Starting phenix.real_space_refine on Thu Mar 21 22:07:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ut1_26744/03_2024/7ut1_26744.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ut1_26744/03_2024/7ut1_26744.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ut1_26744/03_2024/7ut1_26744.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ut1_26744/03_2024/7ut1_26744.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ut1_26744/03_2024/7ut1_26744.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ut1_26744/03_2024/7ut1_26744.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 12 6.06 5 P 294 5.49 5 S 108 5.16 5 C 19070 2.51 5 N 5707 2.21 5 O 6128 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "a TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 134": "OE1" <-> "OE2" Residue "e GLU 3": "OE1" <-> "OE2" Residue "e TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 97": "OE1" <-> "OE2" Residue "e TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 97": "OE1" <-> "OE2" Residue "f TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 122": "OD1" <-> "OD2" Residue "h TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 158": "OE1" <-> "OE2" Residue "h ASP 249": "OD1" <-> "OD2" Residue "A GLU 134": "OE1" <-> "OE2" Residue "E TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 65": "OD1" <-> "OD2" Residue "H GLU 97": "OE1" <-> "OE2" Residue "H ASP 101": "OD1" <-> "OD2" Residue "H TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 251": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 31319 Number of models: 1 Model: "" Number of chains: 40 Chain: "a" Number of atoms: 2114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2114 Classifications: {'peptide': 264} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 245} Chain: "b" Number of atoms: 1957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1957 Classifications: {'peptide': 244} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 229} Chain breaks: 2 Chain: "c" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 385 Classifications: {'peptide': 48} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 42} Chain: "d" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 392 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 43} Chain: "e" Number of atoms: 2114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2114 Classifications: {'peptide': 264} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 245} Chain: "f" Number of atoms: 1951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1951 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 228} Chain breaks: 2 Chain: "g" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1893 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 223} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "h" Number of atoms: 1833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1833 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 218} 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: "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: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 773 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain: "n" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 254 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "A" Number of atoms: 2114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2114 Classifications: {'peptide': 264} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 245} Chain: "B" Number of atoms: 1944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1944 Classifications: {'peptide': 242} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 227} Chain breaks: 2 Chain: "C" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 385 Classifications: {'peptide': 48} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 42} Chain: "D" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 392 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 43} 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: 1896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1896 Classifications: {'peptide': 235} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 222} Chain breaks: 3 Chain: "G" Number of atoms: 1886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1886 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 222} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 1829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1829 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 217} 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: "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: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 793 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain: "N" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 275 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 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: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 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} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 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: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 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 37 125.286 142.773 61.608 1.00 95.44 S ATOM 320 SG CYS a 40 126.733 139.149 61.696 1.00 95.68 S ATOM 2413 SG CYS b 37 128.256 112.529 126.899 1.00120.05 S ATOM 2434 SG CYS b 40 130.337 109.306 126.569 1.00123.54 S ATOM 5147 SG CYS e 37 133.029 89.710 80.176 1.00102.13 S ATOM 5168 SG CYS e 40 134.087 93.455 80.673 1.00102.33 S ATOM 7261 SG CYS f 37 111.121 118.655 17.814 1.00142.84 S ATOM 7282 SG CYS f 40 112.978 121.937 17.354 1.00141.64 S ATOM 9208 SG CYS g 37 148.227 49.657 40.139 1.00163.94 S ATOM 9229 SG CYS g 40 145.863 51.940 37.762 1.00168.87 S ATOM 11069 SG CYS h 37 102.110 70.175 55.288 1.00145.15 S ATOM 11090 SG CYS h 40 105.701 70.006 56.762 1.00142.88 S ATOM 15968 SG CYS A 37 35.450 78.283 86.746 1.00171.04 S ATOM 15989 SG CYS A 40 37.938 75.306 86.852 1.00170.83 S ATOM 18082 SG CYS B 37 58.337 71.714 18.663 1.00223.27 S ATOM 18103 SG CYS B 40 60.406 68.388 18.643 1.00222.73 S ATOM 20803 SG CYS E 37 81.401 54.308 61.881 1.00148.42 S ATOM 20824 SG CYS E 40 78.069 54.189 62.930 1.00150.52 S ATOM 22924 SG CYS F 37 65.713 78.131 129.403 1.00244.27 S ATOM 22945 SG CYS F 40 61.882 77.353 129.916 1.00241.79 S ATOM 24816 SG CYS G 37 116.924 22.712 96.881 1.00208.80 S ATOM 24837 SG CYS G 40 115.546 25.412 99.277 1.00209.59 S ATOM 26670 SG CYS H 37 112.803 74.655 86.409 1.00178.82 S ATOM 26691 SG CYS H 40 110.378 72.151 84.664 1.00175.69 S Time building chain proxies: 16.55, per 1000 atoms: 0.53 Number of scatterers: 31319 At special positions: 0 Unit cell: (191.26, 168.99, 146.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 12 29.99 S 108 16.00 P 294 15.00 O 6128 8.00 N 5707 7.00 C 19070 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: 14.24 Conformation dependent library (CDL) restraints added in 4.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 500 " pdb="ZN ZN A 500 " - pdb=" ND1 HIS A 13 " pdb="ZN ZN A 500 " - pdb=" NE2 HIS A 9 " pdb="ZN ZN A 500 " - pdb=" SG CYS A 40 " pdb="ZN ZN A 500 " - pdb=" SG CYS A 37 " 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 37 " pdb="ZN ZN B 500 " - pdb=" SG CYS B 40 " pdb=" ZN E 500 " pdb="ZN ZN E 500 " - pdb=" NE2 HIS E 13 " pdb="ZN ZN E 500 " - pdb=" NE2 HIS E 9 " 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=" NE2 HIS F 9 " pdb="ZN ZN F 500 " - pdb=" ND1 HIS F 13 " pdb="ZN ZN F 500 " - pdb=" SG CYS F 37 " pdb="ZN ZN F 500 " - pdb=" SG CYS F 40 " pdb=" ZN G 500 " pdb="ZN ZN G 500 " - pdb=" NE2 HIS G 9 " pdb="ZN ZN G 500 " - pdb=" NE2 HIS G 13 " pdb="ZN ZN G 500 " - pdb=" SG CYS G 37 " pdb="ZN ZN G 500 " - pdb=" SG CYS G 40 " pdb=" ZN H 500 " pdb="ZN ZN H 500 " - pdb=" ND1 HIS H 13 " pdb="ZN ZN H 500 " - pdb=" NE2 HIS H 9 " pdb="ZN ZN H 500 " - pdb=" SG CYS H 40 " pdb="ZN ZN H 500 " - pdb=" SG CYS H 37 " 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 40 " pdb="ZN ZN a 500 " - pdb=" SG CYS a 37 " pdb=" ZN b 500 " pdb="ZN ZN b 500 " - pdb=" SG CYS b 37 " pdb="ZN ZN b 500 " - pdb=" ND1 HIS b 13 " pdb="ZN ZN b 500 " - pdb=" SG CYS b 40 " pdb="ZN ZN b 500 " - pdb=" NE2 HIS b 9 " pdb=" ZN e 500 " pdb="ZN ZN e 500 " - pdb=" SG CYS e 40 " pdb="ZN ZN e 500 " - pdb=" NE2 HIS e 13 " pdb="ZN ZN e 500 " - pdb=" NE2 HIS e 9 " pdb="ZN ZN e 500 " - pdb=" SG CYS e 37 " pdb=" ZN f 500 " pdb="ZN ZN f 500 " - pdb=" ND1 HIS f 13 " pdb="ZN ZN f 500 " - pdb=" SG CYS f 37 " pdb="ZN ZN f 500 " - pdb=" NE2 HIS f 9 " pdb="ZN ZN f 500 " - pdb=" SG CYS f 40 " pdb=" ZN g 500 " pdb="ZN ZN g 500 " - pdb=" NE2 HIS g 9 " pdb="ZN ZN g 500 " - pdb=" ND1 HIS g 13 " pdb="ZN ZN g 500 " - pdb=" SG CYS g 37 " pdb="ZN ZN g 500 " - pdb=" SG CYS g 40 " pdb=" ZN h 500 " pdb="ZN ZN h 500 " - pdb=" ND1 HIS h 13 " pdb="ZN ZN h 500 " - pdb=" NE2 HIS h 9 " pdb="ZN ZN h 500 " - pdb=" SG CYS h 40 " pdb="ZN ZN h 500 " - pdb=" SG CYS h 37 " Number of angles added : 21 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5974 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 33 sheets defined 43.6% alpha, 17.6% beta 112 base pairs and 211 stacking pairs defined. Time for finding SS restraints: 12.74 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: 3.520A pdb=" N CYS a 37 " --> pdb=" O ILE a 33 " (cutoff:3.500A) Processing helix chain 'a' and resid 70 through 75 removed outlier: 6.946A pdb=" N LYS a 74 " --> pdb=" O GLU a 71 " (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 209 Processing helix chain 'a' and resid 257 through 261 Processing helix chain 'b' and resid 2 through 13 Processing helix chain 'b' and resid 15 through 23 removed outlier: 3.552A pdb=" N LEU b 19 " --> pdb=" O ASN b 15 " (cutoff:3.500A) Processing helix chain 'b' and resid 26 through 37 Processing helix chain 'b' and resid 70 through 73 Processing helix chain 'b' and resid 98 through 114 Processing helix chain 'b' and resid 124 through 129 Processing helix chain 'b' and resid 129 through 139 removed outlier: 3.606A pdb=" N TRP b 139 " --> pdb=" O PHE b 135 " (cutoff:3.500A) Processing helix chain 'b' and resid 154 through 172 Processing helix chain 'b' and resid 179 through 194 Processing helix chain 'b' and resid 202 through 209 Processing helix chain 'd' and resid 259 through 261 No H-bonds generated for 'chain 'd' and resid 259 through 261' Processing helix chain 'e' and resid 2 through 13 Processing helix chain 'e' and resid 15 through 24 Processing helix chain 'e' and resid 26 through 37 removed outlier: 3.751A pdb=" N CYS e 37 " --> pdb=" O ILE e 33 " (cutoff:3.500A) Processing helix chain 'e' and resid 70 through 75 removed outlier: 6.774A pdb=" N LYS e 74 " --> pdb=" O GLU e 71 " (cutoff:3.500A) Processing helix chain 'e' and resid 98 through 113 Processing helix chain 'e' and resid 124 through 129 Processing helix chain 'e' and resid 129 through 139 removed outlier: 3.680A pdb=" N GLN e 133 " --> pdb=" O SER e 129 " (cutoff:3.500A) 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 13 Processing helix chain 'f' and resid 