Starting phenix.real_space_refine on Thu Feb 22 12:04:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqs_26068/02_2024/7tqs_26068_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqs_26068/02_2024/7tqs_26068.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqs_26068/02_2024/7tqs_26068.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqs_26068/02_2024/7tqs_26068.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqs_26068/02_2024/7tqs_26068_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqs_26068/02_2024/7tqs_26068_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 211 5.16 5 C 21600 2.51 5 N 5788 2.21 5 O 6514 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "a PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 259": "OE1" <-> "OE2" Residue "m ARG 238": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 34113 Number of models: 1 Model: "" Number of chains: 27 Chain: "L" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 480 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'TRANS': 95} Unresolved non-hydrogen bonds: 192 Unresolved non-hydrogen angles: 288 Unresolved non-hydrogen dihedrals: 96 Planarities with less than four sites: {'UNK:plan-1': 96} Unresolved non-hydrogen planarities: 96 Chain: "H" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 530 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'TRANS': 105} Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 318 Unresolved non-hydrogen dihedrals: 106 Planarities with less than four sites: {'UNK:plan-1': 106} Unresolved non-hydrogen planarities: 106 Chain: "a" Number of atoms: 2219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2219 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 20, 'TRANS': 261} Chain: "b" Number of atoms: 2044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2044 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 16, 'TRANS': 246} Chain: "c" Number of atoms: 1857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1857 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 20, 'TRANS': 219} Chain: "d" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 512 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "e" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2226 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 20, 'TRANS': 262} Chain: "f" Number of atoms: 2036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2036 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 16, 'TRANS': 246} Chain breaks: 1 Chain: "g" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1848 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 20, 'TRANS': 218} Chain: "h" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 512 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "i" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2226 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 20, 'TRANS': 262} Chain: "j" Number of atoms: 2030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2030 Classifications: {'peptide': 261} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 244} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "k" Number of atoms: 1810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1810 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 20, 'TRANS': 213} Chain: "l" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 512 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "m" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2226 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 20, 'TRANS': 262} Chain: "n" Number of atoms: 2013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2013 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 242} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "o" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1848 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 20, 'TRANS': 218} Chain: "p" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 512 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "q" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2226 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 20, 'TRANS': 262} Chain: "r" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2006 Classifications: {'peptide': 258} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 241} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "s" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1848 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 20, 'TRANS': 218} Chain: "t" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 512 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "a" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Chain: "m" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Chain: "q" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 17.45, per 1000 atoms: 0.51 Number of scatterers: 34113 At special positions: 0 Unit cell: (126.445, 178.695, 157.795, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 211 16.00 O 6514 8.00 N 5788 7.00 C 21600 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: 12.74 Conformation dependent library (CDL) restraints added in 5.6 seconds 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8382 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 112 helices and 57 sheets defined 12.1% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.08 Creating SS restraints... Processing helix chain 'H' and resid 39 through 41 No H-bonds generated for 'chain 'H' and resid 39 through 41' Processing helix chain 'H' and resid 58 through 60 No H-bonds generated for 'chain 'H' and resid 58 through 60' Processing helix chain 'a' and resid 52 through 55 No H-bonds generated for 'chain 'a' and resid 52 through 55' Processing helix chain 'a' and resid 68 through 70 No H-bonds generated for 'chain 'a' and resid 68 through 70' Processing helix chain 'a' and resid 72 through 75 No H-bonds generated for 'chain 'a' and resid 72 through 75' Processing helix chain 'a' and resid 94 through 99 removed outlier: 3.761A pdb=" N LYS a 98 " --> pdb=" O GLY a 94 " (cutoff:3.500A) Processing helix chain 'a' and resid 111 through 119 removed outlier: 3.548A pdb=" N PHE a 119 " --> pdb=" O ARG a 115 " (cutoff:3.500A) Processing helix chain 'a' and resid 168 through 171 Processing helix chain 'a' and resid 226 through 228 No H-bonds generated for 'chain 'a' and resid 226 through 228' Processing helix chain 'a' and resid 283 through 285 No H-bonds generated for 'chain 'a' and resid 283 through 285' Processing helix chain 'b' and resid 34 through 36 No H-bonds generated for 'chain 'b' and resid 34 through 36' Processing helix chain 'b' and resid 44 through 46 No H-bonds generated for 'chain 'b' and resid 44 through 46' Processing helix chain 'b' and resid 57 through 59 No H-bonds generated for 'chain 'b' and resid 57 through 59' Processing helix chain 'b' and resid 82 through 85 No H-bonds generated for 'chain 'b' and resid 82 through 85' Processing helix chain 'b' and resid 90 through 98 Processing helix chain 'b' and resid 145 through 148 No H-bonds generated for 'chain 'b' and resid 145 through 148' Processing helix chain 'b' and resid 187 through 192 removed outlier: 4.380A pdb=" N PHE b 191 " --> pdb=" O GLY b 188 " (cutoff:3.500A) Processing helix chain 'c' and resid 43 through 47 Processing helix chain 'c' and resid 65 through 68 Processing helix chain 'c' and resid 94 through 96 No H-bonds generated for 'chain 'c' and resid 94 through 96' Processing helix chain 'c' and resid 98 through 105 removed outlier: 4.023A pdb=" N TYR c 105 " --> pdb=" O GLU c 101 " (cutoff:3.500A) Processing helix chain 'c' and resid 144 through 149 removed outlier: 4.322A pdb=" N LEU c 149 " --> pdb=" O LYS c 145 " (cutoff:3.500A) Processing helix chain 'c' and resid 182 through 184 No H-bonds generated for 'chain 'c' and resid 182 through 184' Processing helix chain 'd' and resid 36 through 38 No H-bonds generated for 'chain 'd' and resid 36 through 38' Processing helix chain 'd' and resid 50 through 54 removed outlier: 3.690A pdb=" N THR d 54 " --> pdb=" O SER d 51 " (cutoff:3.500A) Processing helix chain 'e' and resid 52 through 55 No H-bonds generated for 'chain 'e' and resid 52 through 55' Processing helix chain 'e' and resid 72 through 75 No H-bonds generated for 'chain 'e' and resid 72 through 75' Processing helix chain 'e' and resid 93 through 99 removed outlier: 4.882A pdb=" N LYS e 97 " --> pdb=" O GLY e 94 " (cutoff:3.500A) Processing helix chain 'e' and resid 111 through 119 removed outlier: 3.657A pdb=" N PHE e 119 " --> pdb=" O ARG e 115 " (cutoff:3.500A) Processing helix chain 'e' and resid 168 through 171 Processing helix chain 'e' and resid 226 through 229 Processing helix chain 'e' and resid 283 through 285 No H-bonds generated for 'chain 'e' and resid 283 through 285' Processing helix chain 'f' and resid 34 through 36 No H-bonds generated for 'chain 'f' and resid 34 through 36' Processing helix chain 'f' and resid 44 through 46 No H-bonds generated for 'chain 'f' and resid 44 through 46' Processing helix chain 'f' and resid 57 through 59 No H-bonds generated for 'chain 'f' and resid 57 through 59' Processing helix chain 'f' and resid 82 through 85 No H-bonds generated for 'chain 'f' and resid 82 through 85' Processing helix chain 'f' and resid 92 through 98 Processing helix chain 'f' and resid 151 through 153 No H-bonds generated for 'chain 'f' and resid 151 through 153' Processing helix chain 'f' and resid 169 through 171 No H-bonds generated for 'chain 'f' and resid 169 through 171' Processing helix chain 'f' and resid 187 through 192 removed outlier: 4.523A pdb=" N PHE f 191 " --> pdb=" O GLY f 188 " (cutoff:3.500A) Processing helix chain 'g' and resid 43 through 47 Processing helix chain 'g' and resid 65 through 68 Processing helix chain 'g' and resid 94 through 96 No H-bonds generated for 'chain 'g' and resid 94 through 96' Processing helix chain 'g' and resid 98 through 105 removed outlier: 4.141A pdb=" N TYR g 105 " --> pdb=" O GLU g 101 " (cutoff:3.500A) Processing helix chain 'g' and resid 144 through 147 No H-bonds generated for 'chain 'g' and resid 144 through 147' Processing helix chain 'h' and resid 36 through 38 No H-bonds generated for 'chain 'h' and resid 36 through 38' Processing helix chain 'h' and resid 50 through 54 removed outlier: 3.526A pdb=" N THR h 54 " --> pdb=" O SER h 51 " (cutoff:3.500A) Processing helix chain 'i' and resid 52 through 54 No H-bonds generated for 'chain 'i' and resid 52 through 54' Processing helix chain 'i' and resid 68 through 70 No H-bonds generated for 'chain 'i' and resid 68 through 70' Processing helix chain 'i' and resid 72 through 75 No H-bonds generated for 'chain 'i' and resid 72 through 75' Processing helix chain 'i' and resid 93 through 99 removed outlier: 4.995A pdb=" N LYS i 97 " --> pdb=" O GLY i 94 " (cutoff:3.500A) Processing helix chain 'i' and resid 111 through 119 removed outlier: 3.529A pdb=" N PHE i 119 " --> pdb=" O ARG i 115 " (cutoff:3.500A) Processing helix chain 'i' and resid 168 through 171 Processing helix chain 'i' and resid 226 through 229 No H-bonds generated for 'chain 'i' and resid 226 through 229' Processing helix chain 'j' and resid 34 through 36 No H-bonds generated for 'chain 'j' and resid 34 through 36' Processing helix chain 'j' and resid 44 through 46 No H-bonds generated for 'chain 'j' and resid 44 through 46' Processing helix chain 'j' and resid 57 through 60 No H-bonds generated for 'chain 'j' and resid 57 through 60' Processing helix chain 'j' and resid 82 through 88 removed outlier: 3.520A pdb=" N LYS j 87 " --> pdb=" O PRO j 83 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ASP j 88 " --> pdb=" O ASP j 84 " (cutoff:3.500A) Processing helix chain 'j' and resid 93 through 98 Processing helix chain 'j' and resid 145 through 148 No H-bonds generated for 'chain 'j' and resid 145 through 148' Processing helix chain 'j' and resid 187 through 192 removed outlier: 4.280A pdb=" N PHE j 191 " --> pdb=" O GLY j 188 " (cutoff:3.500A) Processing helix chain 'k' and resid 43 through 47 Processing helix chain 'k' and resid 65 through 68 Processing helix chain 'k' and resid 98 through 105 removed outlier: 4.097A pdb=" N TYR k 105 " --> pdb=" O GLU k 101 " (cutoff:3.500A) Processing helix chain 'k' and resid 144 through 149 Processing helix chain 'k' and resid 182 through 184 No H-bonds generated for 'chain 'k' and resid 182 through 184' Processing helix chain 'l' and resid 23 through 25 No H-bonds generated for 'chain 'l' and resid 23 through 25' Processing helix chain 'l' and resid 36 through 38 No H-bonds generated for 'chain 'l' and resid 36 through 38' Processing helix chain 'l' and resid 50 through 54 Processing helix chain 'm' and resid 52 through 54 No H-bonds generated for 'chain 'm' and resid 52 through 54' Processing helix chain 'm' and resid 72 through 75 No H-bonds generated for 'chain 'm' and resid 72 through 75' Processing helix chain 'm' and resid 93 through 98 removed outlier: 4.634A pdb=" N LYS m 97 " --> pdb=" O GLY m 94 " (cutoff:3.500A) Processing helix chain 'm' and resid 111 through 119 removed outlier: 4.384A pdb=" N LYS m 116 " --> pdb=" O GLN m 112 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE m 119 " --> pdb=" O