (tm-30) REVERT: F 220 MET cc_start: 0.7999 (tpt) cc_final: 0.7298 (mmm) REVERT: G 62 TRP cc_start: 0.6484 (m-10) cc_final: 0.4882 (m-10) REVERT: G 65 ASP cc_start: 0.8696 (t0) cc_final: 0.8304 (t0) REVERT: G 85 TYR cc_start: 0.7482 (t80) cc_final: 0.7264 (t80) REVERT: G 92 THR cc_start: 0.2937 (OUTLIER) cc_final: 0.2581 (p) REVERT: G 113 MET cc_start: 0.6758 (mtm) cc_final: 0.5963 (mtm) REVERT: G 169 ASN cc_start: 0.6953 (m-40) cc_final: 0.6177 (t0) REVERT: G 205 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8324 (mt-10) REVERT: H 7 GLU cc_start: 0.8868 (pt0) cc_final: 0.8399 (pm20) REVERT: H 15 ASN cc_start: 0.7840 (m-40) cc_final: 0.7184 (p0) REVERT: H 59 ARG cc_start: 0.7879 (mtm110) cc_final: 0.7481 (mpp80) REVERT: H 134 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8039 (tm-30) REVERT: H 161 HIS cc_start: 0.7429 (m-70) cc_final: 0.6827 (m90) REVERT: H 195 ASN cc_start: 0.8496 (m-40) cc_final: 0.7837 (m-40) REVERT: H 196 MET cc_start: 0.6477 (mmt) cc_final: 0.5844 (mmm) REVERT: H 205 GLU cc_start: 0.8119 (mp0) cc_final: 0.7306 (mp0) REVERT: H 220 MET cc_start: 0.8633 (mmm) cc_final: 0.7234 (mmm) outliers start: 51 outliers final: 27 residues processed: 258 average time/residue: 0.2945 time to fit residues: 116.3178 Evaluate side-chains 238 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 205 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 221 TRP Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 52 ASN Chi-restraints excluded: chain E residue 221 TRP Chi-restraints excluded: chain F residue 12 HIS Chi-restraints excluded: chain F residue 249 ASP Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 39 ASN Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain G residue 218 MET Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 233 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 8.9990 chunk 182 optimal weight: 8.9990 chunk 40 optimal weight: 0.8980 chunk 119 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 203 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 94 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19826 Z= 0.260 Angle : 0.549 7.219 27584 Z= 0.300 Chirality : 0.039 0.132 3002 Planarity : 0.004 0.053 3000 Dihedral : 22.125 85.963 3740 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.50 % Allowed : 16.16 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % 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: 0.76 (0.20), residues: 1936 helix: 1.59 (0.19), residues: 824 sheet: 0.69 (0.30), residues: 368 loop : -0.80 (0.24), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 208 HIS 0.005 0.001 HIS A 9 PHE 0.010 0.001 PHE B 88 TYR 0.011 0.001 TYR E 77 ARG 0.003 0.000 ARG D 159 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 202 time to evaluate : 1.876 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7745 (mm-30) REVERT: B 3 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7576 (mm-30) REVERT: B 7 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7468 (mt-10) REVERT: B 12 HIS cc_start: 0.6204 (OUTLIER) cc_final: 0.5918 (m-70) REVERT: B 134 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8087 (tm-30) REVERT: B 220 MET cc_start: 0.8010 (tpt) cc_final: 0.7303 (mmm) REVERT: C 62 TRP cc_start: 0.6483 (m-10) cc_final: 0.4977 (m-10) REVERT: C 65 ASP cc_start: 0.8721 (t0) cc_final: 0.8351 (t0) REVERT: C 85 TYR cc_start: 0.7526 (t80) cc_final: 0.7292 (t80) REVERT: C 97 GLU cc_start: 0.7635 (mp0) cc_final: 0.7400 (mp0) REVERT: C 169 ASN cc_start: 0.6941 (m-40) cc_final: 0.6186 (t0) REVERT: C 205 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8303 (mt-10) REVERT: D 7 GLU cc_start: 0.8857 (pt0) cc_final: 0.8381 (pm20) REVERT: D 59 ARG cc_start: 0.7928 (mtm110) cc_final: 0.7616 (mpp80) REVERT: D 134 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8038 (tm-30) REVERT: D 205 GLU cc_start: 0.7857 (mp0) cc_final: 0.6981 (mp0) REVERT: D 220 MET cc_start: 0.8554 (mmm) cc_final: 0.7175 (mmm) REVERT: D 251 GLU cc_start: 0.7429 (tp30) cc_final: 0.7213 (tp30) REVERT: E 28 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7744 (mm-30) REVERT: F 3 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7579 (mm-30) REVERT: F 7 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7469 (mt-10) REVERT: F 12 HIS cc_start: 0.6208 (OUTLIER) cc_final: 0.5918 (m-70) REVERT: F 134 GLU cc_start: 0.8499 (tm-30) cc_final: 0.8083 (tm-30) REVERT: F 220 MET cc_start: 0.8010 (tpt) cc_final: 0.7309 (mmm) REVERT: G 62 TRP cc_start: 0.6488 (m-10) cc_final: 0.4979 (m-10) REVERT: G 65 ASP cc_start: 0.8727 (t0) cc_final: 0.8351 (t0) REVERT: G 85 TYR cc_start: 0.7530 (t80) cc_final: 0.7292 (t80) REVERT: G 97 GLU cc_start: 0.7639 (mp0) cc_final: 0.7403 (mp0) REVERT: G 169 ASN cc_start: 0.6943 (m-40) cc_final: 0.6190 (t0) REVERT: G 205 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8309 (mt-10) REVERT: H 7 GLU cc_start: 0.8851 (pt0) cc_final: 0.8370 (pm20) REVERT: H 59 ARG cc_start: 0.7930 (mtm110) cc_final: 0.7619 (mpp80) REVERT: H 134 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8037 (tm-30) REVERT: H 205 GLU cc_start: 0.7858 (mp0) cc_final: 0.6981 (mp0) REVERT: H 220 MET cc_start: 0.8558 (mmm) cc_final: 0.7177 (mmm) REVERT: H 251 GLU cc_start: 0.7428 (tp30) cc_final: 0.7212 (tp30) outliers start: 58 outliers final: 45 residues processed: 243 average time/residue: 0.2879 time to fit residues: 108.4907 Evaluate side-chains 243 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 194 time to evaluate : 1.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 208 TRP Chi-restraints excluded: chain A residue 221 TRP Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 39 ASN Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 52 ASN Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 208 TRP Chi-restraints excluded: chain E residue 221 TRP Chi-restraints excluded: chain F residue 12 HIS Chi-restraints excluded: chain F residue 39 ASN Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 249 ASP Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 39 ASN Chi-restraints excluded: chain G residue 194 VAL Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain G residue 218 MET Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 233 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 114 optimal weight: 0.3980 chunk 171 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 202 optimal weight: 0.2980 chunk 126 optimal weight: 0.9990 chunk 123 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19826 Z= 0.176 Angle : 0.517 7.392 27584 Z= 0.283 Chirality : 0.037 0.131 3002 Planarity : 0.004 0.047 3000 Dihedral : 21.919 81.858 3740 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.96 % Allowed : 17.13 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % 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: 0.91 (0.20), residues: 1936 helix: 1.75 (0.19), residues: 824 sheet: 0.62 (0.30), residues: 364 loop : -0.69 (0.24), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 208 HIS 0.005 0.001 HIS F 105 PHE 0.009 0.001 PHE G 23 TYR 0.012 0.001 TYR C 112 ARG 0.002 0.000 ARG H 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 216 time to evaluate : 1.892 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7668 (mm-30) REVERT: B 3 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7589 (mm-30) REVERT: B 7 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7475 (mt-10) REVERT: B 12 HIS cc_start: 0.5828 (OUTLIER) cc_final: 0.5371 (m-70) REVERT: B 134 GLU cc_start: 0.8462 (tm-30) cc_final: 0.8059 (tm-30) REVERT: B 220 MET cc_start: 0.7991 (tpt) cc_final: 0.7319 (mmm) REVERT: C 62 TRP cc_start: 0.6357 (m-10) cc_final: 0.5628 (m-10) REVERT: C 64 MET cc_start: 0.7999 (ttp) cc_final: 0.7194 (ttp) REVERT: C 65 ASP cc_start: 0.8709 (t0) cc_final: 0.7975 (m-30) REVERT: C 85 TYR cc_start: 0.7632 (t80) cc_final: 0.7392 (t80) REVERT: C 92 THR cc_start: 0.3553 (OUTLIER) cc_final: 0.3191 (p) REVERT: C 113 MET cc_start: 0.6757 (mtm) cc_final: 0.6279 (mtm) REVERT: C 169 ASN cc_start: 0.6861 (m-40) cc_final: 0.6136 (t0) REVERT: C 205 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8263 (mt-10) REVERT: D 7 GLU cc_start: 0.8831 (pt0) cc_final: 0.8358 (pm20) REVERT: D 59 ARG cc_start: 0.7866 (mtm110) cc_final: 0.7526 (mpp80) REVERT: D 134 