15 through 23 removed outlier: 3.598A pdb=" N LEU f 19 " --> pdb=" O ASN f 15 " (cutoff:3.500A) Processing helix chain 'f' and resid 26 through 36 Processing helix chain 'f' and resid 98 through 114 Processing helix chain 'f' and resid 124 through 129 Processing helix chain 'f' and resid 129 through 139 Processing helix chain 'f' and resid 156 through 172 Processing helix chain 'f' and resid 179 through 194 removed outlier: 3.514A pdb=" N LEU f 183 " --> pdb=" O THR f 179 " (cutoff:3.500A) Processing helix chain 'f' and resid 202 through 209 removed outlier: 3.565A pdb=" N ARG f 206 " --> pdb=" O THR f 202 " (cutoff:3.500A) Processing helix chain 'g' and resid 2 through 13 Processing helix chain 'g' and resid 15 through 24 removed outlier: 3.862A pdb=" N LEU g 19 " --> pdb=" O ASN g 15 " (cutoff:3.500A) Processing helix chain 'g' and resid 26 through 37 Processing helix chain 'g' and resid 70 through 75 removed outlier: 3.755A pdb=" N GLY g 73 " --> pdb=" O SER g 70 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LYS g 74 " --> pdb=" O GLU g 71 " (cutoff:3.500A) Processing helix chain 'g' and resid 98 through 113 Processing helix chain 'g' and resid 129 through 139 Processing helix chain 'g' and resid 156 through 172 Processing helix chain 'g' and resid 173 through 175 No H-bonds generated for 'chain 'g' and resid 173 through 175' Processing helix chain 'g' and resid 179 through 193 Processing helix chain 'g' and resid 202 through 207 Processing helix chain 'h' and resid 4 through 13 Processing helix chain 'h' and resid 15 through 23 Processing helix chain 'h' and resid 26 through 37 Processing helix chain 'h' and resid 72 through 75 Processing helix chain 'h' and resid 98 through 114 Processing helix chain 'h' and resid 129 through 139 removed outlier: 3.609A pdb=" N TRP h 139 " --> pdb=" O PHE h 135 " (cutoff:3.500A) Processing helix chain 'h' and resid 155 through 171 Processing helix chain 'h' and resid 179 through 194 removed outlier: 3.540A pdb=" N LEU h 183 " --> pdb=" O THR h 179 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL h 194 " --> pdb=" O VAL h 190 " (cutoff:3.500A) Processing helix chain 'h' and resid 202 through 208 Processing helix chain 'A' and resid 2 through 13 Processing helix chain 'A' and resid 15 through 24 removed outlier: 3.524A pdb=" N LEU A 19 " --> pdb=" O ASN A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 37 removed outlier: 3.823A pdb=" N CYS A 37 " --> pdb=" O ILE A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 76 removed outlier: 3.619A pdb=" N GLY A 73 " --> pdb=" O SER A 70 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LYS A 74 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 3.560A 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 129 Processing helix chain 'A' and resid 129 through 140 removed outlier: 3.572A pdb=" N GLN A 133 " --> pdb=" O SER A 129 " (cutoff:3.500A) 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 'B' and resid 2 through 13 Processing helix chain 'B' and resid 15 through 23 Processing helix chain 'B' and resid 26 through 37 Processing helix chain 'B' and resid 98 through 114 Processing helix chain 'B' and resid 124 through 129 Processing helix chain 'B' and resid 129 through 139 Processing helix chain 'B' and resid 156 through 172 Processing helix chain 'B' and resid 179 through 194 Processing helix chain 'B' and resid 202 through 209 Processing helix chain 'E' and resid 2 through 13 Processing helix chain 'E' and resid 15 through 24 Processing helix chain 'E' and resid 26 through 37 removed outlier: 3.505A pdb=" N CYS E 37 " --> pdb=" O ILE E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 75 removed outlier: 6.228A pdb=" N LYS E 74 " --> pdb=" O GLU E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 113 Processing helix chain 'E' and resid 124 through 129 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 209 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 13 Processing helix chain 'F' and resid 15 through 24 removed outlier: 3.537A pdb=" N LEU F 19 " --> pdb=" O ASN F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 37 removed outlier: 3.571A pdb=" N CYS F 37 " --> pdb=" O ILE F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 114 Processing helix chain 'F' and resid 124 through 129 Processing helix chain 'F' and resid 129 through 139 Processing helix chain 'F' and resid 155 through 172 Processing helix chain 'F' and resid 179 through 194 removed outlier: 3.604A pdb=" N LEU F 183 " --> pdb=" O THR F 179 " (cutoff:3.500A) 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: 3.807A pdb=" N GLY G 73 " --> pdb=" O SER G 70 " (cutoff:3.500A) removed outlier: 7.227A 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 156 through 173 removed outlier: 4.728A pdb=" N LYS G 173 " --> pdb=" O ASN G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 194 removed outlier: 3.777A pdb=" N VAL G 194 " --> pdb=" O VAL G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 208 Processing helix chain 'H' and resid 3 through 13 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: 6.874A 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 removed outlier: 3.646A pdb=" N VAL H 194 " --> pdb=" O VAL H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 208 Processing sheet with id=AA1, first strand: chain 'a' and resid 91 through 93 removed outlier: 3.758A pdb=" N VAL a 78 " --> pdb=" O THR a 67 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N TRP a 62 " --> pdb=" O LYS a 120 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 218 through 219 removed outlier: 4.369A pdb=" N VAL a 234 " --> pdb=" O PHE a 246 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N CYS a 244 " --> pdb=" O ILE a 236 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 222 through 223 Processing sheet with id=AA4, first strand: chain 'b' and resid 89 through 94 removed outlier: 3.649A pdb=" N TYR b 77 " --> pdb=" O ARG b 94 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP b 65 " --> pdb=" O VAL b 80 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'b' and resid 254 through 257 removed outlier: 3.942A pdb=" N THR b 237 " --> pdb=" O CYS b 244 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N PHE b 246 " --> pdb=" O LEU b 235 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N LEU b 235 " --> pdb=" O PHE b 246 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG b 262 " --> pdb=" O MET b 220 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'c' and resid 254 through 257 removed outlier: 3.677A pdb=" N THR c 237 " --> pdb=" O CYS c 244 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP c 233 " --> pdb=" O VAL c 219 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL c 219 " --> pdb=" O ASP c 233 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'd' and resid 219 through 222 removed outlier: 7.263A pdb=" N TRP d 221 " --> pdb=" O GLY d 231 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLY d 231 " --> pdb=" O TRP d 221 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'd' and resid 235 through 237 removed outlier: 4.033A pdb=" N THR d 237 " --> pdb=" O CYS d 244 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'e' and resid 89 through 93 removed outlier: 3.738A pdb=" N VAL e 78 " --> pdb=" O THR e 67 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N TRP e 62 " --> pdb=" O LYS e 120 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE e 119 " --> pdb=" O VAL e 144 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'e' and resid 254 through 256 removed outlier: 6.667A pdb=" N CYS e 244 " --> pdb=" O ILE e 236 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL e 234 " --> pdb=" O PHE e 246 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER e 228 " --> pdb=" O ASP e 223 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL e 219 " --> pdb=" O PRO e 232 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'f' and resid 89 through 94 removed outlier: 3.595A pdb=" N TYR f 77 " --> pdb=" O ARG f 94 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N TRP f 62 " --> pdb=" O LYS f 120 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'f' and resid 254 through 257 removed outlier: 6.699A pdb=" N TYR f 242 " --> pdb=" O ALA f 238 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ALA f 238 " --> pdb=" O TYR f 242 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N CYS f 244 " --> pdb=" O ILE f 236 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL f 234 " --> pdb=" O PHE f 246 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG f 262 " --> pdb=" O MET f 220 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'g' and resid 89 through 94 removed outlier: 3.606A pdb=" N TYR g 77 " --> pdb=" O ARG g 94 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP g 65 " --> pdb=" O VAL g 80 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N TRP g 62 " --> pdb=" O LYS g 120 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ILE g 119 " --> pdb=" O VAL g 144 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'g' and resid 254 through 257 removed outlier: 4.061A pdb=" N THR g 237 " --> pdb=" O CYS g 244 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N PHE g 246 " --> pdb=" O LEU g 235 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N LEU g 235 " --> pdb=" O PHE g 246 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'h' and resid 89 through 94 removed outlier: 3.648A pdb=" N TYR h 77 " --> pdb=" O ARG h 94 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N TRP h 62 " --> pdb=" O LYS h 120 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'h' and resid 254 through 257 removed outlier: 3.666A pdb=" N TYR h 242 " --> pdb=" O GLY h 239 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N THR h 237 " --> pdb=" O CYS h 244 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N PHE h 246 " --> pdb=" O LEU h 235 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU h 235 " --> pdb=" O PHE h 246 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N GLY h 231 " --> pdb=" O TRP h 221 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N TRP h 221 " --> pdb=" O GLY h 231 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 89 through 93 removed outlier: 3.535A pdb=" N HIS A 79 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N TRP A 62 " --> pdb=" O LYS A 120 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 228 through 229 removed outlier: 3.587A pdb=" N SER A 228 " --> pdb=" O ASP A 223 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N CYS A 244 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA A 238 " --> pdb=" O TYR A 242 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N TYR A 242 " --> pdb=" O ALA A 238 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 228 through 229 removed outlier: 3.587A pdb=" N SER A 228 " --> pdb=" O ASP A 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 89 through 94 removed outlier: 3.581A pdb=" N TYR B 77 " --> pdb=" O ARG B 94 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL B 78 " --> pdb=" O