ARG m 115 " (cutoff:3.500A) Processing helix chain 'm' and resid 168 through 171 Processing helix chain 'm' and resid 226 through 229 Processing helix chain 'n' and resid 34 through 36 No H-bonds generated for 'chain 'n' and resid 34 through 36' Processing helix chain 'n' and resid 57 through 59 No H-bonds generated for 'chain 'n' and resid 57 through 59' Processing helix chain 'n' and resid 82 through 85 No H-bonds generated for 'chain 'n' and resid 82 through 85' Processing helix chain 'n' and resid 90 through 97 Processing helix chain 'n' and resid 145 through 148 No H-bonds generated for 'chain 'n' and resid 145 through 148' Processing helix chain 'n' and resid 151 through 153 No H-bonds generated for 'chain 'n' and resid 151 through 153' Processing helix chain 'n' and resid 170 through 172 No H-bonds generated for 'chain 'n' and resid 170 through 172' Processing helix chain 'n' and resid 187 through 192 removed outlier: 4.155A pdb=" N PHE n 191 " --> pdb=" O GLY n 188 " (cutoff:3.500A) Processing helix chain 'o' and resid 43 through 47 Processing helix chain 'o' and resid 65 through 68 Processing helix chain 'o' and resid 98 through 105 removed outlier: 3.740A pdb=" N TYR o 105 " --> pdb=" O GLU o 101 " (cutoff:3.500A) Processing helix chain 'o' and resid 144 through 149 removed outlier: 3.745A pdb=" N LEU o 149 " --> pdb=" O LYS o 145 " (cutoff:3.500A) Processing helix chain 'p' and resid 36 through 38 No H-bonds generated for 'chain 'p' and resid 36 through 38' Processing helix chain 'p' and resid 50 through 54 removed outlier: 3.589A pdb=" N THR p 54 " --> pdb=" O SER p 51 " (cutoff:3.500A) Processing helix chain 'q' and resid 42 through 44 No H-bonds generated for 'chain 'q' and resid 42 through 44' Processing helix chain 'q' and resid 52 through 54 No H-bonds generated for 'chain 'q' and resid 52 through 54' Processing helix chain 'q' and resid 72 through 75 No H-bonds generated for 'chain 'q' and resid 72 through 75' Processing helix chain 'q' and resid 93 through 98 removed outlier: 3.575A pdb=" N LYS q 97 " --> pdb=" O GLY q 94 " (cutoff:3.500A) Processing helix chain 'q' and resid 111 through 119 removed outlier: 3.613A pdb=" N PHE q 119 " --> pdb=" O ARG q 115 " (cutoff:3.500A) Processing helix chain 'q' and resid 168 through 171 Processing helix chain 'q' and resid 221 through 223 No H-bonds generated for 'chain 'q' and resid 221 through 223' Processing helix chain 'q' and resid 226 through 229 No H-bonds generated for 'chain 'q' and resid 226 through 229' Processing helix chain 'r' and resid 34 through 36 No H-bonds generated for 'chain 'r' and resid 34 through 36' Processing helix chain 'r' and resid 44 through 46 No H-bonds generated for 'chain 'r' and resid 44 through 46' Processing helix chain 'r' and resid 57 through 59 No H-bonds generated for 'chain 'r' and resid 57 through 59' Processing helix chain 'r' and resid 82 through 85 No H-bonds generated for 'chain 'r' and resid 82 through 85' Processing helix chain 'r' and resid 90 through 98 Processing helix chain 'r' and resid 145 through 148 No H-bonds generated for 'chain 'r' and resid 145 through 148' Processing helix chain 'r' and resid 151 through 153 No H-bonds generated for 'chain 'r' and resid 151 through 153' Processing helix chain 'r' and resid 187 through 192 removed outlier: 4.292A pdb=" N PHE r 191 " --> pdb=" O GLY r 188 " (cutoff:3.500A) Processing helix chain 's' and resid 43 through 48 Processing helix chain 's' and resid 65 through 68 Processing helix chain 's' and resid 94 through 96 No H-bonds generated for 'chain 's' and resid 94 through 96' Processing helix chain 's' and resid 98 through 105 removed outlier: 3.912A pdb=" N TYR s 105 " --> pdb=" O GLU s 101 " (cutoff:3.500A) Processing helix chain 's' and resid 144 through 147 No H-bonds generated for 'chain 's' and resid 144 through 147' Processing helix chain 't' and resid 36 through 38 No H-bonds generated for 'chain 't' and resid 36 through 38' Processing helix chain 't' and resid 50 through 54 Processing sheet with id= A, first strand: chain 'L' and resid 44 through 46 Processing sheet with id= B, first strand: chain 'H' and resid 16 through 23 Processing sheet with id= C, first strand: chain 'H' and resid 86 through 92 Processing sheet with id= D, first strand: chain 'H' and resid 48 through 50 Processing sheet with id= E, first strand: chain 'a' and resid 87 through 89 Processing sheet with id= F, first strand: chain 'a' and resid 100 through 104 Processing sheet with id= G, first strand: chain 'a' and resid 80 through 83 removed outlier: 6.545A pdb=" N VAL a 254 " --> pdb=" O VAL a 82 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'b' and resid 14 through 18 Processing sheet with id= I, first strand: chain 'b' and resid 63 through 65 Processing sheet with id= J, first strand: chain 'b' and resid 69 through 71 Processing sheet with id= K, first strand: chain 'b' and resid 78 through 81 removed outlier: 6.294A pdb=" N ALA b 121 " --> pdb=" O LEU b 234 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'b' and resid 101 through 103 Processing sheet with id= M, first strand: chain 'c' and resid 70 through 73 Processing sheet with id= N, first strand: chain 'c' and resid 82 through 85 removed outlier: 4.012A pdb=" N PHE c 82 " --> pdb=" O CYS c 191 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'd' and resid 4 through 7 Processing sheet with id= P, first strand: chain 'e' and resid 100 through 104 Processing sheet with id= Q, first strand: chain 'e' and resid 122 through 124 Processing sheet with id= R, first strand: chain 'e' and resid 188 through 191 removed outlier: 5.967A pdb=" N MET e 256 " --> pdb=" O CYS e 81 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N CYS e 81 " --> pdb=" O MET e 256 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'f' and resid 14 through 18 Processing sheet with id= T, first strand: chain 'f' and resid 63 through 65 Processing sheet with id= U, first strand: chain 'f' and resid 69 through 72 Processing sheet with id= V, first strand: chain 'f' and resid 78 through 81 removed outlier: 6.385A pdb=" N ALA f 121 " --> pdb=" O LEU f 234 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'f' and resid 101 through 103 Processing sheet with id= X, first strand: chain 'g' and resid 70 through 73 Processing sheet with id= Y, first strand: chain 'g' and resid 151 through 156 removed outlier: 3.679A pdb=" N PHE g 82 " --> pdb=" O CYS g 191 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N TYR g 193 " --> pdb=" O PRO g 80 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'h' and resid 4 through 7 Processing sheet with id= AA, first strand: chain 'i' and resid 100 through 104 Processing sheet with id= AB, first strand: chain 'i' and resid 122 through 124 Processing sheet with id= AC, first strand: chain 'i' and resid 188 through 191 removed outlier: 5.935A pdb=" N MET i 256 " --> pdb=" O CYS i 81 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N CYS i 81 " --> pdb=" O MET i 256 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'j' and resid 14 through 18 Processing sheet with id= AE, first strand: chain 'j' and resid 69 through 71 Processing sheet with id= AF, first strand: chain 'j' and resid 78 through 81 removed outlier: 6.184A pdb=" N ALA j 121 " --> pdb=" O LEU j 234 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'j' and resid 101 through 103 Processing sheet with id= AH, first strand: chain 'j' and resid 250 through 256 Processing sheet with id= AI, first strand: chain 'k' and resid 70 through 73 Processing sheet with id= AJ, first strand: chain 'k' and resid 151 through 156 removed outlier: 4.094A pdb=" N LYS k 128 " --> pdb=" O THR k 195 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N LEU k 130 " --> pdb=" O TYR k 193 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N TYR k 193 " --> pdb=" O LEU k 130 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N SER k 132 " --> pdb=" O CYS k 191 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N CYS k 191 " --> pdb=" O SER k 132 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N SER k 134 " --> pdb=" O ILE k 189 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ILE k 189 " --> pdb=" O SER k 134 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE k 82 " --> pdb=" O CYS k 191 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N TYR k 193 " --> pdb=" O PRO k 80 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'l' and resid 4 through 7 Processing sheet with id= AL, first strand: chain 'm' and resid 100 through 104 Processing sheet with id= AM, first strand: chain 'm' and resid 188 through 191 removed outlier: 6.158A pdb=" N MET m 256 " --> pdb=" O CYS m 81 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N CYS m 81 " --> pdb=" O MET m 256 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'n' and resid 14 through 18 Processing sheet with id= AO, first strand: chain 'n' and resid 63 through 65 Processing sheet with id= AP, first strand: chain 'n' and resid 69 through 71 Processing sheet with id= AQ, first strand: chain 'n' and resid 78 through 81 removed outlier: 6.257A pdb=" N ALA n 121 " --> pdb=" O LEU n 234 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'n' and resid 101 through 103 Processing sheet with id= AS, first strand: chain 'o' and resid 70 through 73 Processing sheet with id= AT, first strand: chain 'o' and resid 151 through 156 removed outlier: 4.064A pdb=" N LYS o 128 " --> pdb=" O THR o 195 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N LEU o 130 " --> pdb=" O TYR o 193 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N TYR o 193 " --> pdb=" O LEU o 130 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N SER o 132 " --> pdb=" O CYS o 191 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N CYS o 191 " --> pdb=" O SER o 132 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N SER o 134 " --> pdb=" O ILE o 189 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ILE o 189 " --> pdb=" O SER o 134 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE o 82 " --> pdb=" O CYS o 191 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N TYR o 193 " --> pdb=" O PRO o 80 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'p' and resid 4 through 7 Processing sheet with id= AV, first strand: chain 'q' and resid 100 through 104 Processing sheet with id= AW, first strand: chain 'q' and resid 188 through 191 removed outlier: 6.061A pdb=" N MET q 256 " --> pdb=" O CYS q 81 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N CYS q 81 " --> pdb=" O MET q 256 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'r' and resid 14 through 18 Processing sheet with id= AY, first strand: chain 'r' and resid 31 through 33 removed outlier: 9.006A pdb=" N ILE r 32 " --> pdb=" O SER r 205 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N THR r 207 " --> pdb=" O ILE r 32 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'r' and resid 69 through 72 Processing sheet with id= BA, first strand: chain 'r' and resid 78 through 81 removed outlier: 6.221A pdb=" N ALA r 121 " --> pdb=" O LEU r 234 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'r' and resid 101 through 103 Processing sheet with id= BC, first strand: chain 's' and resid 70 through 73 Processing sheet with id= BD, first strand: chain 's' and resid 151 through 156 removed outlier: 3.582A pdb=" N LYS s 128 " --> pdb=" O THR s 195 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N LEU s 130 " --> pdb=" O TYR s 193 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N TYR s 193 " --> pdb=" O LEU s 130 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N SER s 132 " --> pdb=" O CYS s 191 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N CYS s 191 " --> pdb=" O SER s 132 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N SER s 134 " --> pdb=" O ILE s 189 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ILE s 189 " --> pdb=" O SER s 134 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE s 82 " --> pdb=" O CYS s 191 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N TYR s 193 " --> pdb=" O PRO s 80 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 't' and resid 4 through 7 727 hydrogen bonds defined for protein. 1743 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.52 Time building geometry restraints manager: 13.