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8114 (tm-30) REVERT: D 220 MET cc_start: 0.8557 (mmm) cc_final: 0.7274 (mmm) REVERT: E 28 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7667 (mm-30) REVERT: F 3 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7592 (mm-30) REVERT: F 7 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7476 (mt-10) REVERT: F 11 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8328 (tt) REVERT: F 12 HIS cc_start: 0.5836 (OUTLIER) cc_final: 0.5389 (m-70) REVERT: F 134 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8055 (tm-30) REVERT: F 220 MET cc_start: 0.7994 (tpt) cc_final: 0.7322 (mmm) REVERT: G 62 TRP cc_start: 0.6358 (m-10) cc_final: 0.5634 (m-10) REVERT: G 64 MET cc_start: 0.8007 (ttp) cc_final: 0.7193 (ttp) REVERT: G 65 ASP cc_start: 0.8715 (t0) cc_final: 0.7973 (m-30) REVERT: G 85 TYR cc_start: 0.7635 (t80) cc_final: 0.7390 (t80) REVERT: G 92 THR cc_start: 0.3554 (OUTLIER) cc_final: 0.3194 (p) REVERT: G 113 MET cc_start: 0.6752 (mtm) cc_final: 0.6275 (mtm) REVERT: G 169 ASN cc_start: 0.6861 (m-40) cc_final: 0.6139 (t0) REVERT: G 205 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8267 (mt-10) REVERT: H 7 GLU cc_start: 0.8830 (pt0) cc_final: 0.8355 (pm20) REVERT: H 59 ARG cc_start: 0.7866 (mtm110) cc_final: 0.7530 (mpp80) REVERT: H 134 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8116 (tm-30) REVERT: H 220 MET cc_start: 0.8558 (mmm) cc_final: 0.7275 (mmm) outliers start: 49 outliers final: 33 residues processed: 247 average time/residue: 0.2819 time to fit residues: 107.2522 Evaluate side-chains 232 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 192 time to evaluate : 1.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 208 TRP Chi-restraints excluded: chain A residue 221 TRP Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 52 ASN Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 221 TRP Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 12 HIS Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 249 ASP Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 39 ASN Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 194 VAL Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 233 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 chunk 137 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 chunk 18 optimal weight: 0.9980 chunk 159 optimal weight: 8.9990 chunk 184 optimal weight: 0.0470 overall best weight: 1.2082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 161 HIS ** E 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 161 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19826 Z= 0.212 Angle : 0.531 7.601 27584 Z= 0.290 Chirality : 0.038 0.155 3002 Planarity : 0.004 0.045 3000 Dihedral : 21.953 82.226 3740 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.02 % Allowed : 17.07 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % 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: 0.95 (0.20), residues: 1936 helix: 1.78 (0.19), residues: 824 sheet: 0.79 (0.31), residues: 336 loop : -0.69 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 208 HIS 0.007 0.001 HIS E 161 PHE 0.027 0.001 PHE C 21 TYR 0.010 0.001 TYR F 177 ARG 0.006 0.000 ARG H 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 200 time to evaluate : 2.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 134 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8064 (tm-30) REVERT: B 220 MET cc_start: 0.8020 (tpt) cc_final: 0.7366 (mmm) REVERT: C 7 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7849 (tm-30) REVERT: C 62 TRP cc_start: 0.6399 (m-10) cc_final: 0.5894 (m-10) REVERT: C 64 MET cc_start: 0.7958 (ttp) cc_final: 0.7266 (ttp) REVERT: C 65 ASP cc_start: 0.8713 (t0) cc_final: 0.7978 (m-30) REVERT: C 85 TYR cc_start: 0.7811 (t80) cc_final: 0.7565 (t80) REVERT: C 92 THR cc_start: 0.3364 (OUTLIER) cc_final: 0.2983 (p) REVERT: C 158 GLU cc_start: 0.8050 (tp30) cc_final: 0.7666 (tp30) REVERT: C 169 ASN cc_start: 0.6858 (m-40) cc_final: 0.6136 (t0) REVERT: C 205 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8289 (mt-10) REVERT: D 7 GLU cc_start: 0.8824 (pt0) cc_final: 0.8361 (pm20) REVERT: D 59 ARG cc_start: 0.7887 (mtm110) cc_final: 0.7546 (mpp80) REVERT: D 134 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8104 (tm-30) REVERT: D 205 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7379 (mp0) REVERT: D 220 MET cc_start: 0.8503 (mmm) cc_final: 0.7209 (mmm) REVERT: F 11 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8358 (tt) REVERT: F 12 HIS cc_start: 0.6033 (OUTLIER) cc_final: 0.5464 (m-70) REVERT: F 134 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8061 (tm-30) REVERT: F 220 MET cc_start: 0.8022 (tpt) cc_final: 0.7370 (mmm) REVERT: G 7 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7847 (tm-30) REVERT: G 62 TRP cc_start: 0.6399 (m-10) cc_final: 0.5899 (m-10) REVERT: G 64 MET cc_start: 0.7963 (ttp) cc_final: 0.7260 (ttp) REVERT: G 65 ASP cc_start: 0.8716 (t0) cc_final: 0.7971 (m-30) REVERT: G 85 TYR cc_start: 0.7814 (t80) cc_final: 0.7565 (t80) REVERT: G 92 THR cc_start: 0.3363 (OUTLIER) cc_final: 0.2984 (p) REVERT: G 158 GLU cc_start: 0.8050 (tp30) cc_final: 0.7667 (tp30) REVERT: G 169 ASN cc_start: 0.6861 (m-40) cc_final: 0.6141 (t0) REVERT: G 205 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8292 (mt-10) REVERT: H 7 GLU cc_start: 0.8822 (pt0) cc_final: 0.8359 (pm20) REVERT: H 59 ARG cc_start: 0.7892 (mtm110) cc_final: 0.7545 (mpp80) REVERT: H 134 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8104 (tm-30) REVERT: H 205 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7380 (mp0) REVERT: H 220 MET cc_start: 0.8505 (mmm) cc_final: 0.7210 (mmm) outliers start: 50 outliers final: 39 residues processed: 232 average time/residue: 0.2916 time to fit residues: 104.2942 Evaluate side-chains 239 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 194 time to evaluate : 1.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 208 TRP Chi-restraints excluded: chain A residue 221 TRP Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 52 ASN Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 208 TRP Chi-restraints excluded: chain E residue 221 TRP Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 12 HIS Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 249 ASP Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 39 ASN Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 194 VAL Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 233 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 7.9990 chunk 176 optimal weight: 4.9990 chunk 188 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 148 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 170 optimal weight: 3.9990 chunk 178 optimal weight: 0.0570 chunk 187 optimal weight: 9.9990 chunk 123 optimal weight: 0.6980 overall best weight: 1.9504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19826 Z= 0.285 Angle : 0.572 7.887 27584 Z= 0.312 Chirality : 0.039 0.146 3002 Planarity : 0.004 0.040 3000 Dihedral : 22.114 85.089 3740 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.14 % Allowed : 17.37 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % 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: 0.92 (0.20), residues: 1936 helix: 1.72 (0.19), residues: 824 sheet: 0.68 (0.29), residues: 368 loop : -0.66 (0.24), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 208 HIS 0.011 0.001 HIS H 161 PHE 0.023 0.001 PHE G 21 TYR 0.010 0.001 TYR C 77 ARG 0.006 0.000 ARG A 130 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 192 time to evaluate : 1.877 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 134 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8092 (tm-30) REVERT: B 220 MET cc_start: 0.8063 (tpt) cc_final: 0.7389 (mmm) REVERT: C 7 GLU cc_start: 0.8108 (tm-30) cc_final: 0.7884 (tm-30) REVERT: C 62 TRP cc_start: 0.6326 (m-10) cc_final: 0.5851 (m-10) REVERT: C 64 MET cc_start: 0.7951 (ttp) cc_final: 0.7291 (ttp) REVERT: C 65 ASP cc_start: 0.8695 (t0) cc_final: 0.7974 (m-30) REVERT: C 85 TYR cc_start: 0.7834 (t80) cc_final: 0.7577 (t80) REVERT: C 92 THR cc_start: 0.3120 (OUTLIER) cc_final: 0.2814 (p) REVERT: C 158 GLU cc_start: 0.8066 (tp30) cc_final: 0.7688 (tp30) REVERT: C 169 ASN cc_start: 0.6772 (m-40) cc_final: 