THR B 67 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N TRP B 62 " --> pdb=" O LYS B 120 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 254 through 257 removed outlier: 3.546A pdb=" N THR B 237 " --> pdb=" O CYS B 244 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N PHE B 246 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N LEU B 235 " --> pdb=" O PHE B 246 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 245 through 246 removed outlier: 3.962A pdb=" N VAL C 234 " --> pdb=" O PHE C 246 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL C 219 " --> pdb=" O PRO C 232 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 242 through 243 Processing sheet with id=AC6, first strand: chain 'D' and resid 254 through 257 Processing sheet with id=AC7, first strand: chain 'E' and resid 89 through 93 removed outlier: 3.707A pdb=" N HIS E 79 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL E 78 " --> pdb=" O THR E 67 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N TRP E 62 " --> pdb=" O LYS E 120 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 254 through 256 removed outlier: 6.606A pdb=" N CYS E 244 " --> pdb=" O ILE E 236 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL E 234 " --> pdb=" O PHE E 246 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL E 219 " --> pdb=" O ASP E 233 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 89 through 94 removed outlier: 3.704A pdb=" N TYR F 77 " --> pdb=" O ARG F 94 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP F 65 " --> pdb=" O VAL F 80 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N TRP F 62 " --> pdb=" O LYS F 120 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ILE F 119 " --> pdb=" O VAL F 144 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 256 through 257 removed outlier: 3.888A pdb=" N THR F 237 " --> pdb=" O CYS F 244 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N PHE F 246 " --> pdb=" O LEU F 235 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N LEU F 235 " --> pdb=" O PHE F 246 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL F 219 " --> pdb=" O PRO F 232 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 89 through 94 removed outlier: 3.627A pdb=" N TYR G 77 " --> pdb=" O ARG G 94 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL G 80 " --> pdb=" O ASP G 65 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N TRP G 62 " --> pdb=" O LYS G 120 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE G 119 " --> pdb=" O VAL G 144 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 254 through 257 removed outlier: 6.561A pdb=" N TYR G 242 " --> pdb=" O ALA G 238 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ALA G 238 " --> pdb=" O TYR G 242 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N CYS G 244 " --> pdb=" O ILE G 236 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL G 234 " --> pdb=" O PHE G 246 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N GLY G 231 " --> pdb=" O TRP G 221 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N TRP G 221 " --> pdb=" O GLY G 231 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 67 through 68 removed outlier: 4.127A pdb=" N TYR H 77 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS H 79 " --> pdb=" O THR H 92 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR H 92 " --> pdb=" O HIS H 79 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 67 through 68 removed outlier: 6.428A pdb=" N TRP H 62 " --> pdb=" O LYS H 120 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 254 through 257 removed outlier: 3.625A pdb=" N TYR H 242 " --> pdb=" O GLY H 239 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR H 237 " --> pdb=" O CYS H 244 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N PHE H 246 " --> pdb=" O LEU H 235 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU H 235 " --> pdb=" O PHE H 246 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL H 219 " --> pdb=" O PRO H 232 " (cutoff:3.500A) 1159 hydrogen bonds defined for protein. 3294 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 279 hydrogen bonds 538 hydrogen bond angles 0 basepair planarities 112 basepair parallelities 211 stacking parallelities Total time for adding SS restraints: 12.84 Time building geometry restraints manager: 15.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9085 1.34 - 1.46: 9510 1.46 - 1.58: 13460 1.58 - 1.71: 580 1.71 - 1.83: 176 Bond restraints: 32811 Sorted by residual: bond pdb=" CG PRO d 232 " pdb=" CD PRO d 232 " ideal model delta sigma weight residual 1.512 1.482 0.030 2.70e-02 1.37e+03 1.25e+00 bond pdb=" CB LYS E 74 " pdb=" CG LYS E 74 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.21e+00 bond pdb=" CG GLU E 7 " pdb=" CD GLU E 7 " ideal model delta sigma weight residual 1.516 1.490 0.026 2.50e-02 1.60e+03 1.09e+00 bond pdb=" CG LYS E 74 " pdb=" CD LYS E 74 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.09e+00 bond pdb=" CG PRO D 232 " pdb=" CD PRO D 232 " ideal model delta sigma weight residual 1.512 1.484 0.028 2.70e-02 1.37e+03 1.07e+00 ... (remaining 32806 not shown) Histogram of bond angle deviations from ideal: 99.60 - 106.49: 2983 106.49 - 113.37: 17610 113.37 - 120.25: 11767 120.25 - 127.14: 12415 127.14 - 134.02: 1070 Bond angle restraints: 45845 Sorted by residual: angle pdb=" N PRO f 210 " pdb=" CA PRO f 210 " pdb=" C PRO f 210 " ideal model delta sigma weight residual 114.68 110.86 3.82 1.04e+00 9.25e-01 1.35e+01 angle pdb=" CA ASP G 249 " pdb=" CB ASP G 249 " pdb=" CG ASP G 249 " ideal model delta sigma weight residual 112.60 108.93 3.67 1.00e+00 1.00e+00 1.35e+01 angle pdb=" N GLU f 32 " pdb=" CA GLU f 32 " pdb=" CB GLU f 32 " ideal model delta sigma weight residual 110.28 115.83 -5.55 1.55e+00 4.16e-01 1.28e+01 angle pdb=" N GLU E 7 " pdb=" CA GLU E 7 " pdb=" CB GLU E 7 " ideal model delta sigma weight residual 110.39 116.30 -5.91 1.66e+00 3.63e-01 1.27e+01 angle pdb=" C GLN E 6 " pdb=" N GLU E 7 " pdb=" CA GLU E 7 " ideal model delta sigma weight residual 120.72 115.24 5.48 1.67e+00 3.59e-01 1.08e+01 ... (remaining 45840 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.34: 16508 28.34 - 56.68: 1751 56.68 - 85.02: 165 85.02 - 113.36: 7 113.36 - 141.70: 2 Dihedral angle restraints: 18433 sinusoidal: 9259 harmonic: 9174 Sorted by residual: dihedral pdb=" CA TYR H 112 " pdb=" C TYR H 112 " pdb=" N MET H 113 " pdb=" CA MET H 113 " ideal model delta harmonic sigma weight residual 180.00 -156.99 -23.01 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA MET d 218 " pdb=" C MET d 218 " pdb=" N VAL d 219 " pdb=" CA VAL d 219 " ideal model delta harmonic sigma weight residual -180.00 -157.43 -22.57 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA MET a 218 " pdb=" C MET a 218 " pdb=" N VAL a 219 " pdb=" CA VAL a 219 " ideal model delta harmonic sigma weight residual 180.00 -159.02 -20.98 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 18430 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 4092 0.047 - 0.095: 735 0.095 - 0.142: 150 0.142 - 0.189: 6 0.189 - 0.236: 1 Chirality restraints: 4984 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 2.41 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CB ILE G 115 " pdb=" CA ILE G 115 " pdb=" CG1 ILE G 115 " pdb=" CG2 ILE G 115 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.18e-01 chirality pdb=" CB VAL g 194 " pdb=" CA VAL g 194 " pdb=" CG1 VAL g 194 " pdb=" CG2 VAL g 194 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.52e-01 ... (remaining 4981 not shown) Planarity restraints: 4812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS E 13 " 0.021 2.00e-02 2.50e+03 2.73e-02 1.12e+01 pdb=" CG HIS E 13 " -0.058 2.00e-02 2.50e+03 pdb=" ND1 HIS E 13 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 HIS E 13 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 HIS E 13 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS E 13 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE H 115 " 0.047 5.00e-02 4.00e+02 7.07e-02 7.99e+00 pdb=" N PRO H 116 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO H 116 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO H 116 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS G 13 " 0.021 2.00e-02 2.50e+03 1.80e-02 4.84e+00 pdb=" CG HIS G 13 " -0.036 2.00e-02 2.50e+03 pdb=" ND1 HIS G 13 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 HIS G 13 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS G 13 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS G 13 " 0.014 2.00e-02 2.50e+03 ... (remaining 4809 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1076 2.70 - 3.25: 30589 3.25 - 3.80: 55890 3.80 - 4.35: 68488 4.35 - 4.90: 105990 Nonbonded interactions: 262033 Sorted by model distance: nonbonded pdb=" OD1 ASN A 123 " pdb=" OG1 THR A 145 " model vdw 2.148 2.440 nonbonded pdb=" O ALA E 1 " pdb=" OG SER E 4 " model vdw 2.167 2.440 nonbonded pdb=" CG HIS E 13 " pdb="ZN ZN E 500 " model vdw 2.170 1.960 nonbonded pdb=" O ALA e 1 " pdb=" OG SER e 4 " model vdw 2.187 2.440 nonbonded pdb=" OH TYR c 242 " pdb=" OP1 DG l 10 " model vdw 2.200 2.440 ... (remaining 262028 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 155 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 208 or resid 218 through 264 or resid 500)) 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 through 155 \ and (name N or name CA or name C or name O or name CB )) or resid 156 through 1 \ 61 or (resid 162 and (name N or name CA or name C or name O or name CB )) or res \ id 163 through 172 or (resid 173 and (name N or name CA or name C or name O or n \ ame CB )) or resid 177 through 208 or resid 218 through 264 or resid 500)) 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 155 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 208 or resid 218 through 264 or resid 500)) 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 155 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 208 or resid 218 through 264 or resid 500)) 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 through 155 \ and (name N or name CA or name C or name O or name CB )) or resid 156 through 1 \ 72 or (resid 173 and (name N or name CA or name C or name O or name CB )) or res \ id 177 through 208 or resid 218 through 264 or resid 500)) selection = (chain 'H' and (resid 2 through 144 or resid 155 through 161 or (resid 162 and ( \ name N or name CA or name C or name O or name CB )) or resid 163 through 208 or \ resid 218 through 264 or resid 500)) selection = (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 155 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 208 or resid 218 through 264 or resid 500)) 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 155 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 208 or resid 218 through 264 or resid 500)) 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 155 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 208 or resid 218 through 264 or resid 500)) 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 155 