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 5819 1.30 - 1.44: 10161 1.44 - 1.57: 18578 1.57 - 1.71: 78 1.71 - 1.85: 339 Bond restraints: 34975 Sorted by residual: bond pdb=" CB HIS j 224 " pdb=" CG HIS j 224 " ideal model delta sigma weight residual 1.497 1.380 0.117 1.40e-02 5.10e+03 7.01e+01 bond pdb=" CB HIS r 224 " pdb=" CG HIS r 224 " ideal model delta sigma weight residual 1.497 1.395 0.102 1.40e-02 5.10e+03 5.31e+01 bond pdb=" CB PHE i 100 " pdb=" CG PHE i 100 " ideal model delta sigma weight residual 1.502 1.336 0.166 2.30e-02 1.89e+03 5.23e+01 bond pdb=" CB PHE q 100 " pdb=" CG PHE q 100 " ideal model delta sigma weight residual 1.502 1.340 0.162 2.30e-02 1.89e+03 4.96e+01 bond pdb=" CB HIS f 224 " pdb=" CG HIS f 224 " ideal model delta sigma weight residual 1.497 1.400 0.097 1.40e-02 5.10e+03 4.77e+01 ... (remaining 34970 not shown) Histogram of bond angle deviations from ideal: 95.01 - 102.87: 578 102.87 - 110.74: 11795 110.74 - 118.60: 15639 118.60 - 126.47: 19266 126.47 - 134.34: 433 Bond angle restraints: 47711 Sorted by residual: angle pdb=" N VAL g 221 " pdb=" CA VAL g 221 " pdb=" C VAL g 221 " ideal model delta sigma weight residual 113.10 124.42 -11.32 9.70e-01 1.06e+00 1.36e+02 angle pdb=" C PRO o 135 " pdb=" N PRO o 136 " pdb=" CA PRO o 136 " ideal model delta sigma weight residual 120.21 129.62 -9.41 9.60e-01 1.09e+00 9.60e+01 angle pdb=" C PRO k 135 " pdb=" N PRO k 136 " pdb=" CA PRO k 136 " ideal model delta sigma weight residual 120.21 129.17 -8.96 9.60e-01 1.09e+00 8.71e+01 angle pdb=" C PRO s 135 " pdb=" N PRO s 136 " pdb=" CA PRO s 136 " ideal model delta sigma weight residual 120.21 129.13 -8.92 9.60e-01 1.09e+00 8.64e+01 angle pdb=" N LEU b 234 " pdb=" CA LEU b 234 " pdb=" C LEU b 234 " ideal model delta sigma weight residual 113.88 102.52 11.36 1.23e+00 6.61e-01 8.54e+01 ... (remaining 47706 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 20162 17.72 - 35.44: 519 35.44 - 53.16: 113 53.16 - 70.88: 51 70.88 - 88.60: 14 Dihedral angle restraints: 20859 sinusoidal: 7864 harmonic: 12995 Sorted by residual: dihedral pdb=" CA ASN l 15 " pdb=" C ASN l 15 " pdb=" N GLN l 16 " pdb=" CA GLN l 16 " ideal model delta harmonic sigma weight residual 180.00 157.02 22.98 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" C LEU r 82 " pdb=" N LEU r 82 " pdb=" CA LEU r 82 " pdb=" CB LEU r 82 " ideal model delta harmonic sigma weight residual -122.60 -133.44 10.84 0 2.50e+00 1.60e-01 1.88e+01 dihedral pdb=" CA ASP s 218 " pdb=" C ASP s 218 " pdb=" N PHE s 219 " pdb=" CA PHE s 219 " ideal model delta harmonic sigma weight residual 180.00 -160.91 -19.09 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 20856 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 3941 0.103 - 0.207: 1241 0.207 - 0.310: 152 0.310 - 0.414: 21 0.414 - 0.517: 8 Chirality restraints: 5363 Sorted by residual: chirality pdb=" CB VAL i 16 " pdb=" CA VAL i 16 " pdb=" CG1 VAL i 16 " pdb=" CG2 VAL i 16 " both_signs ideal model delta sigma weight residual False -2.63 -3.15 0.52 2.00e-01 2.50e+01 6.69e+00 chirality pdb=" CA TRP a 264 " pdb=" N TRP a 264 " pdb=" C TRP a 264 " pdb=" CB TRP a 264 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.42e+00 chirality pdb=" CB VAL q 16 " pdb=" CA VAL q 16 " pdb=" CG1 VAL q 16 " pdb=" CG2 VAL q 16 " both_signs ideal model delta sigma weight residual False -2.63 -3.13 0.50 2.00e-01 2.50e+01 6.30e+00 ... (remaining 5360 not shown) Planarity restraints: 6193 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR i 168 " -0.050 2.00e-02 2.50e+03 3.26e-02 2.13e+01 pdb=" CG TYR i 168 " 0.004 2.00e-02 2.50e+03 pdb=" CD1 TYR i 168 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR i 168 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR i 168 " 0.030 2.00e-02 2.50e+03 pdb=" CE2 TYR i 168 " 0.024 2.00e-02 2.50e+03 pdb=" CZ TYR i 168 " 0.012 2.00e-02 2.50e+03 pdb=" OH TYR i 168 " -0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR b 179 " -0.054 2.00e-02 2.50e+03 3.15e-02 1.98e+01 pdb=" CG TYR b 179 " 0.002 2.00e-02 2.50e+03 pdb=" CD1 TYR b 179 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR b 179 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR b 179 " 0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR b 179 " 0.020 2.00e-02 2.50e+03 pdb=" CZ TYR b 179 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR b 179 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR e 255 " 0.051 2.00e-02 2.50e+03 3.05e-02 1.86e+01 pdb=" CG TYR e 255 " -0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR e 255 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR e 255 " -0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR e 255 " -0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR e 255 " -0.023 2.00e-02 2.50e+03 pdb=" CZ TYR e 255 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR e 255 " 0.051 2.00e-02 2.50e+03 ... (remaining 6190 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 13185 2.87 - 3.38: 32137 3.38 - 3.89: 61038 3.89 - 4.39: 74155 4.39 - 4.90: 117680 Nonbonded interactions: 298195 Sorted by model distance: nonbonded pdb=" N ASP q 221 " pdb=" OD1 ASP q 221 " model vdw 2.363 2.520 nonbonded pdb=" N LEU b 234 " pdb=" N ALA b 235 " model vdw 2.408 2.560 nonbonded pdb=" NZ LYS i 257 " pdb=" O ASP k 17 " model vdw 2.409 2.520 nonbonded pdb=" O ALA d 41 " pdb=" NZ LYS t 34 " model vdw 2.409 2.520 nonbonded pdb=" N ASP k 218 " pdb=" N PHE k 219 " model vdw 2.411 2.560 ... (remaining 298190 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 'H' and resid 13 through 108) selection = chain 'L' } ncs_group { reference = chain 'a' selection = (chain 'e' and (resid 17 through 298 or resid 300)) selection = (chain 'i' and (resid 17 through 298 or resid 300)) selection = (chain 'm' and (resid 17 through 298 or resid 300)) selection = (chain 'q' and (resid 17 through 298 or resid 300)) } ncs_group { reference = (chain 'b' and (resid 11 through 163 or resid 169 through 271)) selection = (chain 'f' and (resid 11 through 163 or resid 169 through 271)) selection = (chain 'j' and (resid 11 through 163 or resid 169 through 271)) selection = (chain 'n' and (resid 11 through 163 or resid 169 through 271)) selection = (chain 'r' and (resid 11 through 163 or resid 169 through 271)) } ncs_group { reference = (chain 'c' and resid 1 through 234) selection = (chain 'g' and resid 1 through 234) selection = chain 'k' selection = (chain 'o' and resid 1 through 234) selection = (chain 's' and resid 1 through 234) } ncs_group { reference = chain 'd' selection = chain 'h' selection = chain 'l' selection = chain 'p' selection = chain 't' } 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: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 6.690 Check model and map are aligned: 0.510 Set scattering table: 0.310 Process input model: 84.790 Find NCS groups from input model: 2.720 Set up NCS constraints: 0.250 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: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 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 : 0.021 0.166 34975 Z= 1.410 Angle : 1.804 11.580 47711 Z= 1.232 Chirality : 0.096 0.517 5363 Planarity : 0.009 0.052 6193 Dihedral : 9.827 88.605 12477 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % 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: 0.58 (0.12), residues: 4201 helix: -2.79 (0.20), residues: 377 sheet: 1.63 (0.15), residues: 1032 loop : 0.46 (0.11), residues: 2792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.007 TRP r 227 HIS 0.013 0.003 HIS q 246 PHE 0.030 0.006 PHE o 82 TYR 0.060 0.009 TYR i 168 ARG 0.013 0.001 ARG a 275 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1664 residues out of total 3684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1664 time to evaluate : 3.812 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN n 272 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN r 272 " (corrupted residue). Skipping it. REVERT: a 29 SER cc_start: 0.8666 (t) cc_final: 0.8350 (m) REVERT: a 47 SER cc_start: 0.9172 (m) cc_final: 0.8948 (p) REVERT: a 49 GLN cc_start: 0.8732 (mm-40) cc_final: 0.8311 (mm110) REVERT: a 105 ILE cc_start: 0.9599 (mt) cc_final: 0.9353 (mt) REVERT: a 106 THR cc_start: 0.9279 (t) cc_final: 0.8955 (m) REVERT: a 110 THR cc_start: 0.8741 (p) cc_final: 0.8289 (p) REVERT: a 174 SER cc_start: 0.9349 (m) cc_final: 0.8899 (t) REVERT: a 175 ASN cc_start: 0.8950 (m-40) cc_final: 0.8557 (m-40) REVERT: a 205 ASP cc_start: 0.9055 (t0) cc_final: 0.8828 (t70) REVERT: a 267 ARG cc_start: 0.8815 (mtp85) cc_final: 0.8591 (mtt-85) REVERT: a 277 GLU cc_start: 0.7380 (mp0) cc_final: 0.7054 (mp0) REVERT: b 41 TYR cc_start: 0.8595 (m-80) cc_final: 0.8167 (m-10) REVERT: b 97 TYR cc_start: 0.8614 (m-80) cc_final: 0.8378 (m-80) REVERT: b 104 SER cc_start: 0.9120 (t) cc_final: 0.8583 (p) REVERT: b 106 TYR cc_start: 0.9099 (m-80) cc_final: 0.8383 (m-80) REVERT: b 142 TYR cc_start: 0.7909 (t80) cc_final: 0.7703 (t80) REVERT: b 149 ASN cc_start: 0.8889 (m-40) cc_final: 0.8228 (m-40) REVERT: b 170 GLU cc_start: 0.7665 (mm-30) cc_final: 0.6639 (mm-30) REVERT: b 183 SER cc_start: 0.9111 (p) cc_final: 0.8754 (t) REVERT: b 193 TYR cc_start: 0.9072 (m-80) cc_final: 0.8863 (m-10) REVERT: b 198 ILE cc_start: 0.9456 (mt) cc_final: 0.9212 (tt) REVERT: b 249 ILE cc_start: 0.9584 (mt) cc_final: 0.9343 (mm) REVERT: c 10 SER cc_start: 0.9413 (t) cc_final: 0.9038 (p) REVERT: c 21 SER cc_start: 0.9442 (p) cc_final: 0.8994 (m) REVERT: c 56 ASN cc_start: 0.9550 (t0) cc_final: 0.9348 (t0) REVERT: c 112 SER cc_start: 0.9560 (m) cc_final: 0.9252 (p) REVERT: c 146 ASP cc_start: 0.8907 (m-30) cc_final: 0.8689 (m-30) REVERT: c 226 ASP cc_start: 0.8482 (m-30) cc_final: 0.7831 (m-30) REVERT: c 235 LEU cc_start: 0.8517 (mt) cc_final: 0.8201 (mt) REVERT: d 21 ASN cc_start: 0.7786 (p0) cc_final: 0.7203 (p0) REVERT: e 51 ILE cc_start: 0.8917 (pt) cc_final: 0.8593 (pt) REVERT: e 163 SER cc_start: 0.8982 (p) cc_final: 0.8694 (p) REVERT: e 174 SER cc_start: 0.8993 (m) cc_final: 0.8571 (t) REVERT: e 182 TYR cc_start: 0.8653 (t80) cc_final: 0.8399 (t80) REVERT: e 204 TYR cc_start: 0.8645 (t80) cc_final: 0.8399 (t80) REVERT: e 205 ASP cc_start: 0.9146 (t0) cc_final: 0.8720 (t0) REVERT: e 229 ILE cc_start: 0.9062 (tt) cc_final: 0.8696 (tt) REVERT: e 282 ILE cc_start: 0.8007 (tp) cc_final: 0.7767 (pt) REVERT: f 13 VAL cc_start: 0.9581 (t) cc_final: 0.9345 (p) REVERT: f 87 LYS cc_start: 0.9084 (pttp) cc_final: 0.8655 (pttp) REVERT: f 122 LEU cc_start: 0.9410 (mt) cc_final: 0.9144 (mt) REVERT: f 145 TYR cc_start: 0.9071 (t80) cc_final: 0.8784 (t80) REVERT: g 6 ASN cc_start: 0.9067 (m-40) cc_final: 0.8866 (m-40) REVERT: g 42 ASN cc_start: 0.8498 (t0) cc_final: 0.8234 (t0) REVERT: g 74 ASP cc_start: 0.8720 (p0) cc_final: 0.8409 (p0) REVERT: g 85 SER cc_start: 0.8509 (t) cc_final: 0.8110 (m) REVERT: g 106 TYR cc_start: 0.9407 (m-80) cc_final: 0.8332 (m-80) REVERT: g 112 SER cc_start: 0.9114 (m) cc_final: 0.8352 (p) REVERT: g 156 ASP cc_start: 0.8286 (t0) cc_final: 0.7672 (p0) REVERT: g 172 ASN cc_start: 0.9271 (p0) cc_final: 0.8941 (p0) REVERT: g 198 VAL cc_start: 0.9584 (t) cc_final: 0.9325 (p) REVERT: g 216 CYS cc_start: 0.8751 (m) cc_final: 0.7731 (m) REVERT: h 27 TYR cc_start: 0.9154 (p90) cc_final: 0.8822 (p90) REVERT: i 98 LYS cc_start: 0.8998 (mttt) cc_final: 0.8711 (mtpp) REVERT: i 101 ASN cc_start: 0.8468 (t0) cc_final: 0.8211 (t0) REVERT: i 105 ILE cc_start: 0.9092 (mm) cc_final: 0.8789 (mm) REVERT: i 107 TYR cc_start: 0.9038 (p90) cc_final: 0.8729 (p90) REVERT: i 127 LEU cc_start: 0.9299 (tp) cc_final: 0.8519 (tp) REVERT: i 166 ASP cc_start: 0.7404 (p0) cc_final: 0.5743 (p0) REVERT: i 204 TYR cc_start: 0.8719 (t80) cc_final: 0.8185 (t80) REVERT: i 267 ARG cc_start: 0.9220 (mtp85) cc_final: 0.8767 (mtp180) REVERT: i 286 ILE cc_start: 0.8981 (pt) cc_final: 0.8711 (pt) REVERT: j 84 ASP cc_start: 0.8270 (t70) cc_final: 0.7697 (t70) REVERT: j 91 MET cc_start: 0.8322 (mmm) cc_final: 0.8101 (mmt) REVERT: j 131 VAL cc_start: 0.9448 (t) cc_final: 0.9006 (p) REVERT: j 137 GLU cc_start: 0.7294 (pm20) cc_final: 0.6855 (tp30) REVERT: j 179 TYR cc_start: 0.8460 (p90) cc_final: 0.8065 (p90) REVERT: j 192 VAL cc_start: 0.9457 (m) cc_final: 0.9249 (t) REVERT: j 223 LYS cc_start: 0.9233 (mtmt) cc_final: 0.8603 (mtmm) REVERT: j 227 TRP cc_start: 0.8856 (m100) cc_final: 0.8566 (m100) REVERT: j 259 GLU cc_start: 0.7692 (pt0) cc_final: 0.7189 (pt0) REVERT: j 265 ASN cc_start: 0.7796 (t0) cc_final: 0.7528 (t0) REVERT: k 2 LEU cc_start: 0.9267 (tp) cc_final: 0.9015 (tp) REVERT: k 42 ASN cc_start: 0.8708 (t0) cc_final: 0.8217 (t0) REVERT: k 55 MET cc_start: 0.9114 (tpp) cc_final: 0.8789 (tpt) REVERT: k 65 MET cc_start: 0.8380 (tpp) cc_final: 0.8150 (tpp) REVERT: k 107 THR cc_start: 0.9403 (p) cc_final: 0.9104 (t) REVERT: k 119 PHE cc_start: 0.8631 (t80) cc_final: 0.8160 (t80) REVERT: k 128 LYS cc_start: 0.8385 (mttm) cc_final: 0.7897 (mtmt) REVERT: k 155 TRP cc_start: 0.8381 (t60) cc_final: 0.7919 (t60) REVERT: k 169 TRP cc_start: 0.8774 (t-100) cc_final: 0.8125 (t-100) REVERT: k 178 CYS cc_start: 0.8403 (m) cc_final: 0.8152 (m) REVERT: k 183 PHE cc_start: 0.8169 (t80) cc_final: 0.7947 (t80) REVERT: k 196 ARG cc_start: 0.7584 (ttp80) cc_final: 0.6821 (ptt-90) REVERT: k 216 CYS cc_start: 0.8599 (m) cc_final: 0.8340 (m) REVERT: l 53 PHE cc_start: 0.9102 (m-80) cc_final: 0.8870 (m-80) REVERT: m 54 ASP cc_start: 0.8327 (m-30) cc_final: 0.7997 (m-30) REVERT: m 95 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7868 (mm-30) REVERT: m 105 ILE cc_start: 0.9163 (mt) cc_final: 0.8799 (mt) REVERT: m 127 LEU cc_start: 0.8930 (tp) cc_final: 0.8477 (tp) REVERT: m 166 ASP cc_start: 0.8803 (p0) cc_final: 0.8009 (p0) REVERT: m 205 ASP cc_start: 0.8639 (t0) cc_final: 0.7946 (t70) REVERT: m 216 ASN cc_start: 0.6964 (t0) cc_final: 0.6482 (m-40) REVERT: m 218 ASP cc_start: 0.7770 (m-30) cc_final: 0.7450 (m-30) REVERT: n 13 VAL cc_start: 0.9589 (t) cc_final: 0.9229 (p) REVERT: n 33 VAL cc_start: 0.9639 (t) cc_final: 0.9413 (m) REVERT: n 60 SER cc_start: 0.9406 (m) cc_final: 0.8981 (p) REVERT: n 71 TRP cc_start: 0.8653 (t60) cc_final: 0.8450 (t60) REVERT: n 129 GLU cc_start: 0.8406 (tp30) cc_final: 0.8052 (tp30) REVERT: n 180 LEU cc_start: 0.9073 (mt) cc_final: 0.8854 (mt) REVERT: n 213 VAL cc_start: 0.9786 (t) cc_final: 0.9439 (p) REVERT: n 216 LEU cc_start: 0.9249 (mt) cc_final: 0.8862 (mt) REVERT: n 224 HIS cc_start: 0.8735 (t-90) cc_final: 0.8235 (t-90) REVERT: o 87 SER cc_start: 0.9241 (m) cc_final: 0.8869 (p) REVERT: o 98 MET cc_start: 0.8622 (tpp) cc_final: 0.8422 (tpp) REVERT: o 128 LYS cc_start: 0.7191 (mttt) cc_final: 0.6957 (mttt) REVERT: o 153 ILE cc_start: 0.9226 (tt) cc_final: 0.8975 (tp) REVERT: p 46 LEU cc_start: 0.8599 (mt) cc_final: 0.8396 (mt) REVERT: p 64 THR cc_start: 0.9140 (p) cc_final: 0.8108 (p) REVERT: q 47 SER cc_start: 0.9110 (m) cc_final: 0.8871 (p) REVERT: q 62 VAL cc_start: 0.9606 (t) cc_final: 0.9346 (p) REVERT: q 105 ILE cc_start: 0.9088 (mt) cc_final: 0.8750 (mt) REVERT: q 109 ASP cc_start: 0.7807 (m-30) cc_final: 0.7447 (m-30) REVERT: q 126 ASP cc_start: 0.7917 (m-30) cc_final: 0.7589 (m-30) REVERT: q 127 LEU cc_start: 0.9435 (tp) cc_final: 0.9157 (tt) REVERT: q 137 TYR cc_start: 0.8886 (m-80) cc_final: 0.8682 (m-10) REVERT: q 165 TRP cc_start: 0.8400 (p-90) cc_final: 0.7190 (p-90) REVERT: q 168 TYR cc_start: 0.8878 (p90) cc_final: 0.8452 (p90) REVERT: q 171 GLN cc_start: 0.8570 (mt0) cc_final: 0.8051 (mt0) REVERT: q 221 ASP cc_start: 0.7322 (p0) cc_final: 0.7095 (p0) REVERT: q 244 ASN cc_start: 0.8648 (m-40) cc_final: 0.8411 (m110) REVERT: q 264 TRP cc_start: 0.9156 (m-90) cc_final: 0.8590 (m100) REVERT: q 274 TYR cc_start: 0.8411 (m-80) cc_final: 0.8121 (m-80) REVERT: q 280 ASP cc_start: 0.8443 (m-30) cc_final: 0.8153 (m-30) REVERT: r 40 THR cc_start: 0.9256 (p) cc_final: 0.8828 (t) REVERT: r 48 ASN cc_start: 0.9057 (t0) cc_final: 0.8811 (t0) REVERT: r 50 VAL cc_start: 0.9514 (m) cc_final: 0.9250 (p) REVERT: r 212 TYR cc_start: 0.8829 (t80) cc_final: 0.8364 (t80) REVERT: r 214 ASN cc_start: 0.9147 (t0) cc_final: 0.8902 (t0) REVERT: s 10 SER cc_start: 0.9560 (m) cc_final: 0.9273 (p) REVERT: s 42 ASN cc_start: 0.8446 (t0) cc_final: 0.8237 (t0) REVERT: s 43 MET cc_start: 0.9307 (mmm) cc_final: 0.8913 (tpp) REVERT: s 50 ASP cc_start: 0.8352 (m-30) cc_final: 0.8094 (m-30) REVERT: s 74 ASP cc_start: 0.8000 (p0) cc_final: 0.7467 (p0) REVERT: s 91 ASP cc_start: 0.8312 (t70) cc_final: 0.7889 (t0) REVERT: s 120 CYS cc_start: 0.8529 (m) cc_final: 0.8317 (m) REVERT: s 146 ASP cc_start: 0.8249 (m-30) cc_final: 0.8015 (m-30) REVERT: s 154 ILE cc_start: 0.9216 (mt) cc_final: 0.8854 (mt) REVERT: s 234 LYS cc_start: 0.8851 (mtmt) cc_final: 0.8422 (mttp) REVERT: t 28 THR cc_start: 0.9308 (m) cc_final: 0.9015 (p) REVERT: t 42 THR cc_start: 0.9125 (p) cc_final: 0.8781 (p) outliers start: 0 outliers final: 0 residues processed: 1664 average time/residue: 0.4717 time to fit residues: 1262.1430 Evaluate side-chains 1137 residues out of total 3684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1137 time to evaluate : 3.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 365 optimal weight: 6.9990 chunk 328 optimal weight: 5.9990 chunk 182 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 221 optimal weight: 6.9990 chunk 175 optimal weight: 5.9990 chunk 339 optimal weight: 5.9990 chunk 131 optimal weight: 7.9990 chunk 206 optimal weight: 7.9990 chunk 252 optimal weight: 6.9990 chunk 393 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 99 HIS b 111 GLN ** b 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 204 ASN ** c 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 20 GLN c 96 HIS ** c 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 13 HIS ** e 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 99 HIS ** e 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 20 ASN ** f 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 56 ASN g 96 HIS h 13 HIS ** h 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 112 GLN ** i 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 171 GLN ** j 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 118 HIS j 119 GLN ** k 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 160 GLN ** l 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 17 ASN l 26 ASN l 39 ASN m 151 GLN ** m 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 249 HIS ** n 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 118 HIS n 119 GLN n 226 ASN ** o 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 108 HIS p 26 ASN ** p 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 184 ASN r 20 ASN ** r 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 4 GLN t 44 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 34975 Z= 0.407 Angle : 0.740 10.837 47711 Z= 0.388 Chirality : 0.048 0.213 5363 Planarity : 0.005 0.053 6193 Dihedral : 6.109 54.843 4860 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 4.29 % Allowed : 11.81 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.12), residues: 4201 helix: -2.13 (0.24), residues: 344 sheet: 1.21 (0.15), residues: 1035 loop : 0.19 (0.11), residues: 2822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP q 170 HIS 0.015 0.002 HIS k 96 PHE 0.026 0.002 PHE c 115 TYR 0.029 0.002 TYR i 154 ARG 0.013 0.001 ARG g 225 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1444 residues out of total 3684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 1286 time to evaluate : 3.895 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 TARDY: cannot create tardy model for: "GLN n 272 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLN r 272 " (corrupted residue). Skipping it. REVERT: a 49 GLN cc_start: 0.8486 (mm-40) cc_final: 0.8224 (mm110) REVERT: a 105 ILE cc_start: 0.9590 (mt) cc_final: 0.9321 (mt) REVERT: a 106 THR cc_start: 0.9233 (t) cc_final: 0.8989 (m) REVERT: a 169 THR cc_start: 0.9067 (p) cc_final: 0.8540 (t) REVERT: a 179 PHE cc_start: 0.8820 (m-80) cc_final: 0.8565 (m-10) REVERT: b 16 ILE cc_start: 0.9512 (mp) cc_final: 0.9193 (mt) REVERT: b 84 ASP cc_start: 0.8266 (t0) cc_final: 0.7944 (t0) REVERT: b 97 TYR cc_start: 0.8481 (m-80) cc_final: 0.7913 (m-80) REVERT: b 111 GLN cc_start: 0.9206 (OUTLIER) cc_final: 0.8879 (mp10) REVERT: b 183 SER cc_start: 0.9221 (p) cc_final: 0.8761 (t) REVERT: b 203 ASN cc_start: 0.8261 (t0) cc_final: 0.8057 (t0) REVERT: b 214 ASN cc_start: 0.9167 (t0) cc_final: 0.8787 (t0) REVERT: b 215 SER cc_start: 0.9226 (p) cc_final: 0.8922 (p) REVERT: c 101 GLU cc_start: 0.8409 (mm-30) cc_final: 0.7976 (mm-30) REVERT: c 131 LEU cc_start: 0.9295 (tp) cc_final: 0.8982 (tt) REVERT: d 21 ASN cc_start: 0.7585 (p0) cc_final: 0.6969 (p0) REVERT: e 51 ILE cc_start: 0.9158 (pt) cc_final: 0.8915 (pt) REVERT: e 95 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7595 (mm-30) REVERT: e 154 TYR cc_start: 0.8392 (t80) cc_final: 0.8167 (t80) REVERT: e 182 TYR cc_start: 0.8904 (t80) cc_final: 0.8358 (t80) REVERT: e 205 ASP cc_start: 0.8838 (t0) cc_final: 0.8571 (t70) REVERT: e 229 ILE cc_start: 0.9073 (tt) cc_final: 0.8676 (tt) REVERT: e 231 ASP cc_start: 0.8163 (t0) cc_final: 0.7923 (t0) REVERT: f 145 TYR cc_start: 0.8980 (t80) cc_final: 0.8752 (t80) REVERT: f 173 LYS cc_start: 0.9059 (mptt) cc_final: 0.8028 (mptt) REVERT: f 196 GLN cc_start: 0.8770 (tt0) cc_final: 0.8487 (tt0) REVERT: g 42 ASN cc_start: 0.8409 (t0) cc_final: 0.8098 (t0) REVERT: g 44 MET cc_start: 0.8569 (mmm) cc_final: 0.8321 (mmm) REVERT: g 106 TYR cc_start: 0.9410 (m-80) cc_final: 0.8994 (m-80) REVERT: g 112 SER cc_start: 0.8924 (m) cc_final: 0.8208 (p) REVERT: g 154 ILE cc_start: 0.9213 (mm) cc_final: 0.8904 (mm) REVERT: g 156 ASP cc_start: 0.8160 (t0) cc_final: 0.7799 (p0) REVERT: g 194 GLN cc_start: 0.8911 (tp-100) cc_final: 0.8447 (tp-100) REVERT: g 216 CYS cc_start: 0.8684 (m) cc_final: 0.7542 (m) REVERT: g 218 ASP cc_start: 0.8785 (p0) cc_final: 0.8574 (p0) REVERT: h 38 SER cc_start: 0.9241 (m) cc_final: 0.8981 (p) REVERT: h 53 PHE cc_start: 0.8995 (m-80) cc_final: 0.8647 (m-80) REVERT: i 95 GLU cc_start: 0.7250 (mt-10) cc_final: 0.6889 (tt0) REVERT: i 98 LYS cc_start: 0.8940 (mttt) cc_final: 0.8733 (mtpp) REVERT: i 108 THR cc_start: 0.8660 (p) cc_final: 0.8348 (t) REVERT: i 127 LEU cc_start: 0.9163 (tp) cc_final: 0.8882 (tp) REVERT: i 166 ASP cc_start: 0.7805 (p0) cc_final: 0.6528 (p0) REVERT: i 204 TYR cc_start: 0.8669 (t80) cc_final: 0.7835 (t80) REVERT: j 84 ASP cc_start: 0.8222 (t70) cc_final: 0.8020 (t70) REVERT: j 193 TYR cc_start: 0.8965 (m-80) cc_final: 0.8639 (m-10) REVERT: j 200 LEU cc_start: 0.8799 (mt) cc_final: 0.8576 (mt) REVERT: j 223 LYS cc_start: 0.9317 (mtmt) cc_final: 0.8550 (mtmm) REVERT: j 264 ARG cc_start: 0.8605 (pmt100) cc_final: 0.8283 (ptt90) REVERT: k 39 GLU cc_start: 0.8338 (tm-30) cc_final: 0.8069 (tm-30) REVERT: k 55 MET cc_start: 0.9034 (tpp) cc_final: 0.8768 (tpt) REVERT: k 84 LEU cc_start: 0.8930 (tt) cc_final: 0.8562 (tt) REVERT: k 87 SER cc_start: 0.9196 (t) cc_final: 0.8797 (p) REVERT: k 128 LYS cc_start: 0.8381 (mttm) cc_final: 0.7831 (mtmt) REVERT: k 155 TRP cc_start: 0.8268 (t60) cc_final: 0.7742 (t60) REVERT: k 169 TRP cc_start: 0.8930 (t-100) cc_final: 0.8018 (t-100) REVERT: k 177 ARG cc_start: 0.8891 (ttm110) cc_final: 0.8454 (ttm110) REVERT: k 178 CYS cc_start: 0.8509 (m) cc_final: 0.8015 (m) REVERT: k 196 ARG cc_start: 0.7639 (ttp80) cc_final: 0.6669 (ptt-90) REVERT: k 216 CYS cc_start: 0.8715 (m) cc_final: 0.8457 (m) REVERT: m 105 ILE cc_start: 0.9169 (mt) cc_final: 0.8824 (mt) REVERT: m 111 VAL cc_start: 0.9056 (m) cc_final: 0.8824 (p) REVERT: m 166 ASP cc_start: 0.8635 (p0) cc_final: 0.7803 (p0) REVERT: m 204 TYR cc_start: 0.8949 (t80) cc_final: 0.8563 (t80) REVERT: m 216 ASN cc_start: 0.7379 (t0) cc_final: 0.6891 (m-40) REVERT: m 218 ASP cc_start: 0.7961 (m-30) cc_final: 0.7184 (m-30) REVERT: m 235 LEU cc_start: 0.9360 (mt) cc_final: 0.9116 (mp) REVERT: n 13 VAL cc_start: 0.9594 (t) cc_final: 0.9302 (p) REVERT: n 60 SER cc_start: 0.9420 (m) cc_final: 0.9129 (p) REVERT: n 71 TRP cc_start: 0.8791 (t60) cc_final: 0.8475 (t60) REVERT: n 179 TYR cc_start: 0.8444 (p90) cc_final: 0.8160 (p90) REVERT: n 213 VAL cc_start: 0.9738 (t) cc_final: 0.9524 (p) REVERT: n 216 LEU cc_start: 0.9058 (mt) cc_final: 0.8604 (mt) REVERT: n 218 ILE cc_start: 0.9464 (tt) cc_final: 0.9246 (mt) REVERT: o 42 ASN cc_start: 0.8346 (t0) cc_final: 0.8100 (t0) REVERT: o 84 LEU cc_start: 0.8827 (mp) cc_final: 0.8556 (mp) REVERT: o 87 SER cc_start: 0.9087 (m) cc_final: 0.8097 (p) REVERT: o 91 ASP cc_start: 0.7515 (t0) cc_final: 0.7204 (t0) REVERT: o 146 ASP cc_start: 0.7655 (m-30) cc_final: 0.7422 (m-30) REVERT: o 175 TYR cc_start: 0.9013 (m-80) cc_final: 0.8726 (m-10) REVERT: o 207 MET cc_start: 0.8395 (ptp) cc_final: 0.8085 (ptp) REVERT: o 234 LYS cc_start: 0.7834 (tttt) cc_final: 0.6761 (tttt) REVERT: q 47 SER cc_start: 0.9084 (m) cc_final: 0.8798 (p) REVERT: q 171 GLN cc_start: 0.8518 (mt0) cc_final: 0.8126 (mt0) REVERT: q 264 TRP cc_start: 0.8938 (m-90) cc_final: 0.8734 (m-90) REVERT: q 274 TYR cc_start: 0.8392 (m-80) cc_final: 0.8076 (m-80) REVERT: q 280 ASP cc_start: 0.8403 (m-30) cc_final: 0.8053 (m-30) REVERT: r 11 ASP cc_start: 0.7958 (p0) cc_final: 0.7744 (p0) REVERT: r 48 ASN cc_start: 0.8891 (t0) cc_final: 0.8674 (t0) REVERT: r 50 VAL cc_start: 0.9462 (m) cc_final: 0.9188 (p) REVERT: r 112 CYS cc_start: 0.8267 (t) cc_final: 0.8043 (t) REVERT: r 116 LYS cc_start: 0.8840 (mttt) cc_final: 0.8299 (mtmt) REVERT: r 212 TYR cc_start: 0.8629 (t80) cc_final: 0.8293 (t80) REVERT: r 249 ILE cc_start: 0.9638 (mt) cc_final: 0.9388 (mm) REVERT: s 10 SER cc_start: 0.9466 (m) cc_final: 0.9179 (p) REVERT: s 18 ASP cc_start: 0.8319 (t0) cc_final: 0.8095 (t0) REVERT: s 50 ASP cc_start: 0.8530 (m-30) cc_final: 0.8261 (m-30) REVERT: s 74 ASP cc_start: 0.7905 (p0) cc_final: 0.7524 (p0) REVERT: s 156 ASP cc_start: 0.8697 (t0) cc_final: 0.8309 (t0) REVERT: s 234 LYS cc_start: 0.8884 (mtmt) cc_final: 0.8323 (mttt) REVERT: t 28 THR cc_start: 0.9305 (m) cc_final: 0.9087 (p) outliers start: 158 outliers final: 103 residues processed: 1362 average time/residue: 0.4399 time to fit residues: 979.6699 Evaluate side-chains 1189 residues out of total 3684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 1085 time to evaluate : 3.