0.6033 (t0) REVERT: C 205 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8308 (mt-10) REVERT: D 7 GLU cc_start: 0.8840 (pt0) cc_final: 0.8420 (pm20) REVERT: D 59 ARG cc_start: 0.7941 (mtm110) cc_final: 0.7588 (mpp80) REVERT: D 134 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8117 (tm-30) REVERT: D 205 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7333 (mp0) REVERT: D 220 MET cc_start: 0.8507 (mmm) cc_final: 0.7199 (mmm) REVERT: F 12 HIS cc_start: 0.6242 (OUTLIER) cc_final: 0.5660 (m-70) REVERT: F 134 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8087 (tm-30) REVERT: F 220 MET cc_start: 0.8066 (tpt) cc_final: 0.7396 (mmm) REVERT: G 7 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7881 (tm-30) REVERT: G 62 TRP cc_start: 0.6325 (m-10) cc_final: 0.5854 (m-10) REVERT: G 64 MET cc_start: 0.7957 (ttp) cc_final: 0.7289 (ttp) REVERT: G 65 ASP cc_start: 0.8703 (t0) cc_final: 0.7968 (m-30) REVERT: G 85 TYR cc_start: 0.7839 (t80) cc_final: 0.7578 (t80) REVERT: G 92 THR cc_start: 0.3087 (OUTLIER) cc_final: 0.2790 (p) REVERT: G 158 GLU cc_start: 0.8067 (tp30) cc_final: 0.7688 (tp30) REVERT: G 169 ASN cc_start: 0.6770 (m-40) cc_final: 0.6033 (t0) REVERT: G 205 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8311 (mt-10) REVERT: H 7 GLU cc_start: 0.8840 (pt0) cc_final: 0.8418 (pm20) REVERT: H 59 ARG cc_start: 0.7935 (mtm110) cc_final: 0.7584 (mpp80) REVERT: H 134 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8116 (tm-30) REVERT: H 205 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7334 (mp0) REVERT: H 220 MET cc_start: 0.8505 (mmm) cc_final: 0.7197 (mmm) outliers start: 52 outliers final: 41 residues processed: 228 average time/residue: 0.2913 time to fit residues: 102.4485 Evaluate side-chains 232 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 186 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 208 TRP Chi-restraints excluded: chain A residue 221 TRP Chi-restraints excluded: chain B residue 39 ASN Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 52 ASN Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 208 TRP Chi-restraints excluded: chain E residue 221 TRP Chi-restraints excluded: chain F residue 12 HIS Chi-restraints excluded: chain F residue 39 ASN Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 249 ASP Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 39 ASN Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 194 VAL Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 233 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 6.9990 chunk 121 optimal weight: 0.6980 chunk 94 optimal weight: 6.9990 chunk 138 optimal weight: 3.9990 chunk 209 optimal weight: 10.0000 chunk 192 optimal weight: 3.9990 chunk 166 optimal weight: 9.9990 chunk 17 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 19826 Z= 0.322 Angle : 0.606 9.602 27584 Z= 0.327 Chirality : 0.040 0.143 3002 Planarity : 0.004 0.038 3000 Dihedral : 22.256 87.898 3740 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.71 % Allowed : 18.09 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % 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: 0.77 (0.20), residues: 1936 helix: 1.59 (0.19), residues: 822 sheet: 0.60 (0.30), residues: 368 loop : -0.73 (0.24), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 208 HIS 0.009 0.001 HIS E 161 PHE 0.021 0.001 PHE C 21 TYR 0.012 0.001 TYR G 77 ARG 0.006 0.000 ARG E 130 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 191 time to evaluate : 1.939 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 134 GLU cc_start: 0.8549 (tm-30) cc_final: 0.7768 (tm-30) REVERT: B 220 MET cc_start: 0.8063 (tpt) cc_final: 0.7414 (mmm) REVERT: C 7 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7887 (tm-30) REVERT: C 62 TRP cc_start: 0.6427 (m-10) cc_final: 0.5096 (m-10) REVERT: C 64 MET cc_start: 0.8112 (ttp) cc_final: 0.7435 (ttp) REVERT: C 65 ASP cc_start: 0.8670 (t0) cc_final: 0.7973 (m-30) REVERT: C 85 TYR cc_start: 0.7783 (t80) cc_final: 0.7489 (t80) REVERT: C 158 GLU cc_start: 0.8096 (tp30) cc_final: 0.7733 (tp30) REVERT: C 169 ASN cc_start: 0.6716 (m-40) cc_final: 0.6000 (t0) REVERT: C 205 