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 208 or resid 218 through 264 or resid 500)) 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 155 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 208 or resid 218 through 264 or resid 500)) selection = (chain 'h' and (resid 2 through 144 or resid 155 through 161 or (resid 162 and ( \ name N or name CA or name C or name O or name CB )) or resid 163 through 208 or \ resid 218 through 264 or resid 500)) } ncs_group { reference = chain 'C' selection = (chain 'D' and resid 217 through 264) selection = chain 'c' selection = (chain 'd' and resid 217 through 264) } ncs_group { reference = chain 'I' selection = chain 'L' selection = chain 'i' selection = chain 'l' } ncs_group { reference = (chain 'J' and resid 1 through 38) selection = (chain 'M' and resid 1 through 38) selection = (chain 'j' and resid 1 through 38) selection = chain 'm' } ncs_group { reference = (chain 'K' and resid 5 through 16) selection = (chain 'N' and resid 5 through 16) selection = (chain 'k' and resid 5 through 16) 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: 1.050 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: 5.360 Check model and map are aligned: 0.410 Set scattering table: 0.280 Process input model: 97.810 Find NCS groups from input model: 2.540 Set up NCS constraints: 0.180 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 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 0.035 32811 Z= 0.189 Angle : 0.552 8.656 45845 Z= 0.306 Chirality : 0.038 0.236 4984 Planarity : 0.004 0.071 4812 Dihedral : 20.160 141.704 12459 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % 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: 0.17 (0.16), residues: 3069 helix: 1.16 (0.15), residues: 1195 sheet: 0.07 (0.22), residues: 586 loop : -0.82 (0.18), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP b 208 HIS 0.034 0.001 HIS E 13 PHE 0.013 0.001 PHE H 88 TYR 0.012 0.001 TYR e 242 ARG 0.004 0.000 ARG g 138 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 262 time to evaluate : 3.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 218 MET cc_start: 0.8184 (tpt) cc_final: 0.7885 (tpt) REVERT: f 113 MET cc_start: 0.8611 (mtm) cc_final: 0.8287 (mtp) REVERT: f 220 MET cc_start: 0.8848 (mmm) cc_final: 0.8094 (tpp) REVERT: g 32 GLU cc_start: 0.9155 (mp0) cc_final: 0.8793 (mp0) REVERT: A 39 ASN cc_start: 0.8221 (m-40) cc_final: 0.7824 (t0) REVERT: A 113 MET cc_start: 0.7940 (mtm) cc_final: 0.7452 (mtt) REVERT: B 7 GLU cc_start: 0.9489 (mt-10) cc_final: 0.9265 (mt-10) REVERT: B 32 GLU cc_start: 0.9461 (tp30) cc_final: 0.9256 (tp30) REVERT: B 244 CYS cc_start: 0.8835 (t) cc_final: 0.8502 (t) REVERT: C 223 ASP cc_start: 0.7780 (t0) cc_final: 0.7471 (t0) REVERT: C 230 LYS cc_start: 0.8730 (mmtm) cc_final: 0.8350 (mmmt) REVERT: F 7 GLU cc_start: 0.9333 (mp0) cc_final: 0.9106 (mp0) REVERT: F 15 ASN cc_start: 0.6600 (p0) cc_final: 0.6260 (p0) REVERT: F 64 MET cc_start: 0.7586 (mmm) cc_final: 0.7067 (mmt) REVERT: F 77 TYR cc_start: 0.8982 (m-80) cc_final: 0.8493 (m-80) REVERT: F 169 ASN cc_start: 0.9137 (m110) cc_final: 0.8651 (m110) REVERT: F 177 TYR cc_start: 0.7430 (m-80) cc_final: 0.7205 (m-80) REVERT: F 195 ASN cc_start: 0.7459 (m-40) cc_final: 0.7050 (m110) REVERT: F 205 GLU cc_start: 0.8349 (tt0) cc_final: 0.7995 (tt0) REVERT: F 208 TRP cc_start: 0.8137 (m100) cc_final: 0.7645 (m100) REVERT: G 7 GLU cc_start: 0.9117 (mp0) cc_final: 0.8483 (mp0) REVERT: G 134 GLU cc_start: 0.8548 (tm-30) cc_final: 0.8279 (tm-30) REVERT: G 252 SER cc_start: 0.8996 (p) cc_final: 0.8679 (p) REVERT: H 123 ASN cc_start: 0.8147 (m-40) cc_final: 0.7862 (m-40) REVERT: H 242 TYR cc_start: 0.8832 (p90) cc_final: 0.8441 (p90) outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 0.3914 time to fit residues: 169.1510 Evaluate side-chains 209 residues out of total 2668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 3.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 281 optimal weight: 10.0000 chunk 252 optimal weight: 4.9990 chunk 140 optimal weight: 7.9990 chunk 86 optimal weight: 6.9990 chunk 170 optimal weight: 6.9990 chunk 134 optimal weight: 9.9990 chunk 261 optimal weight: 8.9990 chunk 101 optimal weight: 8.9990 chunk 158 optimal weight: 7.9990 chunk 194 optimal weight: 0.9990 chunk 302 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 193 HIS b 163 ASN ** b 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 52 ASN e 161 HIS ** f 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 152 GLN ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN F 193 HIS ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 32811 Z= 0.407 Angle : 0.656 9.233 45845 Z= 0.363 Chirality : 0.043 0.187 4984 Planarity : 0.005 0.049 4812 Dihedral : 22.875 143.680 6532 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.61 % Allowed : 7.72 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % 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: -0.10 (0.15), residues: 3069 helix: 0.94 (0.15), residues: 1226 sheet: 0.01 (0.22), residues: 615 loop : -1.09 (0.18), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP b 208 HIS 0.017 0.002 HIS G 9 PHE 0.015 0.002 PHE F 90 TYR 0.019 0.002 TYR A 112 ARG 0.006 0.001 ARG h 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 220 time to evaluate : 3.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 218 MET cc_start: 0.8432 (mmm) cc_final: 0.8062 (mmm) REVERT: d 218 MET cc_start: 0.8250 (tpt) cc_final: 0.7931 (tpt) REVERT: e 52 ASN cc_start: 0.8696 (OUTLIER) cc_final: 0.8451 (m110) REVERT: f 77 TYR cc_start: 0.8159 (m-80) cc_final: 0.7872 (m-80) REVERT: f 113 MET cc_start: 0.8632 (mtm) cc_final: 0.8188 (mtp) REVERT: f 220 MET cc_start: 0.8615 (mmm) cc_final: 0.8209 (tpp) REVERT: g 32 GLU cc_start: 0.9173 (mp0) cc_final: 0.8649 (mp0) REVERT: g 220 MET cc_start: 0.8594 (mmm) cc_final: 0.8172 (mmm) REVERT: A 39 ASN cc_start: 0.8160 (m-40) cc_final: 0.7842 (m-40) REVERT: B 32 GLU cc_start: 0.9456 (tp30) cc_final: 0.9236 (tp30) REVERT: B 113 MET cc_start: 0.8954 (tpp) cc_final: 0.8620 (tpt) REVERT: B 196 MET cc_start: 0.8296 (tpp) cc_final: 0.7829 (tpp) REVERT: B 220 MET cc_start: 0.7281 (tpp) cc_final: 0.6949 (tpp) REVERT: C 223 ASP cc_start: 0.7717 (t0) cc_final: 0.7422 (t0) REVERT: C 230 LYS cc_start: 0.8683 (mmtm) cc_final: 0.8474 (mmmt) REVERT: F 7 GLU cc_start: 0.9334 (mp0) cc_final: 0.9091 (mp0) REVERT: F 15 ASN cc_start: 0.6806 (p0) cc_final: 0.6505 (p0) REVERT: F 64 MET cc_start: 0.7324 (mmm) cc_final: 0.6565 (mmt) REVERT: F 77 TYR cc_start: 0.8920 (m-80) cc_final: 0.8496 (m-80) REVERT: F 169 ASN cc_start: 0.9244 (m110) cc_final: 0.8752 (m110) REVERT: F 177 TYR cc_start: 0.7556 (m-80) cc_final: 0.7279 (m-80) REVERT: F 195 ASN cc_start: 0.7549 (m-40) cc_final: 0.7078 (m110) REVERT: F 196 MET cc_start: 0.6580 (tmm) cc_final: 0.5414 (tmm) REVERT: F 205 GLU cc_start: 0.8412 (tt0) cc_final: 0.8088 (tt0) REVERT: F 220 MET cc_start: 0.8372 (tpp) cc_final: 0.7385 (tpp) REVERT: G 7 GLU cc_start: 0.9347 (mp0) cc_final: 0.8800 (mp0) REVERT: G 134 GLU cc_start: 0.8533 (tm-30) cc_final: 0.8210 (tm-30) REVERT: H 158 GLU cc_start: 0.7866 (mp0) cc_final: 0.7619 (mp0) REVERT: H 242 TYR cc_start: 0.8778 (p90) cc_final: 0.8467 (p90) outliers start: 16 outliers final: 11 residues processed: 227 average time/residue: 0.3675 time to fit residues: 141.3075 Evaluate side-chains 219 residues out of total 2668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 207 time to evaluate : 3.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 249 ASP Chi-restraints excluded: chain e residue 52 ASN Chi-restraints excluded: chain f residue 32 GLU Chi-restraints excluded: chain g residue 7 GLU Chi-restraints excluded: chain g residue 64 MET Chi-restraints excluded: chain g residue 188 LEU Chi-restraints excluded: chain g residue 249 ASP Chi-restraints excluded: chain h residue 101 ASP Chi-restraints excluded: chain h residue 171 LEU Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain H residue 249 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 168 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 chunk 251 optimal weight: 6.9990 chunk 205 optimal weight: 7.9990 chunk 83 optimal weight: 9.9990 chunk 302 optimal weight: 3.9990 chunk 327 optimal weight: 10.0000 chunk 269 optimal weight: 20.0000 chunk 300 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 243 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 143 HIS ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 HIS ** E 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 207 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 32811 Z= 0.360 Angle : 0.618 8.890 45845 Z= 0.342 Chirality : 0.041 0.162 4984 Planarity : 0.004 0.042 4812 Dihedral : 22.908 142.021 6532 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.40 % Allowed : 12.98 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % 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: -0.20 (0.15), residues: 3069 helix: 0.89 (0.15), residues: 1226 sheet: -0.04 (0.22), residues: 606 loop : -1.17 (0.18), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP b 208 HIS 0.013 0.001 HIS G 9 PHE 0.015 0.002 PHE F 246 TYR 0.016 0.002 TYR D 242 ARG 0.004 0.000 ARG h 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 225 time to evaluate : 2.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 218 MET cc_start: 0.8184 (mmm) cc_final: 0.7579 (tmm) REVERT: c 218 MET cc_start: 0.8924 (mmm) cc_final: 0.8723 (mmm) REVERT: f 77 TYR cc_start: 0.8190 (m-80) cc_final: 0.7751 (m-80) REVERT: f 220 MET cc_start: 0.8556 (mmm) cc_final: 0.8133 (tpp) REVERT: g 32 GLU cc_start: 0.9173 (mp0) cc_final: 0.8593 (mp0) REVERT: g 218 MET cc_start: 0.8973 (mmp) cc_final: 0.8691 (mmp) REVERT: g 220 MET cc_start: 0.8506 (mmm) cc_final: 0.8074 (mmm) REVERT: A 39 ASN cc_start: 0.8188 (m-40) cc_final: 0.7854 (m-40) REVERT: A 169 ASN cc_start: 0.9248 (t0) cc_final: 0.8943 (t0) REVERT: B 32 GLU cc_start: 0.9454 (tp30) cc_final: 0.9237 (tp30) REVERT: B 64 MET cc_start: 0.8644 (ttp) cc_final: 0.8117 (ttm) REVERT: B 113 MET cc_start: 0.8898 (tpp) cc_final: 0.8654 (mmm) REVERT: B 196 MET cc_start: 0.8670 (tpp) cc_final: 0.8229 (tpp) REVERT: B 220 MET cc_start: 0.7899 (tpp) cc_final: 0.7524 (tpp) REVERT: C 223 ASP cc_start: 0.7684 (t0) cc_final: 0.7393 (t0) REVERT: D 224 LEU cc_start: 0.8789 (tt) cc_final: 0.8586 (tt) REVERT: E 7 GLU cc_start: 0.8888 (pm20) cc_final: 0.8649 (pm20) REVERT: F 15 ASN cc_start: 0.6964 (p0) cc_final: 0.6725 (p0) REVERT: F 64 MET cc_start: 0.7191 (mmm) cc_final: 0.6983 (mmt) REVERT: F 77 TYR cc_start: 0.8899 (m-80) cc_final: 0.8408 (m-80) REVERT: F 113 MET cc_start: 0.8987 (tpp) cc_final: 0.8716 (tpp) REVERT: F 169 ASN cc_start: 0.9207 (m110) cc_final: 0.8739 (m110) REVERT: F 177 TYR cc_start: 0.7503 (m-80) cc_final: 0.7150 (m-80) REVERT: F 195 ASN cc_start: 0.7532 (m-40) cc_final: 0.7186 (m110) REVERT: F 196 MET cc_start: 0.6473 (tmm) cc_final: 0.5328 (tmm) REVERT: F 205 GLU cc_start: 0.8399 (tt0) cc_final: 0.8169 (tt0) REVERT: F 220 MET cc_start: 0.8644 (tpp) cc_final: 0.7786 (tpp) REVERT: G 7 GLU cc_start: 0.9393 (mp0) cc_final: 0.8886 (mp0) REVERT: G 113 MET cc_start: 0.8030 (mtt) cc_final: 0.7647 (mtt) REVERT: G 134 GLU cc_start: 0.8570 (tm-30) cc_final: 0.8195 (tm-30) REVERT: H 113 MET cc_start: 0.8444 (mtt) cc_final: 0.8240 (mtt) REVERT: H 242 TYR cc_start: 0.8881 (p90) cc_final: 0.8495 (p90) outliers start: 37 outliers final: 27 residues processed: 247 average time/residue: 0.3766 time to fit residues: 159.0337 Evaluate side-chains 233 residues out of total 2668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 206 time to evaluate : 3.