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 61 VAL Chi-restraints excluded: chain a residue 71 CYS Chi-restraints excluded: chain a residue 134 THR Chi-restraints excluded: chain a residue 152 ILE Chi-restraints excluded: chain a residue 250 THR Chi-restraints excluded: chain a residue 282 ILE Chi-restraints excluded: chain a residue 296 THR Chi-restraints excluded: chain b residue 21 SER Chi-restraints excluded: chain b residue 74 THR Chi-restraints excluded: chain b residue 111 GLN Chi-restraints excluded: chain b residue 202 THR Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 184 THR Chi-restraints excluded: chain d residue 60 LEU Chi-restraints excluded: chain e residue 66 THR Chi-restraints excluded: chain e residue 104 ASN Chi-restraints excluded: chain e residue 123 SER Chi-restraints excluded: chain e residue 134 THR Chi-restraints excluded: chain e residue 135 GLU Chi-restraints excluded: chain e residue 237 VAL Chi-restraints excluded: chain e residue 248 ILE Chi-restraints excluded: chain e residue 280 ASP Chi-restraints excluded: chain e residue 293 ASP Chi-restraints excluded: chain f residue 20 ASN Chi-restraints excluded: chain f residue 40 THR Chi-restraints excluded: chain f residue 45 SER Chi-restraints excluded: chain f residue 88 ASP Chi-restraints excluded: chain f residue 112 CYS Chi-restraints excluded: chain f residue 140 THR Chi-restraints excluded: chain f residue 263 LEU Chi-restraints excluded: chain g residue 56 ASN Chi-restraints excluded: chain g residue 118 LEU Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain g residue 203 THR Chi-restraints excluded: chain g residue 207 MET Chi-restraints excluded: chain h residue 7 THR Chi-restraints excluded: chain h residue 10 THR Chi-restraints excluded: chain i residue 40 THR Chi-restraints excluded: chain i residue 88 THR Chi-restraints excluded: chain i residue 171 GLN Chi-restraints excluded: chain i residue 173 SER Chi-restraints excluded: chain i residue 251 SER Chi-restraints excluded: chain i residue 296 THR Chi-restraints excluded: chain j residue 38 TRP Chi-restraints excluded: chain j residue 45 SER Chi-restraints excluded: chain j residue 50 VAL Chi-restraints excluded: chain j residue 126 LEU Chi-restraints excluded: chain j residue 246 GLN Chi-restraints excluded: chain k residue 10 SER Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain k residue 189 ILE Chi-restraints excluded: chain k residue 218 ASP Chi-restraints excluded: chain k residue 223 LEU Chi-restraints excluded: chain k residue 233 SER Chi-restraints excluded: chain l residue 24 THR Chi-restraints excluded: chain l residue 26 ASN Chi-restraints excluded: chain l residue 44 GLN Chi-restraints excluded: chain m residue 68 SER Chi-restraints excluded: chain m residue 106 THR Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 173 SER Chi-restraints excluded: chain m residue 174 SER Chi-restraints excluded: chain m residue 198 ASN Chi-restraints excluded: chain m residue 272 VAL Chi-restraints excluded: chain m residue 282 ILE Chi-restraints excluded: chain n residue 54 THR Chi-restraints excluded: chain n residue 74 THR Chi-restraints excluded: chain n residue 84 ASP Chi-restraints excluded: chain n residue 140 THR Chi-restraints excluded: chain n residue 141 SER Chi-restraints excluded: chain o residue 30 VAL Chi-restraints excluded: chain o residue 51 THR Chi-restraints excluded: chain o residue 107 THR Chi-restraints excluded: chain o residue 122 SER Chi-restraints excluded: chain o residue 126 THR Chi-restraints excluded: chain o residue 166 VAL Chi-restraints excluded: chain o residue 190 THR Chi-restraints excluded: chain o residue 198 VAL Chi-restraints excluded: chain p residue 7 THR Chi-restraints excluded: chain p residue 57 VAL Chi-restraints excluded: chain q residue 36 VAL Chi-restraints excluded: chain q residue 71 CYS Chi-restraints excluded: chain q residue 96 GLU Chi-restraints excluded: chain q residue 99 HIS Chi-restraints excluded: chain q residue 100 PHE Chi-restraints excluded: chain q residue 153 MET Chi-restraints excluded: chain q residue 174 SER Chi-restraints excluded: chain q residue 191 ILE Chi-restraints excluded: chain q residue 265 CYS Chi-restraints excluded: chain q residue 296 THR Chi-restraints excluded: chain r residue 18 LEU Chi-restraints excluded: chain r residue 25 THR Chi-restraints excluded: chain r residue 51 ASP Chi-restraints excluded: chain r residue 59 SER Chi-restraints excluded: chain r residue 84 ASP Chi-restraints excluded: chain r residue 131 VAL Chi-restraints excluded: chain r residue 192 VAL Chi-restraints excluded: chain r residue 252 THR Chi-restraints excluded: chain s residue 53 ILE Chi-restraints excluded: chain s residue 86 LEU Chi-restraints excluded: chain s residue 189 ILE Chi-restraints excluded: chain s residue 190 THR Chi-restraints excluded: chain s residue 203 THR Chi-restraints excluded: chain t residue 7 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 218 optimal weight: 0.9990 chunk 122 optimal weight: 9.9990 chunk 327 optimal weight: 8.9990 chunk 267 optimal weight: 20.0000 chunk 108 optimal weight: 5.9990 chunk 393 optimal weight: 10.0000 chunk 425 optimal weight: 6.9990 chunk 350 optimal weight: 0.0070 chunk 390 optimal weight: 1.9990 chunk 134 optimal weight: 8.9990 chunk 316 optimal weight: 0.9990 overall best weight: 2.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 112 GLN ** b 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 11 ASN c 12 GLN ** c 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 4 GLN ** e 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 175 ASN ** e 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 20 ASN f 135 ASN f 162 ASN ** f 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 21 ASN ** j 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 99 HIS ** k 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 26 ASN ** m 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 119 GLN n 261 ASN o 27 ASN ** p 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 26 ASN ** p 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 6 ASN ** s 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 4 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 34975 Z= 0.221 Angle : 0.630 9.363 47711 Z= 0.324 Chirality : 0.046 0.230 5363 Planarity : 0.004 0.042 6193 Dihedral : 5.741 53.309 4860 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.72 % Allowed : 16.78 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.12), residues: 4201 helix: -2.04 (0.24), residues: 351 sheet: 1.11 (0.15), residues: 1021 loop : 0.08 (0.11), residues: 2829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP o 169 HIS 0.010 0.001 HIS j 224 PHE 0.031 0.002 PHE c 19 TYR 0.027 0.002 TYR i 154 ARG 0.007 0.000 ARG a 262 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1390 residues out of total 3684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 1253 time to evaluate : 4.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN n 272 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN r 272 " (corrupted residue). Skipping it. REVERT: a 105 ILE cc_start: 0.9629 (mt) cc_final: 0.8835 (tt) REVERT: a 106 THR cc_start: 0.9252 (t) cc_final: 0.8960 (m) REVERT: a 169 THR cc_start: 0.9080 (p) cc_final: 0.8642 (t) REVERT: a 205 ASP cc_start: 0.8573 (t0) cc_final: 0.8291 (t0) REVERT: b 84 ASP cc_start: 0.8020 (t70) cc_final: 0.7696 (t0) REVERT: b 97 TYR cc_start: 0.8300 (m-80) cc_final: 0.8009 (m-10) REVERT: b 183 SER cc_start: 0.9138 (p) cc_final: 0.8694 (t) REVERT: b 214 ASN cc_start: 0.9170 (t0) cc_final: 0.8928 (t0) REVERT: c 56 ASN cc_start: 0.9541 (t0) cc_final: 0.9245 (t0) REVERT: c 101 GLU cc_start: 0.8353 (mm-30) cc_final: 0.7936 (mm-30) REVERT: c 131 LEU cc_start: 0.9287 (tp) cc_final: 0.8926 (tt) REVERT: c 165 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.8292 (ttm) REVERT: d 5 VAL cc_start: 0.9460 (t) cc_final: 0.9179 (m) REVERT: d 21 ASN cc_start: 0.7537 (p0) cc_final: 0.6782 (p0) REVERT: e 51 ILE cc_start: 0.9159 (pt) cc_final: 0.8924 (pt) REVERT: e 95 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7594 (mm-30) REVERT: e 173 SER cc_start: 0.9150 (p) cc_final: 0.8772 (p) REVERT: e 174 SER cc_start: 0.9092 (m) cc_final: 0.8655 (p) REVERT: e 182 TYR cc_start: 0.8703 (t80) cc_final: 0.8469 (t80) REVERT: e 204 TYR cc_start: 0.8505 (t80) cc_final: 0.7713 (t80) REVERT: e 205 ASP cc_start: 0.8811 (t0) cc_final: 0.8510 (t70) REVERT: e 286 ILE cc_start: 0.9011 (pt) cc_final: 0.8700 (mt) REVERT: f 23 ILE cc_start: 0.9352 (mt) cc_final: 0.9025 (mm) REVERT: f 116 LYS cc_start: 0.9178 (mttt) cc_final: 0.8941 (mttp) REVERT: f 145 TYR cc_start: 0.8999 (t80) cc_final: 0.8754 (t80) REVERT: f 196 GLN cc_start: 0.8583 (tt0) cc_final: 0.8320 (tp40) REVERT: f 264 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7121 (ptt180) REVERT: g 42 ASN cc_start: 0.8372 (t0) cc_final: 0.8088 (t0) REVERT: g 91 ASP cc_start: 0.7996 (t0) cc_final: 0.7648 (t0) REVERT: g 106 TYR cc_start: 0.9303 (m-80) cc_final: 0.9063 (m-80) REVERT: g 112 SER cc_start: 0.8903 (m) cc_final: 0.8532 (p) REVERT: g 154 ILE cc_start: 0.9230 (mm) cc_final: 0.8727 (mm) REVERT: g 156 ASP cc_start: 0.8308 (t0) cc_final: 0.7798 (p0) REVERT: g 177 ARG cc_start: 0.8817 (ttm110) cc_final: 0.8291 (mtm110) REVERT: g 194 GLN cc_start: 0.8933 (tp40) cc_final: 0.8395 (tp40) REVERT: g 216 CYS cc_start: 0.8733 (m) cc_final: 0.8041 (m) REVERT: g 218 ASP cc_start: 0.8747 (p0) cc_final: 0.8516 (p0) REVERT: i 78 ARG cc_start: 0.8705 (mmt90) cc_final: 0.8476 (mmt90) REVERT: i 108 THR cc_start: 0.8671 (p) cc_final: 0.8415 (t) REVERT: i 166 ASP cc_start: 0.7881 (OUTLIER) cc_final: 0.6348 (p0) REVERT: i 204 TYR cc_start: 0.8367 (t80) cc_final: 0.7913 (t80) REVERT: i 256 MET cc_start: 0.8505 (mmm) cc_final: 0.8266 (mmm) REVERT: i 280 ASP cc_start: 0.7457 (OUTLIER) cc_final: 0.7183 (m-30) REVERT: j 84 ASP cc_start: 0.8119 (t70) cc_final: 0.7899 (t70) REVERT: j 223 LYS cc_start: 0.9260 (mtmt) cc_final: 0.8622 (mtmm) REVERT: k 39 GLU cc_start: 0.8326 (tm-30) cc_final: 0.7990 (tm-30) REVERT: k 55 MET cc_start: 0.8941 (tpp) cc_final: 0.8558 (tpt) REVERT: k 87 SER cc_start: 0.9180 (t) cc_final: 0.8778 (p) REVERT: k 128 LYS cc_start: 0.8293 (mttm) cc_final: 0.7692 (mtmt) REVERT: k 155 TRP cc_start: 0.8185 (t60) cc_final: 0.7598 (t60) REVERT: k 165 MET cc_start: 0.8770 (tmm) cc_final: 0.8557 (ttt) REVERT: k 169 TRP cc_start: 0.8829 (t-100) cc_final: 0.7769 (t-100) REVERT: k 178 CYS cc_start: 0.8506 (m) cc_final: 0.8001 (m) REVERT: k 196 ARG cc_start: 0.7854 (ttp80) cc_final: 0.6771 (ptt-90) REVERT: l 32 TYR cc_start: 0.8850 (m-80) cc_final: 0.8634 (m-10) REVERT: m 105 ILE cc_start: 0.9213 (mt) cc_final: 0.8950 (mt) REVERT: m 111 VAL cc_start: 0.9039 (m) cc_final: 0.8740 (p) REVERT: m 166 ASP cc_start: 0.8585 (p0) cc_final: 0.7733 (p0) REVERT: m 205 ASP cc_start: 0.8649 (t0) cc_final: 0.8140 (t0) REVERT: m 216 ASN cc_start: 0.7468 (t0) cc_final: 0.6899 (m-40) REVERT: m 218 ASP cc_start: 0.7974 (m-30) cc_final: 0.7196 (m-30) REVERT: n 13 VAL cc_start: 0.9618 (t) cc_final: 0.9341 (p) REVERT: n 50 VAL cc_start: 0.9312 (m) cc_final: 0.9042 (t) REVERT: n 60 SER cc_start: 0.9342 (m) cc_final: 0.9101 (p) REVERT: n 129 GLU cc_start: 0.8444 (tp30) cc_final: 0.7671 (tp30) REVERT: n 213 VAL cc_start: 0.9704 (t) cc_final: 0.9483 (p) REVERT: n 216 LEU cc_start: 0.9133 (mt) cc_final: 0.8817 (mt) REVERT: n 249 ILE cc_start: 0.9342 (mt) cc_final: 0.8970 (mt) REVERT: o 20 GLN cc_start: 0.8593 (mt0) cc_final: 0.8304 (mt0) REVERT: o 87 SER cc_start: 0.9092 (m) cc_final: 0.8107 (p) REVERT: o 91 ASP cc_start: 0.7606 (t0) cc_final: 0.7342 (t0) REVERT: o 144 ARG cc_start: 0.7953 (ttp-170) cc_final: 0.7731 (ttp-170) REVERT: o 169 TRP cc_start: 0.9000 (t-100) cc_final: 0.8420 (t-100) REVERT: o 207 MET cc_start: 0.8384 (ptp) cc_final: 0.8073 (ptp) REVERT: o 234 LYS cc_start: 0.7739 (tttt) cc_final: 0.6768 (mttt) REVERT: p 48 GLN cc_start: 0.8547 (pm20) cc_final: 0.8130 (pt0) REVERT: q 47 SER cc_start: 0.9058 (m) cc_final: 0.8627 (p) REVERT: q 66 THR cc_start: 0.8842 (m) cc_final: 0.8101 (p) REVERT: q 105 ILE cc_start: 0.8840 (mt) cc_final: 0.8285 (tt) REVERT: q 154 TYR cc_start: 0.9076 (t80) cc_final: 0.8785 (t80) REVERT: q 166 ASP cc_start: 0.7076 (p0) cc_final: 0.6571 (p0) REVERT: q 168 TYR cc_start: 0.9052 (p90) cc_final: 0.8491 (p90) REVERT: q 171 GLN cc_start: 0.8542 (mt0) cc_final: 0.8068 (mt0) REVERT: r 48 ASN cc_start: 0.8876 (t0) cc_final: 0.8666 (t0) REVERT: r 50 VAL cc_start: 0.9353 (m) cc_final: 0.9151 (p) REVERT: r 116 LYS cc_start: 0.8862 (mttt) cc_final: 0.8393 (mtmt) REVERT: r 212 TYR cc_start: 0.8454 (t80) cc_final: 0.8081 (t80) REVERT: r 249 ILE cc_start: 0.9652 (mt) cc_final: 0.9428 (mm) REVERT: s 10 SER cc_start: 0.9387 (m) cc_final: 0.9107 (p) REVERT: s 18 ASP cc_start: 0.8259 (t0) cc_final: 0.7994 (t0) REVERT: s 50 ASP cc_start: 0.8540 (m-30) cc_final: 0.8135 (m-30) REVERT: s 74 ASP cc_start: 0.7855 (p0) cc_final: 0.7479 (p0) REVERT: s 154 ILE cc_start: 0.8870 (mt) cc_final: 0.8636 (pt) REVERT: s 156 ASP cc_start: 0.8800 (t0) cc_final: 0.8368 (t0) REVERT: s 234 LYS cc_start: 0.8852 (mtmt) cc_final: 0.8320 (mttt) REVERT: t 28 THR cc_start: 0.9301 (m) cc_final: 0.9097 (p) outliers start: 137 outliers final: 98 residues processed: 1314 average time/residue: 0.4935 time to fit residues: 1068.9020 Evaluate side-chains 1228 residues out of total 3684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 1126 time to evaluate : 3.