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8299 (mt-10) REVERT: D 7 GLU cc_start: 0.8856 (pt0) cc_final: 0.8460 (pm20) REVERT: D 59 ARG cc_start: 0.7964 (mtm110) cc_final: 0.7611 (mpp80) REVERT: D 134 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8123 (pp20) REVERT: D 138 ARG cc_start: 0.6748 (tpt-90) cc_final: 0.6437 (tpt-90) REVERT: D 143 HIS cc_start: 0.8592 (t70) cc_final: 0.8128 (t-90) REVERT: D 205 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7490 (mp0) REVERT: D 220 MET cc_start: 0.8525 (mmm) cc_final: 0.7169 (mmm) REVERT: F 12 HIS cc_start: 0.6065 (OUTLIER) cc_final: 0.5785 (m-70) REVERT: F 134 GLU cc_start: 0.8544 (tm-30) cc_final: 0.7759 (tm-30) REVERT: F 220 MET cc_start: 0.8063 (tpt) cc_final: 0.7410 (mmm) REVERT: G 7 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7879 (tm-30) REVERT: G 62 TRP cc_start: 0.6430 (m-10) cc_final: 0.5098 (m-10) REVERT: G 64 MET cc_start: 0.8121 (ttp) cc_final: 0.7439 (ttp) REVERT: G 65 ASP cc_start: 0.8679 (t0) cc_final: 0.7967 (m-30) REVERT: G 85 TYR cc_start: 0.7791 (t80) cc_final: 0.7489 (t80) REVERT: G 158 GLU cc_start: 0.8094 (tp30) cc_final: 0.7732 (tp30) REVERT: G 169 ASN cc_start: 0.6715 (m-40) cc_final: 0.6001 (t0) REVERT: G 205 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8302 (mt-10) REVERT: H 7 GLU cc_start: 0.8854 (pt0) cc_final: 0.8457 (pm20) REVERT: H 59 ARG cc_start: 0.7990 (mtm110) cc_final: 0.7626 (mpp80) REVERT: H 134 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8117 (pp20) REVERT: H 138 ARG cc_start: 0.6722 (tpt-90) cc_final: 0.6392 (tpt-90) REVERT: H 143 HIS cc_start: 0.8578 (t70) cc_final: 0.8119 (t-90) REVERT: H 205 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7490 (mp0) REVERT: H 220 MET cc_start: 0.8523 (mmm) cc_final: 0.7167 (mmm) outliers start: 45 outliers final: 42 residues processed: 220 average time/residue: 0.3077 time to fit residues: 103.1115 Evaluate side-chains 231 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 186 time to evaluate : 1.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 208 TRP Chi-restraints excluded: chain A residue 221 TRP Chi-restraints excluded: chain B residue 39 ASN Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 52 ASN Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 208 TRP Chi-restraints excluded: chain E residue 221 TRP Chi-restraints excluded: chain F residue 12 HIS Chi-restraints excluded: chain F residue 39 ASN Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 249 ASP Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 39 ASN Chi-restraints excluded: chain G residue 194 VAL Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 233 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.9990 chunk 51 optimal weight: 30.0000 chunk 153 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 166 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 171 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 30 optimal weight: 0.0970 chunk 146 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 HIS ** E 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.143972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.101054 restraints weight = 44094.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.104014 restraints weight = 20804.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.105555 restraints weight = 13310.697| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19826 Z= 0.200 Angle : 0.561 10.173 27584 Z= 0.302 Chirality : 0.038 0.173 3002 Planarity : 0.004 0.043 3000 Dihedral : 22.005 84.114 3740 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.53 % Allowed : 18.76 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % 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: 0.90 (0.20), residues: 1936 helix: 1.73 (0.19), residues: 824 sheet: 0.50 (0.29), residues: 372 loop : -0.60 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 208 HIS 0.007 0.001 HIS E 161 PHE 0.024 0.001 PHE G 21 TYR 0.011 0.001 TYR C 112 ARG 0.006 0.000 ARG E 130 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3253.99 seconds wall clock time: 60 minutes 12.35 seconds (3612.35 seconds total)