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 191 LEU Chi-restraints excluded: chain b residue 249 ASP Chi-restraints excluded: chain e residue 26 THR Chi-restraints excluded: chain e residue 51 VAL Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 115 ILE Chi-restraints excluded: chain e residue 161 HIS Chi-restraints excluded: chain e residue 218 MET Chi-restraints excluded: chain f residue 32 GLU Chi-restraints excluded: chain g residue 7 GLU Chi-restraints excluded: chain g residue 64 MET Chi-restraints excluded: chain g residue 82 VAL Chi-restraints excluded: chain g residue 188 LEU Chi-restraints excluded: chain g residue 249 ASP Chi-restraints excluded: chain h residue 82 VAL Chi-restraints excluded: chain h residue 101 ASP Chi-restraints excluded: chain h residue 121 THR Chi-restraints excluded: chain h residue 249 ASP Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain F residue 233 ASP Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 249 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 299 optimal weight: 6.9990 chunk 227 optimal weight: 0.9990 chunk 157 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 144 optimal weight: 5.9990 chunk 203 optimal weight: 10.0000 chunk 304 optimal weight: 10.0000 chunk 321 optimal weight: 10.0000 chunk 158 optimal weight: 7.9990 chunk 288 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 52 ASN ** f 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 HIS B 182 HIS ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 GLN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 199 GLN ** H 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 32811 Z= 0.300 Angle : 0.581 8.427 45845 Z= 0.321 Chirality : 0.040 0.141 4984 Planarity : 0.004 0.044 4812 Dihedral : 22.907 140.596 6532 Min Nonbonded Distance : 1.723 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.20 % Allowed : 14.50 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % 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: -0.04 (0.15), residues: 3069 helix: 1.04 (0.15), residues: 1228 sheet: 0.12 (0.23), residues: 566 loop : -1.13 (0.18), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 62 HIS 0.010 0.001 HIS G 9 PHE 0.012 0.001 PHE F 246 TYR 0.017 0.001 TYR D 242 ARG 0.006 0.000 ARG H 138 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 225 time to evaluate : 3.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 208 TRP cc_start: 0.8942 (OUTLIER) cc_final: 0.7716 (m-10) REVERT: a 218 MET cc_start: 0.8150 (mmm) cc_final: 0.7658 (mmm) REVERT: f 28 GLU cc_start: 0.7515 (tm-30) cc_final: 0.7270 (tm-30) REVERT: f 64 MET cc_start: 0.8768 (ttm) cc_final: 0.8535 (ttm) REVERT: f 77 TYR cc_start: 0.8245 (m-80) cc_final: 0.7807 (m-80) REVERT: f 220 MET cc_start: 0.8544 (mmm) cc_final: 0.8121 (tpp) REVERT: g 32 GLU cc_start: 0.9222 (OUTLIER) cc_final: 0.8905 (mp0) REVERT: g 218 MET cc_start: 0.8997 (mmp) cc_final: 0.8707 (mmp) REVERT: g 220 MET cc_start: 0.8664 (mmm) cc_final: 0.8226 (mmm) REVERT: h 134 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8483 (pm20) REVERT: A 39 ASN cc_start: 0.8179 (m-40) cc_final: 0.7840 (m-40) REVERT: A 134 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8728 (pp20) REVERT: A 169 ASN cc_start: 0.9264 (t0) cc_final: 0.8961 (t0) REVERT: A 205 GLU cc_start: 0.9205 (pp20) cc_final: 0.8785 (pp20) REVERT: B 32 GLU cc_start: 0.9454 (tp30) cc_final: 0.9231 (tp30) REVERT: B 64 MET cc_start: 0.8421 (ttp) cc_final: 0.8197 (ttm) REVERT: B 113 MET cc_start: 0.8898 (tpp) cc_final: 0.8669 (mmm) REVERT: B 196 MET cc_start: 0.8626 (tpp) cc_final: 0.8174 (tpp) REVERT: B 244 CYS cc_start: 0.8576 (t) cc_final: 0.7722 (p) REVERT: C 230 LYS cc_start: 0.8168 (mmmt) cc_final: 0.7962 (mmmt) REVERT: E 97 GLU cc_start: 0.7647 (tp30) cc_final: 0.7407 (tp30) REVERT: E 196 MET cc_start: 0.7592 (ptt) cc_final: 0.6931 (ttp) REVERT: F 15 ASN cc_start: 0.6965 (p0) cc_final: 0.6747 (p0) REVERT: F 77 TYR cc_start: 0.8865 (m-80) cc_final: 0.8414 (m-80) REVERT: F 113 MET cc_start: 0.8875 (tpp) cc_final: 0.8434 (tpp) REVERT: F 169 ASN cc_start: 0.9257 (m110) cc_final: 0.8809 (m110) REVERT: F 177 TYR cc_start: 0.7467 (m-80) cc_final: 0.7160 (m-80) REVERT: F 195 ASN cc_start: 0.7590 (m-40) cc_final: 0.7245 (m110) REVERT: F 196 MET cc_start: 0.6553 (tmm) cc_final: 0.5450 (tmm) REVERT: F 205 GLU cc_start: 0.8387 (tt0) cc_final: 0.8142 (tt0) REVERT: F 220 MET cc_start: 0.8889 (tpp) cc_final: 0.8272 (tpp) REVERT: G 7 GLU cc_start: 0.9402 (OUTLIER) cc_final: 0.9003 (mp0) REVERT: G 113 MET cc_start: 0.8181 (mtt) cc_final: 0.7833 (mtt) REVERT: G 134 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8237 (tm-30) REVERT: H 134 GLU cc_start: 0.8575 (pt0) cc_final: 0.8353 (pp20) REVERT: H 242 TYR cc_start: 0.8893 (p90) cc_final: 0.8523 (p90) outliers start: 58 outliers final: 33 residues processed: 264 average time/residue: 0.3756 time to fit residues: 169.3163 Evaluate side-chains 252 residues out of total 2668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 214 time to evaluate : 3.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 64 MET Chi-restraints excluded: chain a residue 208 TRP Chi-restraints excluded: chain b residue 32 GLU Chi-restraints excluded: chain b residue 92 THR Chi-restraints excluded: chain b residue 249 ASP Chi-restraints excluded: chain e residue 26 THR Chi-restraints excluded: chain e residue 32 GLU Chi-restraints excluded: chain e residue 51 VAL Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 161 HIS Chi-restraints excluded: chain e residue 190 VAL Chi-restraints excluded: chain e residue 218 MET Chi-restraints excluded: chain f residue 32 GLU Chi-restraints excluded: chain g residue 7 GLU Chi-restraints excluded: chain g residue 12 HIS Chi-restraints excluded: chain g residue 32 GLU Chi-restraints excluded: chain g residue 82 VAL Chi-restraints excluded: chain g residue 188 LEU Chi-restraints excluded: chain g residue 249 ASP Chi-restraints excluded: chain h residue 82 VAL Chi-restraints excluded: chain h residue 101 ASP Chi-restraints excluded: chain h residue 121 THR Chi-restraints excluded: chain h residue 134 GLU Chi-restraints excluded: chain h residue 171 LEU Chi-restraints excluded: chain h residue 249 ASP Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain F residue 233 ASP Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 188 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 249 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 268 optimal weight: 9.9990 chunk 182 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 239 optimal weight: 10.0000 chunk 132 optimal weight: 6.9990 chunk 274 optimal weight: 20.0000 chunk 222 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 164 optimal weight: 7.9990 chunk 288 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 199 GLN ** b 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 195 ASN ** f 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 ASN ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.089 32811 Z= 0.477 Angle : 0.694 9.887 45845 Z= 0.379 Chirality : 0.043 0.173 4984 Planarity : 0.005 0.046 4812 Dihedral : 23.043 140.295 6532 Min Nonbonded Distance : 1.665 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 3.22 % Allowed : 16.43 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % 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: -0.50 (0.15), residues: 3069 helix: 0.59 (0.15), residues: 1222 sheet: -0.01 (0.23), residues: 541 loop : -1.32 (0.17), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 62 HIS 0.009 0.002 HIS a 9 PHE 0.019 0.002 PHE F 246 TYR 0.017 0.002 TYR b 177 ARG 0.006 0.001 ARG g 27 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 210 time to evaluate : 2.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 208 TRP cc_start: 0.9047 (OUTLIER) cc_final: 0.8015 (m-10) REVERT: a 218 MET cc_start: 0.8349 (mmm) cc_final: 0.7819 (mmm) REVERT: d 224 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8523 (mp) REVERT: f 77 TYR cc_start: 0.8475 (m-80) cc_final: 0.8037 (m-80) REVERT: f 220 MET cc_start: 0.8579 (mmm) cc_final: 0.8176 (tpp) REVERT: g 32 GLU cc_start: 0.9162 (OUTLIER) cc_final: 0.8817 (mp0) REVERT: g 220 MET cc_start: 0.8422 (mmm) cc_final: 0.8013 (mmm) REVERT: g 233 ASP cc_start: 0.8263 (OUTLIER) cc_final: 0.8031 (p0) REVERT: h 134 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8527 (pm20) REVERT: A 39 ASN cc_start: 0.8266 (m-40) cc_final: 0.7989 (m-40) REVERT: A 169 ASN cc_start: 0.9287 (t0) cc_final: 0.8952 (t0) REVERT: A 205 GLU cc_start: 0.9224 (pp20) cc_final: 0.8802 (pp20) REVERT: B 32 GLU cc_start: 0.9446 (tp30) cc_final: 0.9236 (tp30) REVERT: B 64 MET cc_start: 0.8496 (ttp) cc_final: 0.8021 (ttm) REVERT: B 127 TYR cc_start: 0.7633 (m-80) cc_final: 0.7333 (m-80) REVERT: B 196 MET cc_start: 0.8472 (tpp) cc_final: 0.8135 (tpp) REVERT: B 220 MET cc_start: 0.7510 (tpp) cc_final: 0.7036 (tpp) REVERT: C 218 MET cc_start: 0.8104 (ptt) cc_final: 0.7659 (ptt) REVERT: E 196 MET cc_start: 0.7916 (ptt) cc_final: 0.7091 (ttp) REVERT: F 64 MET cc_start: 0.7416 (mmt) cc_final: 0.7043 (mmt) REVERT: F 77 TYR cc_start: 0.8881 (m-80) cc_final: 0.8433 (m-80) REVERT: F 169 ASN cc_start: 0.9246 (m110) cc_final: 0.8759 (m110) REVERT: F 177 TYR cc_start: 0.7507 (m-80) cc_final: 0.7192 (m-80) REVERT: F 195 ASN cc_start: 0.7656 (m-40) cc_final: 0.7318 (m110) REVERT: F 196 MET cc_start: 0.6861 (tmm) cc_final: 0.5768 (tmm) REVERT: G 7 GLU cc_start: 0.9359 (mp0) cc_final: 0.8868 (mp0) REVERT: G 113 MET cc_start: 0.8057 (mtt) cc_final: 0.7613 (mtt) REVERT: G 134 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8173 (tm-30) REVERT: G 196 MET cc_start: 0.8697 (ptp) cc_final: 0.8395 (ptp) REVERT: H 113 MET cc_start: 0.8503 (mtt) cc_final: 0.8269 (mtt) REVERT: H 242 TYR cc_start: 0.8938 (p90) cc_final: 0.8531 (p90) outliers start: 85 outliers final: 59 residues processed: 274 average time/residue: 0.3725 time to fit residues: 174.6380 Evaluate side-chains 268 residues out of total 2668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 204 time to evaluate : 3.