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 61 VAL Chi-restraints excluded: chain a residue 134 THR Chi-restraints excluded: chain a residue 293 ASP Chi-restraints excluded: chain a residue 295 ILE Chi-restraints excluded: chain b residue 15 GLN Chi-restraints excluded: chain b residue 21 SER Chi-restraints excluded: chain b residue 40 THR Chi-restraints excluded: chain b residue 74 THR Chi-restraints excluded: chain b residue 160 THR Chi-restraints excluded: chain b residue 172 ARG Chi-restraints excluded: chain b residue 200 LEU Chi-restraints excluded: chain b residue 202 THR Chi-restraints excluded: chain c residue 10 SER Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 62 VAL Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 159 LEU Chi-restraints excluded: chain c residue 165 MET Chi-restraints excluded: chain c residue 184 THR Chi-restraints excluded: chain c residue 213 VAL Chi-restraints excluded: chain c residue 239 THR Chi-restraints excluded: chain d residue 60 LEU Chi-restraints excluded: chain e residue 104 ASN Chi-restraints excluded: chain e residue 227 VAL Chi-restraints excluded: chain e residue 237 VAL Chi-restraints excluded: chain e residue 280 ASP Chi-restraints excluded: chain f residue 45 SER Chi-restraints excluded: chain f residue 60 SER Chi-restraints excluded: chain f residue 88 ASP Chi-restraints excluded: chain f residue 263 LEU Chi-restraints excluded: chain f residue 264 ARG Chi-restraints excluded: chain g residue 198 VAL Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain g residue 203 THR Chi-restraints excluded: chain g residue 207 MET Chi-restraints excluded: chain h residue 10 THR Chi-restraints excluded: chain h residue 23 SER Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 61 MET Chi-restraints excluded: chain i residue 26 GLU Chi-restraints excluded: chain i residue 40 THR Chi-restraints excluded: chain i residue 88 THR Chi-restraints excluded: chain i residue 99 HIS Chi-restraints excluded: chain i residue 128 GLU Chi-restraints excluded: chain i residue 166 ASP Chi-restraints excluded: chain i residue 280 ASP Chi-restraints excluded: chain j residue 38 TRP Chi-restraints excluded: chain j residue 50 VAL Chi-restraints excluded: chain j residue 126 LEU Chi-restraints excluded: chain j residue 181 LEU Chi-restraints excluded: chain j residue 183 SER Chi-restraints excluded: chain j residue 247 VAL Chi-restraints excluded: chain k residue 21 SER Chi-restraints excluded: chain k residue 81 ILE Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain k residue 103 LEU Chi-restraints excluded: chain k residue 116 THR Chi-restraints excluded: chain k residue 199 VAL Chi-restraints excluded: chain k residue 218 ASP Chi-restraints excluded: chain k residue 223 LEU Chi-restraints excluded: chain l residue 26 ASN Chi-restraints excluded: chain l residue 44 GLN Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 173 SER Chi-restraints excluded: chain m residue 196 ILE Chi-restraints excluded: chain m residue 198 ASN Chi-restraints excluded: chain n residue 74 THR Chi-restraints excluded: chain n residue 84 ASP Chi-restraints excluded: chain n residue 152 GLU Chi-restraints excluded: chain n residue 226 ASN Chi-restraints excluded: chain n residue 265 ASN Chi-restraints excluded: chain o residue 27 ASN Chi-restraints excluded: chain o residue 51 THR Chi-restraints excluded: chain o residue 126 THR Chi-restraints excluded: chain o residue 161 SER Chi-restraints excluded: chain o residue 166 VAL Chi-restraints excluded: chain o residue 190 THR Chi-restraints excluded: chain p residue 57 VAL Chi-restraints excluded: chain q residue 35 GLU Chi-restraints excluded: chain q residue 36 VAL Chi-restraints excluded: chain q residue 68 SER Chi-restraints excluded: chain q residue 71 CYS Chi-restraints excluded: chain q residue 100 PHE Chi-restraints excluded: chain q residue 153 MET Chi-restraints excluded: chain q residue 190 SER Chi-restraints excluded: chain q residue 265 CYS Chi-restraints excluded: chain q residue 296 THR Chi-restraints excluded: chain r residue 40 THR Chi-restraints excluded: chain r residue 46 GLU Chi-restraints excluded: chain r residue 51 ASP Chi-restraints excluded: chain r residue 84 ASP Chi-restraints excluded: chain r residue 111 GLN Chi-restraints excluded: chain r residue 131 VAL Chi-restraints excluded: chain r residue 192 VAL Chi-restraints excluded: chain r residue 205 SER Chi-restraints excluded: chain r residue 252 THR Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain s residue 76 LEU Chi-restraints excluded: chain s residue 86 LEU Chi-restraints excluded: chain s residue 189 ILE Chi-restraints excluded: chain s residue 203 THR Chi-restraints excluded: chain t residue 7 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 389 optimal weight: 20.0000 chunk 296 optimal weight: 0.9980 chunk 204 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 187 optimal weight: 30.0000 chunk 264 optimal weight: 4.9990 chunk 395 optimal weight: 7.9990 chunk 418 optimal weight: 10.0000 chunk 206 optimal weight: 9.9990 chunk 374 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 111 GLN ** c 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 230 ASN ** e 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 135 ASN ** f 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 21 ASN ** i 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 162 ASN ** l 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 26 ASN ** m 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 26 ASN q 60 HIS ** q 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 232 GLN t 4 GLN ** t 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 34975 Z= 0.380 Angle : 0.654 8.588 47711 Z= 0.336 Chirality : 0.046 0.264 5363 Planarity : 0.004 0.049 6193 Dihedral : 5.782 58.339 4860 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 6.00 % Allowed : 16.75 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.12), residues: 4201 helix: -1.98 (0.25), residues: 345 sheet: 0.91 (0.15), residues: 1049 loop : -0.14 (0.11), residues: 2807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP f 227 HIS 0.009 0.002 HIS j 109 PHE 0.031 0.002 PHE f 191 TYR 0.033 0.002 TYR i 154 ARG 0.005 0.001 ARG a 262 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1390 residues out of total 3684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 1169 time to evaluate : 3.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN n 272 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN r 272 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: a 54 ASP cc_start: 0.8797 (OUTLIER) cc_final: 0.8464 (m-30) REVERT: a 105 ILE cc_start: 0.9633 (mt) cc_final: 0.9385 (mt) REVERT: a 106 THR cc_start: 0.9261 (t) cc_final: 0.8945 (m) REVERT: a 169 THR cc_start: 0.9150 (p) cc_final: 0.8703 (t) REVERT: b 48 ASN cc_start: 0.9309 (t0) cc_final: 0.8963 (t0) REVERT: b 97 TYR cc_start: 0.8441 (m-80) cc_final: 0.8139 (m-10) REVERT: b 104 SER cc_start: 0.9328 (OUTLIER) cc_final: 0.9042 (p) REVERT: b 170 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7457 (mm-30) REVERT: b 172 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7256 (mtt90) REVERT: b 183 SER cc_start: 0.9187 (p) cc_final: 0.8753 (t) REVERT: b 221 MET cc_start: 0.7624 (mtm) cc_final: 0.7406 (mtm) REVERT: b 237 LEU cc_start: 0.9254 (tp) cc_final: 0.9029 (tp) REVERT: c 56 ASN cc_start: 0.9576 (t0) cc_final: 0.9313 (t0) REVERT: c 95 SER cc_start: 0.8889 (p) cc_final: 0.8677 (t) REVERT: d 21 ASN cc_start: 0.7720 (p0) cc_final: 0.6861 (p0) REVERT: e 173 SER cc_start: 0.9198 (p) cc_final: 0.8919 (p) REVERT: e 182 TYR cc_start: 0.8868 (t80) cc_final: 0.8246 (t80) REVERT: e 204 TYR cc_start: 0.8621 (t80) cc_final: 0.7771 (t80) REVERT: e 205 ASP cc_start: 0.8832 (t0) cc_final: 0.8502 (t70) REVERT: f 23 ILE cc_start: 0.9328 (mt) cc_final: 0.9033 (mm) REVERT: f 30 ASN cc_start: 0.8300 (t0) cc_final: 0.8066 (t0) REVERT: f 41 TYR cc_start: 0.8302 (m-10) cc_final: 0.7967 (m-80) REVERT: f 116 LYS cc_start: 0.9192 (mttt) cc_final: 0.8903 (mttp) REVERT: f 145 TYR cc_start: 0.9086 (t80) cc_final: 0.8851 (t80) REVERT: f 196 GLN cc_start: 0.8669 (tt0) cc_final: 0.8455 (tp40) REVERT: g 42 ASN cc_start: 0.8393 (t0) cc_final: 0.8187 (t0) REVERT: g 148 MET cc_start: 0.4512 (ttt) cc_final: 0.3962 (ttt) REVERT: g 154 ILE cc_start: 0.9300 (mm) cc_final: 0.8775 (mm) REVERT: g 156 ASP cc_start: 0.8293 (t0) cc_final: 0.7865 (p0) REVERT: g 194 GLN cc_start: 0.9001 (tp40) cc_final: 0.8408 (tp40) REVERT: g 216 CYS cc_start: 0.8773 (m) cc_final: 0.8350 (m) REVERT: h 38 SER cc_start: 0.9327 (m) cc_final: 0.8971 (p) REVERT: i 43 GLU cc_start: 0.8032 (mp0) cc_final: 0.7404 (mp0) REVERT: i 98 LYS cc_start: 0.9078 (mttt) cc_final: 0.8763 (mtpp) REVERT: i 166 ASP cc_start: 0.7863 (OUTLIER) cc_final: 0.6714 (p0) REVERT: i 204 TYR cc_start: 0.8598 (t80) cc_final: 0.8021 (t80) REVERT: i 280 ASP cc_start: 0.7742 (OUTLIER) cc_final: 0.7461 (m-30) REVERT: j 129 GLU cc_start: 0.8430 (mm-30) cc_final: 0.7997 (mm-30) REVERT: j 223 LYS cc_start: 0.9343 (mtmt) cc_final: 0.8619 (mtmm) REVERT: k 39 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8179 (tm-30) REVERT: k 87 SER cc_start: 0.9225 (t) cc_final: 0.8845 (p) REVERT: k 128 LYS cc_start: 0.8246 (mttm) cc_final: 0.7890 (mtmt) REVERT: k 155 TRP cc_start: 0.8391 (t60) cc_final: 0.7727 (t60) REVERT: k 169 TRP cc_start: 0.8890 (t-100) cc_final: 0.8061 (t-100) REVERT: k 178 CYS cc_start: 0.8532 (m) cc_final: 0.7939 (m) REVERT: m 105 ILE cc_start: 0.9278 (mt) cc_final: 0.9015 (mt) REVERT: m 111 VAL cc_start: 0.9155 (m) cc_final: 0.8935 (p) REVERT: m 166 ASP cc_start: 0.8589 (p0) cc_final: 0.7618 (p0) REVERT: m 216 ASN cc_start: 0.7551 (t0) cc_final: 0.6850 (m-40) REVERT: m 218 ASP cc_start: 0.8096 (m-30) cc_final: 0.7274 (m-30) REVERT: m 256 MET cc_start: 0.8082 (ttm) cc_final: 0.7757 (tpp) REVERT: n 13 VAL cc_start: 0.9622 (t) cc_final: 0.9330 (p) REVERT: n 50 VAL cc_start: 0.9370 (m) cc_final: 0.9044 (t) REVERT: n 60 SER cc_start: 0.9376 (m) cc_final: 0.9107 (p) REVERT: n 71 TRP cc_start: 0.8556 (t60) cc_final: 0.8323 (t60) REVERT: n 213 VAL cc_start: 0.9709 (t) cc_final: 0.9508 (p) REVERT: n 216 LEU cc_start: 0.9299 (mt) cc_final: 0.8976 (mt) REVERT: n 249 ILE cc_start: 0.9385 (mt) cc_final: 0.9025 (mt) REVERT: o 42 ASN cc_start: 0.8521 (t0) cc_final: 0.8306 (t0) REVERT: o 87 SER cc_start: 0.9132 (m) cc_final: 0.8196 (p) REVERT: o 91 ASP cc_start: 0.7671 (t0) cc_final: 0.7435 (t0) REVERT: o 104 ASN cc_start: 0.8939 (m-40) cc_final: 0.8697 (m-40) REVERT: o 145 LYS cc_start: 0.8669 (mptt) cc_final: 0.8452 (mptt) REVERT: o 146 ASP cc_start: 0.8098 (m-30) cc_final: 0.7701 (m-30) REVERT: o 148 MET cc_start: 0.6101 (ttm) cc_final: 0.5833 (ttt) REVERT: o 157 LEU cc_start: 0.8254 (mt) cc_final: 0.7946 (mt) REVERT: o 169 TRP cc_start: 0.9109 (t-100) cc_final: 0.8438 (t-100) REVERT: o 175 TYR cc_start: 0.9077 (m-80) cc_final: 0.8874 (m-10) REVERT: o 207 MET cc_start: 0.8481 (ptp) cc_final: 0.8113 (ptp) REVERT: o 234 LYS cc_start: 0.7830 (tttt) cc_final: 0.6816 (mttt) REVERT: p 48 GLN cc_start: 0.8619 (pm20) cc_final: 0.8251 (pt0) REVERT: q 47 SER cc_start: 0.9071 (m) cc_final: 0.8756 (p) REVERT: q 105 ILE cc_start: 0.8981 (mt) cc_final: 0.8472 (tt) REVERT: q 126 ASP cc_start: 0.8195 (m-30) cc_final: 0.7983 (m-30) REVERT: q 171 GLN cc_start: 0.8579 (mt0) cc_final: 0.8219 (mt0) REVERT: q 264 TRP cc_start: 0.8766 (m-90) cc_final: 0.8552 (m-90) REVERT: r 48 ASN cc_start: 0.8902 (t0) cc_final: 0.8647 (t0) REVERT: r 116 LYS cc_start: 0.8698 (mttt) cc_final: 0.8466 (mtmt) REVERT: r 249 ILE cc_start: 0.9640 (mt) cc_final: 0.9403 (mm) REVERT: s 10 SER cc_start: 0.9459 (m) cc_final: 0.9211 (p) REVERT: s 18 ASP cc_start: 0.8181 (t0) cc_final: 0.7920 (t0) REVERT: s 50 ASP cc_start: 0.8690 (m-30) cc_final: 0.8339 (m-30) REVERT: s 74 ASP cc_start: 0.7814 (p0) cc_final: 0.7402 (p0) REVERT: s 154 ILE cc_start: 0.8739 (mt) cc_final: 0.8415 (pt) REVERT: s 234 LYS cc_start: 0.8767 (mtmt) cc_final: 0.8214 (mttp) REVERT: t 28 THR cc_start: 0.9336 (m) cc_final: 0.9085 (p) outliers start: 221 outliers final: 167 residues processed: 1271 average time/residue: 0.4474 time to fit residues: 930.1329 Evaluate side-chains 1252 residues out of total 3684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 1080 time to evaluate : 3.