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 64 MET Chi-restraints excluded: chain a residue 81 THR Chi-restraints excluded: chain a residue 89 THR Chi-restraints excluded: chain a residue 128 VAL 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 11 LEU Chi-restraints excluded: chain b residue 32 GLU Chi-restraints excluded: chain b residue 92 THR Chi-restraints excluded: chain b residue 102 VAL Chi-restraints excluded: chain b residue 191 LEU Chi-restraints excluded: chain b residue 202 THR Chi-restraints excluded: chain b residue 249 ASP Chi-restraints excluded: chain d residue 220 MET Chi-restraints excluded: chain d residue 224 LEU Chi-restraints excluded: chain d residue 244 CYS Chi-restraints excluded: chain d residue 256 VAL Chi-restraints excluded: chain e residue 26 THR Chi-restraints excluded: chain e residue 32 GLU Chi-restraints excluded: chain e residue 51 VAL Chi-restraints excluded: chain e residue 64 MET Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 115 ILE Chi-restraints excluded: chain e residue 152 GLN Chi-restraints excluded: chain e residue 161 HIS Chi-restraints excluded: chain e residue 190 VAL Chi-restraints excluded: chain e residue 211 ILE Chi-restraints excluded: chain e residue 218 MET Chi-restraints excluded: chain e residue 221 TRP Chi-restraints excluded: chain e residue 258 ASP Chi-restraints excluded: chain f residue 32 GLU Chi-restraints excluded: chain f residue 202 THR Chi-restraints excluded: chain f residue 258 ASP Chi-restraints excluded: chain g residue 7 GLU Chi-restraints excluded: chain g residue 12 HIS Chi-restraints excluded: chain g residue 32 GLU Chi-restraints excluded: chain g residue 82 VAL Chi-restraints excluded: chain g residue 92 THR Chi-restraints excluded: chain g residue 188 LEU Chi-restraints excluded: chain g residue 233 ASP Chi-restraints excluded: chain g residue 249 ASP Chi-restraints excluded: chain h residue 82 VAL Chi-restraints excluded: chain h residue 101 ASP Chi-restraints excluded: chain h residue 121 THR Chi-restraints excluded: chain h residue 134 GLU Chi-restraints excluded: chain h residue 249 ASP Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain E residue 15 ASN Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 152 GLN Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain F residue 233 ASP Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 188 LEU Chi-restraints excluded: chain G residue 220 MET Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 249 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 108 optimal weight: 10.0000 chunk 289 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 188 optimal weight: 50.0000 chunk 79 optimal weight: 2.9990 chunk 322 optimal weight: 20.0000 chunk 267 optimal weight: 5.9990 chunk 149 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 169 optimal weight: 9.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 39 ASN ** g 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 207 HIS ** h 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 HIS ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN ** F 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 199 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 32811 Z= 0.258 Angle : 0.576 8.509 45845 Z= 0.316 Chirality : 0.039 0.142 4984 Planarity : 0.004 0.047 4812 Dihedral : 22.983 139.745 6532 Min Nonbonded Distance : 1.691 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.07 % Allowed : 17.26 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % 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: -0.07 (0.15), residues: 3069 helix: 1.00 (0.15), residues: 1223 sheet: 0.27 (0.24), residues: 520 loop : -1.15 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP b 208 HIS 0.008 0.001 HIS G 9 PHE 0.014 0.001 PHE F 246 TYR 0.021 0.001 TYR D 242 ARG 0.004 0.000 ARG E 138 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 220 time to evaluate : 3.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 208 TRP cc_start: 0.8986 (OUTLIER) cc_final: 0.7758 (m-10) REVERT: a 218 MET cc_start: 0.8298 (mmm) cc_final: 0.7892 (mmm) REVERT: e 152 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8306 (mm-40) REVERT: f 28 GLU cc_start: 0.7516 (tm-30) cc_final: 0.7192 (tm-30) REVERT: f 32 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7298 (pm20) REVERT: f 77 TYR cc_start: 0.8351 (m-80) cc_final: 0.7924 (m-80) REVERT: f 220 MET cc_start: 0.8562 (mmm) cc_final: 0.8154 (tpp) REVERT: g 7 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8341 (tm-30) REVERT: g 32 GLU cc_start: 0.9148 (OUTLIER) cc_final: 0.8823 (mp0) REVERT: g 220 MET cc_start: 0.8636 (mmm) cc_final: 0.8213 (mmm) REVERT: h 64 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7453 (tmm) REVERT: h 134 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8491 (pm20) REVERT: A 39 ASN cc_start: 0.8186 (m-40) cc_final: 0.7868 (m-40) REVERT: A 205 GLU cc_start: 0.9209 (OUTLIER) cc_final: 0.8938 (pp20) REVERT: A 218 MET cc_start: 0.7919 (tpt) cc_final: 0.7668 (tpt) REVERT: B 32 GLU cc_start: 0.9458 (tp30) cc_final: 0.9248 (tp30) REVERT: B 64 MET cc_start: 0.8531 (ttp) cc_final: 0.7557 (ttm) REVERT: B 113 MET cc_start: 0.8736 (mmm) cc_final: 0.8176 (mmm) REVERT: B 196 MET cc_start: 0.8460 (tpp) cc_final: 0.8100 (tpp) REVERT: B 220 MET cc_start: 0.7854 (tpp) cc_final: 0.7493 (tpp) REVERT: B 244 CYS cc_start: 0.8531 (t) cc_final: 0.7663 (p) REVERT: C 218 MET cc_start: 0.8226 (ptt) cc_final: 0.7683 (mmp) REVERT: E 152 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7825 (mm-40) REVERT: F 77 TYR cc_start: 0.8812 (m-80) cc_final: 0.8366 (m-80) REVERT: F 113 MET cc_start: 0.8746 (tpp) cc_final: 0.8000 (mmm) REVERT: F 169 ASN cc_start: 0.9230 (m110) cc_final: 0.8732 (m110) REVERT: F 195 ASN cc_start: 0.7793 (m-40) cc_final: 0.7427 (m110) REVERT: F 196 MET cc_start: 0.6585 (tmm) cc_final: 0.5864 (tmm) REVERT: F 220 MET cc_start: 0.8529 (tpp) cc_final: 0.7556 (tpp) REVERT: G 7 GLU cc_start: 0.9377 (OUTLIER) cc_final: 0.8962 (mp0) REVERT: G 113 MET cc_start: 0.7971 (mtt) cc_final: 0.7689 (mtt) REVERT: G 134 GLU cc_start: 0.8577 (tm-30) cc_final: 0.8145 (tm-30) REVERT: H 113 MET cc_start: 0.8459 (mtt) cc_final: 0.8255 (mtt) REVERT: H 242 TYR cc_start: 0.8916 (p90) cc_final: 0.8566 (p90) outliers start: 81 outliers final: 45 residues processed: 279 average time/residue: 0.3623 time to fit residues: 171.5449 Evaluate side-chains 261 residues out of total 2668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 206 time to evaluate : 3.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 95 THR Chi-restraints excluded: chain a residue 128 VAL Chi-restraints excluded: chain a residue 205 GLU Chi-restraints excluded: chain a residue 208 TRP Chi-restraints excluded: chain b residue 32 GLU Chi-restraints excluded: chain b residue 92 THR Chi-restraints excluded: chain b residue 202 THR Chi-restraints excluded: chain b residue 234 VAL Chi-restraints excluded: chain b residue 249 ASP Chi-restraints excluded: chain c residue 254 ILE Chi-restraints excluded: chain d residue 244 CYS Chi-restraints excluded: chain d residue 256 VAL Chi-restraints excluded: chain e residue 14 GLN Chi-restraints excluded: chain e residue 26 THR Chi-restraints excluded: chain e residue 51 VAL Chi-restraints excluded: chain e residue 64 MET Chi-restraints excluded: chain e residue 152 GLN Chi-restraints excluded: chain e residue 161 HIS Chi-restraints excluded: chain e residue 211 ILE Chi-restraints excluded: chain e residue 218 MET Chi-restraints excluded: chain e residue 258 ASP Chi-restraints excluded: chain f residue 32 GLU Chi-restraints excluded: chain f residue 258 ASP Chi-restraints excluded: chain g residue 7 GLU Chi-restraints excluded: chain g residue 12 HIS Chi-restraints excluded: chain g residue 32 GLU Chi-restraints excluded: chain g residue 82 VAL Chi-restraints excluded: chain g residue 188 LEU Chi-restraints excluded: chain g residue 233 ASP Chi-restraints excluded: chain g residue 249 ASP Chi-restraints excluded: chain h residue 64 MET Chi-restraints excluded: chain h residue 82 VAL Chi-restraints excluded: chain h residue 101 ASP Chi-restraints excluded: chain h residue 121 THR Chi-restraints excluded: chain h residue 134 GLU Chi-restraints excluded: chain h residue 236 ILE Chi-restraints excluded: chain h residue 249 ASP Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 152 GLN Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 233 ASP Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 188 LEU Chi-restraints excluded: chain G residue 220 MET Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 249 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 310 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 183 optimal weight: 0.7980 chunk 235 optimal weight: 0.7980 chunk 182 optimal weight: 4.9990 chunk 271 optimal weight: 20.0000 chunk 179 optimal weight: 10.0000 chunk 320 optimal weight: 8.9990 chunk 200 optimal weight: 3.9990 chunk 195 optimal weight: 9.9990 chunk 148 optimal weight: 10.0000 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 199 GLN ** H 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 32811 Z= 0.313 Angle : 0.605 8.236 45845 Z= 0.331 Chirality : 0.040 0.157 4984 Planarity : 0.004 0.047 4812 Dihedral : 22.929 140.801 6532 Min Nonbonded Distance : 1.668 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.37 % Allowed : 18.21 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % 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: -0.09 (0.15), residues: 3069 helix: 0.96 (0.15), residues: 1227 sheet: 0.24 (0.24), residues: 530 loop : -1.15 (0.17), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP b 208 HIS 0.007 0.001 HIS G 9 PHE 0.016 0.001 PHE F 246 TYR 0.024 0.001 TYR F 127 ARG 0.009 0.000 ARG C 262 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 212 time to evaluate : 3.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 208 TRP cc_start: 0.9019 (OUTLIER) cc_final: 0.7798 (m-10) REVERT: a 218 MET cc_start: 0.8331 (mmm) cc_final: 0.7955 (mmm) REVERT: e 152 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8394 (mm-40) REVERT: f 28 GLU cc_start: 0.7692 (tm-30) cc_final: 0.7375 (tm-30) REVERT: f 77 TYR cc_start: 0.8395 (m-80) cc_final: 0.7958 (m-80) REVERT: f 220 MET cc_start: 0.8562 (mmm) cc_final: 0.8143 (tpp) REVERT: g 7 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8371 (tm-30) REVERT: h 64 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7521 (tmm) REVERT: h 134 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8502 (pm20) REVERT: A 39 ASN cc_start: 0.8259 (m-40) cc_final: 0.7941 (m-40) REVERT: A 169 ASN cc_start: 0.9285 (t0) cc_final: 0.8960 (t0) REVERT: A 205 GLU cc_start: 0.9214 (OUTLIER) cc_final: 0.8903 (pp20) REVERT: B 32 GLU cc_start: 0.9461 (tp30) cc_final: 0.9249 (tp30) REVERT: B 64 MET cc_start: 0.8447 (ttp) cc_final: 0.7759 (ttm) REVERT: B 196 MET cc_start: 0.8417 (tpp) cc_final: 0.8081 (tpp) REVERT: B 244 CYS cc_start: 0.8603 (t) cc_final: 0.7718 (p) REVERT: E 152 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.7845 (mm-40) REVERT: F 77 TYR cc_start: 0.8813 (m-80) cc_final: 0.8382 (m-80) REVERT: F 113 MET cc_start: 0.8542 (tpp) cc_final: 0.7842 (mmm) REVERT: F 127 TYR cc_start: 0.7880 (t80) cc_final: 0.7265 (t80) REVERT: F 169 ASN cc_start: 0.9312 (m110) cc_final: 0.8815 (m110) REVERT: F 195 ASN cc_start: 0.7815 (m-40) cc_final: 0.7467 (m110) REVERT: F 196 MET cc_start: 0.6564 (tmm) cc_final: 0.5853 (tmm) REVERT: F 220 MET cc_start: 0.8580 (tpp) cc_final: 0.7582 (tpp) REVERT: G 7 GLU cc_start: 0.9340 (OUTLIER) cc_final: 0.8956 (mp0) REVERT: G 113 MET cc_start: 0.8012 (mtt) cc_final: 0.7725 (mtt) REVERT: G 134 GLU cc_start: 0.8581 (tm-30) cc_final: 0.8147 (tm-30) REVERT: G 196 MET cc_start: 0.7746 (ptp) cc_final: 0.7489 (ptp) REVERT: H 113 MET cc_start: 0.8472 (mtt) cc_final: 0.8251 (mtt) REVERT: H 242 TYR cc_start: 0.8921 (p90) cc_final: 0.8569 (p90) outliers start: 89 outliers final: 70 residues processed: 277 average time/residue: 0.3976 time to fit residues: 188.3857 Evaluate side-chains 286 residues out of total 2668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 208 time to evaluate : 3.