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 51 ILE Chi-restraints excluded: chain a residue 54 ASP Chi-restraints excluded: chain a residue 61 VAL Chi-restraints excluded: chain a residue 66 THR Chi-restraints excluded: chain a residue 71 CYS Chi-restraints excluded: chain a residue 130 THR Chi-restraints excluded: chain a residue 134 THR Chi-restraints excluded: chain a residue 250 THR Chi-restraints excluded: chain a residue 293 ASP Chi-restraints excluded: chain a residue 295 ILE Chi-restraints excluded: chain a residue 296 THR Chi-restraints excluded: chain b residue 21 SER Chi-restraints excluded: chain b residue 26 GLN Chi-restraints excluded: chain b residue 45 SER Chi-restraints excluded: chain b residue 74 THR Chi-restraints excluded: chain b residue 104 SER Chi-restraints excluded: chain b residue 172 ARG Chi-restraints excluded: chain b residue 202 THR Chi-restraints excluded: chain b residue 256 MET Chi-restraints excluded: chain b residue 268 VAL Chi-restraints excluded: chain c residue 7 THR Chi-restraints excluded: chain c residue 10 SER Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 62 VAL Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 159 LEU Chi-restraints excluded: chain c residue 184 THR Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain c residue 239 THR Chi-restraints excluded: chain d residue 60 LEU Chi-restraints excluded: chain e residue 104 ASN Chi-restraints excluded: chain e residue 110 THR Chi-restraints excluded: chain e residue 134 THR Chi-restraints excluded: chain e residue 135 GLU Chi-restraints excluded: chain e residue 196 ILE Chi-restraints excluded: chain e residue 237 VAL Chi-restraints excluded: chain e residue 252 VAL Chi-restraints excluded: chain e residue 280 ASP Chi-restraints excluded: chain e residue 282 ILE Chi-restraints excluded: chain f residue 40 THR Chi-restraints excluded: chain f residue 45 SER Chi-restraints excluded: chain f residue 88 ASP Chi-restraints excluded: chain f residue 140 THR Chi-restraints excluded: chain f residue 146 ILE Chi-restraints excluded: chain f residue 180 LEU Chi-restraints excluded: chain f residue 256 MET Chi-restraints excluded: chain f residue 263 LEU Chi-restraints excluded: chain f residue 265 ASN Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain g residue 132 SER Chi-restraints excluded: chain g residue 190 THR Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain g residue 203 THR Chi-restraints excluded: chain g residue 205 THR Chi-restraints excluded: chain g residue 207 MET Chi-restraints excluded: chain g residue 224 LEU Chi-restraints excluded: chain h residue 7 THR Chi-restraints excluded: chain h residue 10 THR Chi-restraints excluded: chain h residue 23 SER Chi-restraints excluded: chain h residue 26 ASN Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain i residue 40 THR Chi-restraints excluded: chain i residue 88 THR Chi-restraints excluded: chain i residue 99 HIS Chi-restraints excluded: chain i residue 128 GLU Chi-restraints excluded: chain i residue 132 VAL Chi-restraints excluded: chain i residue 166 ASP Chi-restraints excluded: chain i residue 190 SER Chi-restraints excluded: chain i residue 229 ILE Chi-restraints excluded: chain i residue 280 ASP Chi-restraints excluded: chain i residue 296 THR Chi-restraints excluded: chain j residue 25 THR Chi-restraints excluded: chain j residue 38 TRP Chi-restraints excluded: chain j residue 40 THR Chi-restraints excluded: chain j residue 58 VAL Chi-restraints excluded: chain j residue 126 LEU Chi-restraints excluded: chain j residue 181 LEU Chi-restraints excluded: chain j residue 183 SER Chi-restraints excluded: chain j residue 246 GLN Chi-restraints excluded: chain j residue 247 VAL Chi-restraints excluded: chain k residue 5 MET Chi-restraints excluded: chain k residue 10 SER Chi-restraints excluded: chain k residue 21 SER Chi-restraints excluded: chain k residue 81 ILE Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain k residue 103 LEU Chi-restraints excluded: chain k residue 199 VAL Chi-restraints excluded: chain k residue 218 ASP Chi-restraints excluded: chain k residue 223 LEU Chi-restraints excluded: chain k residue 233 SER Chi-restraints excluded: chain l residue 24 THR Chi-restraints excluded: chain l residue 26 ASN Chi-restraints excluded: chain l residue 44 GLN Chi-restraints excluded: chain l residue 64 THR Chi-restraints excluded: chain m residue 68 SER Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain m residue 106 THR Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 173 SER Chi-restraints excluded: chain m residue 177 SER Chi-restraints excluded: chain m residue 196 ILE Chi-restraints excluded: chain m residue 198 ASN Chi-restraints excluded: chain m residue 272 VAL Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 69 VAL Chi-restraints excluded: chain n residue 74 THR Chi-restraints excluded: chain n residue 84 ASP Chi-restraints excluded: chain n residue 141 SER Chi-restraints excluded: chain n residue 152 GLU Chi-restraints excluded: chain n residue 183 SER Chi-restraints excluded: chain n residue 198 ILE Chi-restraints excluded: chain n residue 217 VAL Chi-restraints excluded: chain n residue 226 ASN Chi-restraints excluded: chain n residue 265 ASN Chi-restraints excluded: chain o residue 27 ASN Chi-restraints excluded: chain o residue 30 VAL Chi-restraints excluded: chain o residue 51 THR Chi-restraints excluded: chain o residue 103 LEU Chi-restraints excluded: chain o residue 118 LEU Chi-restraints excluded: chain o residue 122 SER Chi-restraints excluded: chain o residue 126 THR Chi-restraints excluded: chain o residue 132 SER Chi-restraints excluded: chain o residue 153 ILE Chi-restraints excluded: chain o residue 161 SER Chi-restraints excluded: chain o residue 164 SER Chi-restraints excluded: chain o residue 190 THR Chi-restraints excluded: chain o residue 198 VAL Chi-restraints excluded: chain o residue 226 ASP Chi-restraints excluded: chain p residue 7 THR Chi-restraints excluded: chain p residue 25 ILE Chi-restraints excluded: chain p residue 32 TYR Chi-restraints excluded: chain p residue 39 ASN Chi-restraints excluded: chain p residue 57 VAL Chi-restraints excluded: chain q residue 35 GLU Chi-restraints excluded: chain q residue 36 VAL Chi-restraints excluded: chain q residue 62 VAL Chi-restraints excluded: chain q residue 68 SER Chi-restraints excluded: chain q residue 71 CYS Chi-restraints excluded: chain q residue 96 GLU Chi-restraints excluded: chain q residue 99 HIS Chi-restraints excluded: chain q residue 100 PHE Chi-restraints excluded: chain q residue 106 THR Chi-restraints excluded: chain q residue 178 ILE Chi-restraints excluded: chain q residue 190 SER Chi-restraints excluded: chain q residue 217 THR Chi-restraints excluded: chain q residue 265 CYS Chi-restraints excluded: chain q residue 296 THR Chi-restraints excluded: chain r residue 18 LEU Chi-restraints excluded: chain r residue 40 THR Chi-restraints excluded: chain r residue 44 ASP Chi-restraints excluded: chain r residue 46 GLU Chi-restraints excluded: chain r residue 51 ASP Chi-restraints excluded: chain r residue 84 ASP Chi-restraints excluded: chain r residue 86 LEU Chi-restraints excluded: chain r residue 111 GLN Chi-restraints excluded: chain r residue 131 VAL Chi-restraints excluded: chain r residue 192 VAL Chi-restraints excluded: chain r residue 205 SER Chi-restraints excluded: chain r residue 252 THR Chi-restraints excluded: chain s residue 30 VAL Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain s residue 53 ILE Chi-restraints excluded: chain s residue 76 LEU Chi-restraints excluded: chain s residue 86 LEU Chi-restraints excluded: chain s residue 97 THR Chi-restraints excluded: chain s residue 159 LEU Chi-restraints excluded: chain s residue 189 ILE Chi-restraints excluded: chain s residue 203 THR Chi-restraints excluded: chain s residue 205 THR Chi-restraints excluded: chain s residue 232 GLN Chi-restraints excluded: chain t residue 7 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 348 optimal weight: 10.0000 chunk 237 optimal weight: 9.9990 chunk 6 optimal weight: 40.0000 chunk 311 optimal weight: 3.9990 chunk 172 optimal weight: 10.0000 chunk 357 optimal weight: 10.0000 chunk 289 optimal weight: 20.0000 chunk 0 optimal weight: 40.0000 chunk 213 optimal weight: 7.9990 chunk 375 optimal weight: 8.9990 chunk 105 optimal weight: 5.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 111 GLN b 147 ASN ** c 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 151 GLN ** e 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 21 ASN i 23 GLN ** i 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 26 ASN ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 27 ASN ** o 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 26 ASN ** q 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 4 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 34975 Z= 0.448 Angle : 0.696 10.024 47711 Z= 0.357 Chirality : 0.048 0.289 5363 Planarity : 0.005 0.056 6193 Dihedral : 5.846 59.241 4860 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 6.73 % Allowed : 17.45 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.43 (0.12), residues: 4201 helix: -2.04 (0.25), residues: 349 sheet: 0.56 (0.15), residues: 1107 loop : -0.37 (0.11), residues: 2745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP f 227 HIS 0.010 0.002 HIS j 109 PHE 0.032 0.002 PHE f 191 TYR 0.038 0.002 TYR i 154 ARG 0.006 0.001 ARG f 14 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1363 residues out of total 3684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 1115 time to evaluate : 3.669 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 TARDY: cannot create tardy model for: "GLN n 272 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLN r 272 " (corrupted residue). Skipping it. REVERT: a 54 ASP cc_start: 0.8858 (OUTLIER) cc_final: 0.8442 (m-30) REVERT: a 106 THR cc_start: 0.9292 (t) cc_final: 0.8943 (m) REVERT: a 169 THR cc_start: 0.9176 (p) cc_final: 0.8731 (t) REVERT: a 277 GLU cc_start: 0.7728 (mp0) cc_final: 0.7295 (mp0) REVERT: b 48 ASN cc_start: 0.9273 (t0) cc_final: 0.9045 (t0) REVERT: b 97 TYR cc_start: 0.8560 (m-80) cc_final: 0.7997 (m-10) REVERT: b 104 SER cc_start: 0.9347 (OUTLIER) cc_final: 0.9105 (p) REVERT: b 172 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.6920 (mtt90) REVERT: b 183 SER cc_start: 0.9260 (p) cc_final: 0.8954 (t) REVERT: d 21 ASN cc_start: 0.7772 (p0) cc_final: 0.6901 (p0) REVERT: e 182 TYR cc_start: 0.8873 (t80) cc_final: 0.8364 (t80) REVERT: e 204 TYR cc_start: 0.8697 (t80) cc_final: 0.7878 (t80) REVERT: e 205 ASP cc_start: 0.8852 (t0) cc_final: 0.8505 (t70) REVERT: e 231 ASP cc_start: 0.8332 (t0) cc_final: 0.8120 (t0) REVERT: f 23 ILE cc_start: 0.9328 (mt) cc_final: 0.9031 (mm) REVERT: f 30 ASN cc_start: 0.8478 (t0) cc_final: 0.8277 (t0) REVERT: f 116 LYS cc_start: 0.9179 (mttt) cc_final: 0.8855 (mttp) REVERT: f 264 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7474 (ptt90) REVERT: g 154 ILE cc_start: 0.9337 (mm) cc_final: 0.8987 (mm) REVERT: g 156 ASP cc_start: 0.8397 (t0) cc_final: 0.7892 (p0) REVERT: g 216 CYS cc_start: 0.8919 (m) cc_final: 0.8530 (m) REVERT: i 98 LYS cc_start: 0.9010 (mttt) cc_final: 0.8723 (mtpp) REVERT: i 166 ASP cc_start: 0.7952 (OUTLIER) cc_final: 0.7015 (p0) REVERT: i 204 TYR cc_start: 0.8667 (t80) cc_final: 0.7968 (t80) REVERT: j 223 LYS cc_start: 0.9405 (mtmt) cc_final: 0.9055 (mtmm) REVERT: j 264 ARG cc_start: 0.8636 (ptt90) cc_final: 0.8296 (ptt90) REVERT: k 39 GLU cc_start: 0.8509 (tm-30) cc_final: 0.8128 (tm-30) REVERT: k 41 LYS cc_start: 0.9072 (mttm) cc_final: 0.8844 (mttm) REVERT: k 87 SER cc_start: 0.9188 (t) cc_final: 0.8895 (p) REVERT: k 128 LYS cc_start: 0.8225 (mttm) cc_final: 0.7864 (mtmt) REVERT: k 155 TRP cc_start: 0.8473 (t60) cc_final: 0.7938 (t60) REVERT: k 169 TRP cc_start: 0.8963 (t-100) cc_final: 0.8072 (t-100) REVERT: k 177 ARG cc_start: 0.8909 (ttm110) cc_final: 0.8469 (ttm110) REVERT: k 178 CYS cc_start: 0.8482 (m) cc_final: 0.7755 (m) REVERT: k 222 ARG cc_start: 0.8804 (mtp180) cc_final: 0.8448 (mtp85) REVERT: l 53 PHE cc_start: 0.8979 (m-80) cc_final: 0.8728 (m-80) REVERT: m 105 ILE cc_start: 0.9318 (mt) cc_final: 0.9050 (mt) REVERT: m 111 VAL cc_start: 0.9284 (m) cc_final: 0.9052 (p) REVERT: m 166 ASP cc_start: 0.8575 (p0) cc_final: 0.7756 (p0) REVERT: m 216 ASN cc_start: 0.7713 (t0) cc_final: 0.6787 (m-40) REVERT: m 218 ASP cc_start: 0.8106 (m-30) cc_final: 0.7356 (m-30) REVERT: m 240 VAL cc_start: 0.9656 (OUTLIER) cc_final: 0.9296 (t) REVERT: n 13 VAL cc_start: 0.9596 (t) cc_final: 0.9341 (p) REVERT: n 50 VAL cc_start: 0.9413 (m) cc_final: 0.9041 (t) REVERT: n 60 SER cc_start: 0.9434 (m) cc_final: 0.9091 (p) REVERT: n 71 TRP cc_start: 0.8667 (t60) cc_final: 0.8412 (t60) REVERT: n 216 LEU cc_start: 0.9370 (mt) cc_final: 0.9071 (mt) REVERT: n 249 ILE cc_start: 0.9463 (mt) cc_final: 0.9156 (mt) REVERT: o 86 LEU cc_start: 0.9349 (tp) cc_final: 0.9130 (tp) REVERT: o 87 SER cc_start: 0.9145 (m) cc_final: 0.8229 (p) REVERT: o 104 ASN cc_start: 0.9035 (m-40) cc_final: 0.8814 (m-40) REVERT: o 105 TYR cc_start: 0.8913 (m-80) cc_final: 0.8671 (m-80) REVERT: o 157 LEU cc_start: 0.8341 (mt) cc_final: 0.8035 (mt) REVERT: o 175 TYR cc_start: 0.9055 (m-80) cc_final: 0.8837 (m-10) REVERT: o 207 MET cc_start: 0.8503 (ptp) cc_final: 0.8105 (ptp) REVERT: o 234 LYS cc_start: 0.7976 (tttt) cc_final: 0.7251 (mttt) REVERT: p 48 GLN cc_start: 0.8552 (pm20) cc_final: 0.8223 (pt0) REVERT: q 105 ILE cc_start: 0.9072 (mt) cc_final: 0.8534 (tt) REVERT: q 126 ASP cc_start: 0.8395 (m-30) cc_final: 0.8144 (m-30) REVERT: q 171 GLN cc_start: 0.8577 (mt0) cc_final: 0.8214 (mt0) REVERT: r 26 GLN cc_start: 0.7351 (mt0) cc_final: 0.7003 (mt0) REVERT: r 41 TYR cc_start: 0.8701 (m-80) cc_final: 0.8168 (m-10) REVERT: r 48 ASN cc_start: 0.8954 (t0) cc_final: 0.8720 (t0) REVERT: r 116 LYS cc_start: 0.8809 (mttt) cc_final: 0.8559 (mtmt) REVERT: r 212 TYR cc_start: 0.8521 (t80) cc_final: 0.8253 (t80) REVERT: r 259 GLU cc_start: 0.8567 (tt0) cc_final: 0.8286 (tt0) REVERT: s 10 SER cc_start: 0.9462 (m) cc_final: 0.9229 (p) REVERT: s 18 ASP cc_start: 0.8182 (t0) cc_final: 0.7952 (t0) REVERT: s 50 ASP cc_start: 0.8806 (m-30) cc_final: 0.8434 (m-30) REVERT: s 74 ASP cc_start: 0.7789 (p0) cc_final: 0.7440 (p0) REVERT: s 92 LYS cc_start: 0.8731 (mtmm) cc_final: 0.8497 (mtmm) REVERT: s 146 ASP cc_start: 0.8359 (m-30) cc_final: 0.7940 (m-30) REVERT: s 154 ILE cc_start: 0.8794 (mt) cc_final: 0.8453 (pt) REVERT: s 234 LYS cc_start: 0.8606 (mtmt) cc_final: 0.8074 (mttp) REVERT: t 28 THR cc_start: 0.9317 (m) cc_final: 0.9059 (p) outliers start: 248 outliers final: 199 residues processed: 1237 average time/residue: 0.4768 time to fit residues: 962.5774 Evaluate side-chains 1264 residues out of total 3684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 1059 time to evaluate : 3.