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 64 MET Chi-restraints excluded: chain a residue 81 THR Chi-restraints excluded: chain a residue 95 THR Chi-restraints excluded: chain a residue 101 ASP Chi-restraints excluded: chain a residue 128 VAL 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 11 LEU Chi-restraints excluded: chain b residue 15 ASN Chi-restraints excluded: chain b residue 32 GLU Chi-restraints excluded: chain b residue 92 THR Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain b residue 202 THR Chi-restraints excluded: chain b residue 234 VAL Chi-restraints excluded: chain b residue 249 ASP Chi-restraints excluded: chain c residue 254 ILE Chi-restraints excluded: chain d residue 220 MET Chi-restraints excluded: chain d residue 244 CYS Chi-restraints excluded: chain d residue 256 VAL Chi-restraints excluded: chain e residue 14 GLN Chi-restraints excluded: chain e residue 26 THR Chi-restraints excluded: chain e residue 51 VAL Chi-restraints excluded: chain e residue 64 MET Chi-restraints excluded: chain e residue 66 VAL Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 115 ILE Chi-restraints excluded: chain e residue 152 GLN Chi-restraints excluded: chain e residue 161 HIS Chi-restraints excluded: chain e residue 190 VAL Chi-restraints excluded: chain e residue 211 ILE Chi-restraints excluded: chain e residue 218 MET Chi-restraints excluded: chain e residue 221 TRP Chi-restraints excluded: chain e residue 258 ASP Chi-restraints excluded: chain f residue 32 GLU Chi-restraints excluded: chain f residue 258 ASP Chi-restraints excluded: chain g residue 7 GLU Chi-restraints excluded: chain g residue 12 HIS Chi-restraints excluded: chain g residue 32 GLU Chi-restraints excluded: chain g residue 39 ASN Chi-restraints excluded: chain g residue 82 VAL Chi-restraints excluded: chain g residue 188 LEU Chi-restraints excluded: chain g residue 249 ASP Chi-restraints excluded: chain h residue 64 MET Chi-restraints excluded: chain h residue 82 VAL Chi-restraints excluded: chain h residue 101 ASP Chi-restraints excluded: chain h residue 121 THR Chi-restraints excluded: chain h residue 134 GLU Chi-restraints excluded: chain h residue 244 CYS Chi-restraints excluded: chain h residue 249 ASP Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 152 GLN Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 221 TRP Chi-restraints excluded: chain F residue 233 ASP Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 188 LEU Chi-restraints excluded: chain G residue 220 MET Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 249 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 198 optimal weight: 9.9990 chunk 128 optimal weight: 2.9990 chunk 191 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 204 optimal weight: 5.9990 chunk 218 optimal weight: 2.9990 chunk 158 optimal weight: 7.9990 chunk 29 optimal weight: 0.3980 chunk 252 optimal weight: 5.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 68 HIS ** A 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 182 HIS ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 HIS F 161 HIS ** H 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 32811 Z= 0.195 Angle : 0.564 13.195 45845 Z= 0.305 Chirality : 0.038 0.130 4984 Planarity : 0.004 0.048 4812 Dihedral : 22.805 140.668 6532 Min Nonbonded Distance : 1.707 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.35 % Allowed : 19.00 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % 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: 0.23 (0.16), residues: 3069 helix: 1.26 (0.15), residues: 1219 sheet: 0.36 (0.23), residues: 545 loop : -0.98 (0.18), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP b 208 HIS 0.007 0.001 HIS G 9 PHE 0.012 0.001 PHE F 246 TYR 0.024 0.001 TYR D 242 ARG 0.009 0.000 ARG H 138 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 216 time to evaluate : 3.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 218 MET cc_start: 0.8313 (mmm) cc_final: 0.7983 (mmm) REVERT: e 152 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8502 (mm-40) REVERT: f 32 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7653 (pm20) REVERT: f 77 TYR cc_start: 0.8280 (m-80) cc_final: 0.7864 (m-80) REVERT: f 220 MET cc_start: 0.8516 (mmm) cc_final: 0.8075 (tpp) REVERT: g 7 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8342 (tm-30) REVERT: g 32 GLU cc_start: 0.9043 (OUTLIER) cc_final: 0.8735 (mp0) REVERT: h 64 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7714 (tmm) REVERT: h 134 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8398 (pm20) REVERT: A 39 ASN cc_start: 0.8239 (m-40) cc_final: 0.7913 (m-40) REVERT: A 205 GLU cc_start: 0.9193 (OUTLIER) cc_final: 0.8924 (pp20) REVERT: A 220 MET cc_start: 0.8629 (tpp) cc_final: 0.7959 (tpp) REVERT: B 32 GLU cc_start: 0.9460 (tp30) cc_final: 0.9250 (tp30) REVERT: B 88 PHE cc_start: 0.7821 (OUTLIER) cc_final: 0.6112 (t80) REVERT: B 113 MET cc_start: 0.8540 (mmm) cc_final: 0.7745 (mmm) REVERT: B 220 MET cc_start: 0.6794 (tpp) cc_final: 0.6423 (tpp) REVERT: B 244 CYS cc_start: 0.8573 (t) cc_final: 0.7700 (p) REVERT: D 218 MET cc_start: 0.8266 (mmm) cc_final: 0.7729 (mmm) REVERT: D 220 MET cc_start: 0.7935 (tpt) cc_final: 0.7509 (tpt) REVERT: E 97 GLU cc_start: 0.7671 (tp30) cc_final: 0.7378 (tp30) REVERT: E 196 MET cc_start: 0.7782 (ptt) cc_final: 0.6897 (ttp) REVERT: F 77 TYR cc_start: 0.8764 (m-80) cc_final: 0.8241 (m-80) REVERT: F 113 MET cc_start: 0.8663 (tpp) cc_final: 0.7902 (mmm) REVERT: F 127 TYR cc_start: 0.7538 (t80) cc_final: 0.7006 (t80) REVERT: F 169 ASN cc_start: 0.9318 (m110) cc_final: 0.8833 (m110) REVERT: F 195 ASN cc_start: 0.7762 (m-40) cc_final: 0.7484 (m110) REVERT: F 196 MET cc_start: 0.6553 (tmm) cc_final: 0.5835 (tmm) REVERT: F 220 MET cc_start: 0.8608 (tpp) cc_final: 0.7677 (tpp) REVERT: G 7 GLU cc_start: 0.9279 (OUTLIER) cc_final: 0.8946 (mp0) REVERT: G 113 MET cc_start: 0.8094 (mtt) cc_final: 0.7737 (mtt) REVERT: G 134 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8124 (tm-30) REVERT: G 196 MET cc_start: 0.7562 (ptp) cc_final: 0.7280 (ptp) REVERT: H 113 MET cc_start: 0.8439 (mtt) cc_final: 0.8210 (mtt) REVERT: H 242 TYR cc_start: 0.8905 (p90) cc_final: 0.8592 (p90) outliers start: 62 outliers final: 46 residues processed: 261 average time/residue: 0.3692 time to fit residues: 164.3987 Evaluate side-chains 260 residues out of total 2668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 205 time to evaluate : 3.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 95 THR Chi-restraints excluded: chain a residue 109 SER Chi-restraints excluded: chain a residue 128 VAL Chi-restraints excluded: chain a residue 205 GLU Chi-restraints excluded: chain b residue 32 GLU Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain b residue 202 THR Chi-restraints excluded: chain b residue 234 VAL Chi-restraints excluded: chain b residue 249 ASP Chi-restraints excluded: chain d residue 218 MET Chi-restraints excluded: chain d residue 244 CYS Chi-restraints excluded: chain d residue 256 VAL Chi-restraints excluded: chain e residue 14 GLN Chi-restraints excluded: chain e residue 26 THR Chi-restraints excluded: chain e residue 51 VAL Chi-restraints excluded: chain e residue 64 MET Chi-restraints excluded: chain e residue 66 VAL Chi-restraints excluded: chain e residue 152 GLN Chi-restraints excluded: chain e residue 218 MET Chi-restraints excluded: chain e residue 258 ASP Chi-restraints excluded: chain f residue 32 GLU Chi-restraints excluded: chain f residue 258 ASP Chi-restraints excluded: chain g residue 7 GLU Chi-restraints excluded: chain g residue 32 GLU Chi-restraints excluded: chain g residue 39 ASN Chi-restraints excluded: chain g residue 249 ASP Chi-restraints excluded: chain h residue 64 MET Chi-restraints excluded: chain h residue 82 VAL Chi-restraints excluded: chain h residue 101 ASP Chi-restraints excluded: chain h residue 134 GLU Chi-restraints excluded: chain h residue 236 ILE Chi-restraints excluded: chain h residue 244 CYS Chi-restraints excluded: chain h residue 249 ASP Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 233 ASP Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 188 LEU Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 249 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 291 optimal weight: 0.0050 chunk 307 optimal weight: 5.9990 chunk 280 optimal weight: 9.9990 chunk 299 optimal weight: 20.0000 chunk 180 optimal weight: 2.9990 chunk 130 optimal weight: 0.0570 chunk 234 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 270 optimal weight: 6.9990 chunk 282 optimal weight: 6.9990 chunk 298 optimal weight: 6.9990 overall best weight: 2.2118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 198 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 32811 Z= 0.222 Angle : 0.570 11.513 45845 Z= 0.309 Chirality : 0.038 0.208 4984 Planarity : 0.004 0.046 4812 Dihedral : 22.744 141.037 6532 Min Nonbonded Distance : 1.694 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.50 % Allowed : 19.08 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % 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: 0.30 (0.16), residues: 3069 helix: 1.33 (0.15), residues: 1219 sheet: 0.35 (0.23), residues: 551 loop : -0.95 (0.18), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP b 208 HIS 0.006 0.001 HIS G 9 PHE 0.014 0.001 PHE F 246 TYR 0.028 0.001 TYR F 127 ARG 0.005 0.000 ARG C 262 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 212 time to evaluate : 3.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 208 TRP cc_start: 0.9011 (OUTLIER) cc_final: 0.7636 (m-10) REVERT: a 218 MET cc_start: 0.8348 (mmm) cc_final: 0.8017 (mmm) REVERT: d 220 MET cc_start: 0.8194 (mmp) cc_final: 0.7781 (mmp) REVERT: e 152 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8501 (mm-40) REVERT: f 77 TYR cc_start: 0.8296 (m-80) cc_final: 0.7852 (m-80) REVERT: f 220 MET cc_start: 0.8503 (mmm) cc_final: 0.8032 (tpp) REVERT: g 7 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8368 (tm-30) REVERT: g 32 GLU cc_start: 0.9044 (OUTLIER) cc_final: 0.8737 (mp0) REVERT: h 64 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.7724 (tmm) REVERT: A 39 ASN cc_start: 0.8255 (m-40) cc_final: 0.7918 (m-40) REVERT: A 205 GLU cc_start: 0.9190 (OUTLIER) cc_final: 0.8881 (pp20) REVERT: A 220 MET cc_start: 0.8696 (tpp) cc_final: 0.8106 (tpp) REVERT: B 32 GLU cc_start: 0.9464 (tp30) cc_final: 0.9253 (tp30) REVERT: B 88 PHE cc_start: 0.7824 (OUTLIER) cc_final: 0.6125 (t80) REVERT: B 113 MET cc_start: 0.8565 (mmm) cc_final: 0.7774 (mmm) REVERT: B 220 MET cc_start: 0.6609 (tpp) cc_final: 0.6331 (tpp) REVERT: B 244 CYS cc_start: 0.8470 (t) cc_final: 0.7652 (p) REVERT: C 218 MET cc_start: 0.7998 (ptt) cc_final: 0.7435 (mmp) REVERT: D 218 MET cc_start: 0.8268 (mmm) cc_final: 0.7734 (mmm) REVERT: D 220 MET cc_start: 0.7790 (tpt) cc_final: 0.7587 (tpt) REVERT: E 15 ASN cc_start: 0.6474 (p0) cc_final: 0.6231 (p0) REVERT: E 97 GLU cc_start: 0.7659 (tp30) cc_final: 0.7375 (tp30) REVERT: E 196 MET cc_start: 0.7947 (ptt) cc_final: 0.7038 (ttp) REVERT: F 77 TYR cc_start: 0.8763 (m-80) cc_final: 0.8241 (m-80) REVERT: F 113 MET cc_start: 0.8589 (tpp) cc_final: 0.7828 (mmm) REVERT: F 169 ASN cc_start: 0.9311 (m110) cc_final: 0.8825 (m110) REVERT: F 195 ASN cc_start: 0.7872 (m-40) cc_final: 0.7616 (m110) REVERT: F 196 MET cc_start: 0.6584 (tmm) cc_final: 0.5877 (tmm) REVERT: F 220 MET cc_start: 0.8650 (tpp) cc_final: 0.7791 (tpp) REVERT: G 7 GLU cc_start: 0.9314 (OUTLIER) cc_final: 0.8965 (mp0) REVERT: G 113 MET cc_start: 0.8081 (mtt) cc_final: 0.7713 (mtt) REVERT: G 134 GLU cc_start: 0.8556 (tm-30) cc_final: 0.8122 (tm-30) REVERT: G 196 MET cc_start: 0.7712 (ptp) cc_final: 0.7449 (ptp) REVERT: H 113 MET cc_start: 0.8435 (mtt) cc_final: 0.8233 (mtt) REVERT: H 242 TYR cc_start: 0.8904 (p90) cc_final: 0.8650 (p90) outliers start: 66 outliers final: 50 residues processed: 262 average time/residue: 0.3657 time to fit residues: 164.9841 Evaluate side-chains 269 residues out of total 2668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 211 time to evaluate : 3.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 109 SER Chi-restraints excluded: chain a residue 128 VAL Chi-restraints excluded: chain a residue 205 GLU Chi-restraints excluded: chain a residue 208 TRP Chi-restraints excluded: chain b residue 32 GLU Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain b residue 202 THR Chi-restraints excluded: chain b residue 234 VAL Chi-restraints excluded: chain b residue 249 ASP Chi-restraints excluded: chain d residue 218 MET Chi-restraints excluded: chain d residue 244 CYS Chi-restraints excluded: chain d residue 256 VAL Chi-restraints excluded: chain e residue 14 GLN Chi-restraints excluded: chain e residue 26 THR Chi-restraints excluded: chain e residue 51 VAL Chi-restraints excluded: chain e residue 64 MET Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 152 GLN Chi-restraints excluded: chain e residue 211 ILE Chi-restraints excluded: chain e residue 218 MET Chi-restraints excluded: chain e residue 221 TRP Chi-restraints excluded: chain e residue 258 ASP Chi-restraints excluded: chain f residue 32 GLU Chi-restraints excluded: chain f residue 258 ASP Chi-restraints excluded: chain g residue 7 GLU Chi-restraints excluded: chain g residue 32 GLU Chi-restraints excluded: chain g residue 39 ASN Chi-restraints excluded: chain g residue 82 VAL Chi-restraints excluded: chain g residue 188 LEU Chi-restraints excluded: chain g residue 249 ASP Chi-restraints excluded: chain h residue 64 MET Chi-restraints excluded: chain h residue 82 VAL Chi-restraints excluded: chain h residue 101 ASP Chi-restraints excluded: chain h residue 134 GLU Chi-restraints excluded: chain h residue 236 ILE Chi-restraints excluded: chain h residue 244 CYS Chi-restraints excluded: chain h residue 249 ASP Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 221 TRP Chi-restraints excluded: chain F residue 233 ASP Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 188 LEU Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 249 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 196 optimal weight: 8.9990 chunk 316 optimal weight: 9.9990 chunk 193 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 chunk 219 optimal weight: 0.9980 chunk 331 optimal weight: 10.0000 chunk 305 optimal weight: 1.9990 chunk 264 optimal weight: 20.0000 chunk 27 optimal weight: 10.0000 chunk 204 optimal weight: 2.9990 chunk 161 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 161 HIS ** g 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 32811 Z= 0.272 Angle : 0.598 11.308 45845 Z= 0.323 Chirality : 0.039 0.234 4984 Planarity : 0.004 0.045 4812 Dihedral : 22.758 141.547 6532 Min Nonbonded Distance : 1.676 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.42 % Allowed : 19.34 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % 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: 0.22 (0.16), residues: 3069 helix: 1.25 (0.15), residues: 1227 sheet: 0.31 (0.23), residues: 570 loop : -1.00 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP b 208 HIS 0.007 0.001 HIS G 9 PHE 0.015 0.001 PHE F 246 TYR 0.026 0.001 TYR D 242 ARG 0.004 0.000 ARG C 262 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6138 Ramachandran restraints generated. 3069 Oldfield, 0 Emsley, 3069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 211 time to evaluate : 3.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 196 MET cc_start: 0.8207 (ttm) cc_final: 0.7763 (ptm) REVERT: a 208 TRP cc_start: 0.9011 (OUTLIER) cc_final: 0.7764 (m-10) REVERT: a 218 MET cc_start: 0.8347 (mmm) cc_final: 0.8060 (mmm) REVERT: d 220 MET cc_start: 0.8307 (mmp) cc_final: 0.7904 (mmp) REVERT: e 152 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8480 (mm-40) REVERT: f 77 TYR cc_start: 0.8363 (m-80) cc_final: 0.7948 (m-80) REVERT: f 220 MET cc_start: 0.8516 (mmm) cc_final: 0.8092 (tpp) REVERT: g 7 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8393 (tm-30) REVERT: h 64 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.7723 (tmm) REVERT: A 39 ASN cc_start: 0.8229 (m-40) cc_final: 0.7863 (m-40) REVERT: A 205 GLU cc_start: 0.9190 (OUTLIER) cc_final: 0.8904 (pp20) REVERT: A 220 MET cc_start: 0.8753 (tpp) cc_final: 0.8428 (tpp) REVERT: B 88 PHE cc_start: 0.7845 (OUTLIER) cc_final: 0.6131 (t80) REVERT: B 113 MET cc_start: 0.8471 (mmm) cc_final: 0.7717 (mmm) REVERT: B 220 MET cc_start: 0.6641 (tpp) cc_final: 0.6366 (tpp) REVERT: B 244 CYS cc_start: 0.8526 (t) cc_final: 0.7671 (p) REVERT: E 97 GLU cc_start: 0.7655 (tp30) cc_final: 0.7389 (tp30) REVERT: E 196 MET cc_start: 0.7940 (ptt) cc_final: 0.7053 (ttp) REVERT: F 77 TYR cc_start: 0.8725 (m-80) cc_final: 0.8194 (m-80) REVERT: F 113 MET cc_start: 0.8528 (tpp) cc_final: 0.8035 (mmm) REVERT: F 127 TYR cc_start: 0.7560 (m-80) cc_final: 0.7116 (t80) REVERT: F 169 ASN cc_start: 0.9316 (m110) cc_final: 0.8824 (m110) REVERT: F 195 ASN cc_start: 0.7791 (m-40) cc_final: 0.7504 (m110) REVERT: F 196 MET cc_start: 0.6632 (tmm) cc_final: 0.5874 (tmm) REVERT: F 220 MET cc_start: 0.8666 (tpp) cc_final: 0.7777 (tpp) REVERT: G 7 GLU cc_start: 0.9318 (OUTLIER) cc_final: 0.8954 (mp0) REVERT: G 113 MET cc_start: 0.7993 (mtt) cc_final: 0.7594 (mtt) REVERT: G 134 GLU cc_start: 0.8562 (tm-30) cc_final: 0.8127 (tm-30) REVERT: H 113 MET cc_start: 0.8443 (mtt) cc_final: 0.8236 (mtt) REVERT: H 242 TYR cc_start: 0.8924 (p90) cc_final: 0.8637 (p90) outliers start: 64 outliers final: 54 residues processed: 258 average time/residue: 0.3676 time to fit residues: 162.2635 Evaluate side-chains 266 residues out of total 2668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 205 time to evaluate : 3.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 81 THR Chi-restraints excluded: chain a residue 95 THR Chi-restraints excluded: chain a residue 109 SER Chi-restraints excluded: chain a residue 128 VAL Chi-restraints excluded: chain a residue 205 GLU Chi-restraints excluded: chain a residue 208 TRP Chi-restraints excluded: chain b residue 15 ASN Chi-restraints excluded: chain b residue 32 GLU Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain b residue 202 THR Chi-restraints excluded: chain b residue 234 VAL Chi-restraints excluded: chain b residue 249 ASP Chi-restraints excluded: chain d residue 218 MET Chi-restraints excluded: chain d residue 244 CYS Chi-restraints excluded: chain d residue 256 VAL Chi-restraints excluded: chain e residue 14 GLN Chi-restraints excluded: chain e residue 26 THR Chi-restraints excluded: chain e residue 51 VAL Chi-restraints excluded: chain e residue 64 MET Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 152 GLN Chi-restraints excluded: chain e residue 211 ILE Chi-restraints excluded: chain e residue 218 MET Chi-restraints excluded: chain e residue 221 TRP Chi-restraints excluded: chain e residue 258 ASP Chi-restraints excluded: chain f residue 32 GLU Chi-restraints excluded: chain f residue 258 ASP Chi-restraints excluded: chain g residue 7 GLU Chi-restraints excluded: chain g residue 32 GLU Chi-restraints excluded: chain g residue 39 ASN Chi-restraints excluded: chain g residue 82 VAL Chi-restraints excluded: chain g residue 188 LEU Chi-restraints excluded: chain g residue 190 VAL Chi-restraints excluded: chain g residue 249 ASP Chi-restraints excluded: chain h residue 64 MET Chi-restraints excluded: chain h residue 82 VAL Chi-restraints excluded: chain h residue 101 ASP Chi-restraints excluded: chain h residue 134 GLU Chi-restraints excluded: chain h residue 244 CYS Chi-restraints excluded: chain h residue 249 ASP Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 221 TRP Chi-restraints excluded: chain F residue 233 ASP Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 188 LEU Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 249 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 209 optimal weight: 9.9990 chunk 281 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 243 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 73 optimal weight: 0.8980 chunk 264 optimal weight: 20.0000 chunk 110 optimal weight: 5.9990 chunk 271 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 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 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 GLN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.068111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.049386 restraints weight = 145084.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.050645 restraints weight = 75370.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.051489 restraints weight = 50714.298| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 32811 Z= 0.259 Angle : 0.596 12.746 45845 Z= 0.320 Chirality : 0.039 0.205 4984 Planarity : 0.004 0.046 4812 Dihedral : 22.759 141.437 6532 Min Nonbonded Distance : 1.675 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.54 % Allowed : 19.38 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % 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: 0.23 (0.16), residues: 3069 helix: 1.25 (0.15), residues: 1226 sheet: 0.29 (0.23), residues: 575 loop : -0.98 (0.18), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP b 208 HIS 0.006 0.001 HIS G 9 PHE 0.015 0.001 PHE F 246 TYR 0.025 0.001 TYR D 242 ARG 0.009 0.000 ARG H 138 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4801.33 seconds wall clock time: 89 minutes 8.13 seconds (5348.13 seconds total)