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 51 ILE Chi-restraints excluded: chain a residue 54 ASP Chi-restraints excluded: chain a residue 61 VAL Chi-restraints excluded: chain a residue 66 THR Chi-restraints excluded: chain a residue 68 SER Chi-restraints excluded: chain a residue 71 CYS Chi-restraints excluded: chain a residue 130 THR Chi-restraints excluded: chain a residue 134 THR Chi-restraints excluded: chain a residue 190 SER Chi-restraints excluded: chain a residue 250 THR Chi-restraints excluded: chain a residue 280 ASP Chi-restraints excluded: chain a residue 293 ASP Chi-restraints excluded: chain a residue 295 ILE Chi-restraints excluded: chain a residue 296 THR Chi-restraints excluded: chain b residue 21 SER Chi-restraints excluded: chain b residue 26 GLN Chi-restraints excluded: chain b residue 45 SER Chi-restraints excluded: chain b residue 74 THR Chi-restraints excluded: chain b residue 104 SER Chi-restraints excluded: chain b residue 172 ARG Chi-restraints excluded: chain b residue 202 THR Chi-restraints excluded: chain b residue 268 VAL Chi-restraints excluded: chain c residue 7 THR Chi-restraints excluded: chain c residue 10 SER Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 62 VAL Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 159 LEU Chi-restraints excluded: chain c residue 184 THR Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain c residue 213 VAL Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain d residue 60 LEU Chi-restraints excluded: chain e residue 22 THR Chi-restraints excluded: chain e residue 66 THR Chi-restraints excluded: chain e residue 104 ASN Chi-restraints excluded: chain e residue 110 THR Chi-restraints excluded: chain e residue 134 THR Chi-restraints excluded: chain e residue 135 GLU Chi-restraints excluded: chain e residue 163 SER Chi-restraints excluded: chain e residue 189 MET Chi-restraints excluded: chain e residue 196 ILE Chi-restraints excluded: chain e residue 227 VAL Chi-restraints excluded: chain e residue 229 ILE Chi-restraints excluded: chain e residue 237 VAL Chi-restraints excluded: chain e residue 252 VAL Chi-restraints excluded: chain e residue 282 ILE Chi-restraints excluded: chain f residue 37 GLU Chi-restraints excluded: chain f residue 40 THR Chi-restraints excluded: chain f residue 45 SER Chi-restraints excluded: chain f residue 58 VAL Chi-restraints excluded: chain f residue 88 ASP Chi-restraints excluded: chain f residue 140 THR Chi-restraints excluded: chain f residue 146 ILE Chi-restraints excluded: chain f residue 180 LEU Chi-restraints excluded: chain f residue 208 ILE Chi-restraints excluded: chain f residue 256 MET Chi-restraints excluded: chain f residue 263 LEU Chi-restraints excluded: chain f residue 264 ARG Chi-restraints excluded: chain f residue 265 ASN Chi-restraints excluded: chain g residue 67 MET Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain g residue 107 THR Chi-restraints excluded: chain g residue 112 SER Chi-restraints excluded: chain g residue 132 SER Chi-restraints excluded: chain g residue 153 ILE Chi-restraints excluded: chain g residue 190 THR Chi-restraints excluded: chain g residue 198 VAL Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain g residue 203 THR Chi-restraints excluded: chain g residue 205 THR Chi-restraints excluded: chain g residue 207 MET Chi-restraints excluded: chain g residue 224 LEU Chi-restraints excluded: chain h residue 7 THR Chi-restraints excluded: chain h residue 10 THR Chi-restraints excluded: chain h residue 23 SER Chi-restraints excluded: chain h residue 26 ASN Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 51 SER Chi-restraints excluded: chain h residue 55 GLU Chi-restraints excluded: chain h residue 57 VAL Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain i residue 25 THR Chi-restraints excluded: chain i residue 40 THR Chi-restraints excluded: chain i residue 44 THR Chi-restraints excluded: chain i residue 84 ILE Chi-restraints excluded: chain i residue 88 THR Chi-restraints excluded: chain i residue 100 PHE Chi-restraints excluded: chain i residue 128 GLU Chi-restraints excluded: chain i residue 132 VAL Chi-restraints excluded: chain i residue 166 ASP Chi-restraints excluded: chain i residue 190 SER Chi-restraints excluded: chain i residue 229 ILE Chi-restraints excluded: chain i residue 296 THR Chi-restraints excluded: chain j residue 25 THR Chi-restraints excluded: chain j residue 38 TRP Chi-restraints excluded: chain j residue 40 THR Chi-restraints excluded: chain j residue 58 VAL Chi-restraints excluded: chain j residue 84 ASP Chi-restraints excluded: chain j residue 126 LEU Chi-restraints excluded: chain j residue 181 LEU Chi-restraints excluded: chain j residue 183 SER Chi-restraints excluded: chain j residue 246 GLN Chi-restraints excluded: chain j residue 247 VAL Chi-restraints excluded: chain k residue 5 MET Chi-restraints excluded: chain k residue 10 SER Chi-restraints excluded: chain k residue 21 SER Chi-restraints excluded: chain k residue 30 VAL Chi-restraints excluded: chain k residue 69 GLN Chi-restraints excluded: chain k residue 76 LEU Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain k residue 103 LEU Chi-restraints excluded: chain k residue 116 THR Chi-restraints excluded: chain k residue 189 ILE Chi-restraints excluded: chain k residue 199 VAL Chi-restraints excluded: chain k residue 218 ASP Chi-restraints excluded: chain k residue 223 LEU Chi-restraints excluded: chain k residue 227 THR Chi-restraints excluded: chain k residue 233 SER Chi-restraints excluded: chain l residue 24 THR Chi-restraints excluded: chain l residue 26 ASN Chi-restraints excluded: chain l residue 44 GLN Chi-restraints excluded: chain l residue 64 THR Chi-restraints excluded: chain m residue 68 SER Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain m residue 83 THR Chi-restraints excluded: chain m residue 84 ILE Chi-restraints excluded: chain m residue 95 GLU Chi-restraints excluded: chain m residue 106 THR Chi-restraints excluded: chain m residue 110 THR Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 173 SER Chi-restraints excluded: chain m residue 181 MET Chi-restraints excluded: chain m residue 196 ILE Chi-restraints excluded: chain m residue 240 VAL Chi-restraints excluded: chain m residue 272 VAL Chi-restraints excluded: chain n residue 54 THR Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 69 VAL Chi-restraints excluded: chain n residue 74 THR Chi-restraints excluded: chain n residue 84 ASP Chi-restraints excluded: chain n residue 141 SER Chi-restraints excluded: chain n residue 152 GLU Chi-restraints excluded: chain n residue 183 SER Chi-restraints excluded: chain n residue 198 ILE Chi-restraints excluded: chain n residue 217 VAL Chi-restraints excluded: chain n residue 226 ASN Chi-restraints excluded: chain n residue 252 THR Chi-restraints excluded: chain n residue 265 ASN Chi-restraints excluded: chain o residue 30 VAL Chi-restraints excluded: chain o residue 51 THR Chi-restraints excluded: chain o residue 126 THR Chi-restraints excluded: chain o residue 132 SER Chi-restraints excluded: chain o residue 153 ILE Chi-restraints excluded: chain o residue 164 SER Chi-restraints excluded: chain o residue 190 THR Chi-restraints excluded: chain o residue 198 VAL Chi-restraints excluded: chain o residue 199 VAL Chi-restraints excluded: chain o residue 226 ASP Chi-restraints excluded: chain p residue 25 ILE Chi-restraints excluded: chain p residue 40 SER Chi-restraints excluded: chain p residue 57 VAL Chi-restraints excluded: chain q residue 22 THR Chi-restraints excluded: chain q residue 36 VAL Chi-restraints excluded: chain q residue 62 VAL Chi-restraints excluded: chain q residue 68 SER Chi-restraints excluded: chain q residue 99 HIS Chi-restraints excluded: chain q residue 100 PHE Chi-restraints excluded: chain q residue 106 THR Chi-restraints excluded: chain q residue 177 SER Chi-restraints excluded: chain q residue 178 ILE Chi-restraints excluded: chain q residue 190 SER Chi-restraints excluded: chain q residue 217 THR Chi-restraints excluded: chain q residue 265 CYS Chi-restraints excluded: chain q residue 296 THR Chi-restraints excluded: chain r residue 18 LEU Chi-restraints excluded: chain r residue 24 THR Chi-restraints excluded: chain r residue 32 ILE Chi-restraints excluded: chain r residue 40 THR Chi-restraints excluded: chain r residue 44 ASP Chi-restraints excluded: chain r residue 46 GLU Chi-restraints excluded: chain r residue 50 VAL Chi-restraints excluded: chain r residue 51 ASP Chi-restraints excluded: chain r residue 84 ASP Chi-restraints excluded: chain r residue 86 LEU Chi-restraints excluded: chain r residue 111 GLN Chi-restraints excluded: chain r residue 131 VAL Chi-restraints excluded: chain r residue 192 VAL Chi-restraints excluded: chain r residue 205 SER Chi-restraints excluded: chain r residue 218 ILE Chi-restraints excluded: chain r residue 252 THR Chi-restraints excluded: chain s residue 30 VAL Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain s residue 53 ILE Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain s residue 76 LEU Chi-restraints excluded: chain s residue 85 SER Chi-restraints excluded: chain s residue 86 LEU Chi-restraints excluded: chain s residue 103 LEU Chi-restraints excluded: chain s residue 159 LEU Chi-restraints excluded: chain s residue 173 THR Chi-restraints excluded: chain s residue 189 ILE Chi-restraints excluded: chain s residue 205 THR Chi-restraints excluded: chain t residue 7 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 140 optimal weight: 8.9990 chunk 376 optimal weight: 3.9990 chunk 82 optimal weight: 20.0000 chunk 245 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 418 optimal weight: 9.9990 chunk 347 optimal weight: 9.9990 chunk 193 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 138 optimal weight: 4.9990 chunk 219 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 111 GLN ** c 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 49 GLN e 151 GLN ** e 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 230 ASN h 21 ASN ** i 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 184 ASN ** i 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 196 GLN ** k 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 26 ASN ** m 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 26 ASN ** q 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 4 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.4713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 34975 Z= 0.365 Angle : 0.663 10.399 47711 Z= 0.336 Chirality : 0.047 0.291 5363 Planarity : 0.004 0.046 6193 Dihedral : 5.851 59.323 4860 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 6.19 % Allowed : 19.33 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.12), residues: 4201 helix: -1.90 (0.25), residues: 337 sheet: 0.49 (0.15), residues: 1090 loop : -0.45 (0.11), residues: 2774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP f 227 HIS 0.009 0.001 HIS j 109 PHE 0.035 0.002 PHE e 120 TYR 0.035 0.002 TYR i 154 ARG 0.008 0.001 ARG k 176 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1330 residues out of total 3684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 1102 time to evaluate : 3.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN n 272 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN r 272 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: a 54 ASP cc_start: 0.8846 (OUTLIER) cc_final: 0.8384 (m-30) REVERT: a 105 ILE cc_start: 0.9546 (mt) cc_final: 0.8995 (tt) REVERT: a 169 THR cc_start: 0.9188 (p) cc_final: 0.8735 (t) REVERT: a 205 ASP cc_start: 0.8683 (t70) cc_final: 0.8235 (t70) REVERT: b 48 ASN cc_start: 0.9258 (t0) cc_final: 0.9023 (t0) REVERT: b 104 SER cc_start: 0.9375 (OUTLIER) cc_final: 0.9127 (p) REVERT: b 172 ARG cc_start: 0.7294 (OUTLIER) cc_final: 0.6583 (mtt90) REVERT: b 173 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7789 (ptpt) REVERT: b 183 SER cc_start: 0.9259 (p) cc_final: 0.8966 (t) REVERT: c 101 GLU cc_start: 0.8535 (mm-30) cc_final: 0.7827 (mm-30) REVERT: c 177 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.8191 (mpt-90) REVERT: d 21 ASN cc_start: 0.7769 (p0) cc_final: 0.6860 (p0) REVERT: e 182 TYR cc_start: 0.8857 (t80) cc_final: 0.8384 (t80) REVERT: e 204 TYR cc_start: 0.8672 (t80) cc_final: 0.7778 (t80) REVERT: e 205 ASP cc_start: 0.8823 (t0) cc_final: 0.8448 (t70) REVERT: f 23 ILE cc_start: 0.9282 (mt) cc_final: 0.9018 (mm) REVERT: f 30 ASN cc_start: 0.8506 (t0) cc_final: 0.8301 (t0) REVERT: f 116 LYS cc_start: 0.9179 (mttt) cc_final: 0.8887 (mttp) REVERT: g 99 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.9051 (tt) REVERT: g 154 ILE cc_start: 0.9322 (mm) cc_final: 0.8953 (mm) REVERT: g 156 ASP cc_start: 0.8396 (t0) cc_final: 0.7956 (p0) REVERT: g 216 CYS cc_start: 0.8878 (m) cc_final: 0.8515 (m) REVERT: g 218 ASP cc_start: 0.8602 (p0) cc_final: 0.8358 (p0) REVERT: h 36 SER cc_start: 0.9025 (p) cc_final: 0.8562 (t) REVERT: i 95 GLU cc_start: 0.7123 (tt0) cc_final: 0.6898 (tt0) REVERT: i 98 LYS cc_start: 0.9011 (mttt) cc_final: 0.8767 (mtpp) REVERT: i 166 ASP cc_start: 0.7982 (OUTLIER) cc_final: 0.7057 (p0) REVERT: i 204 TYR cc_start: 0.8498 (t80) cc_final: 0.7936 (t80) REVERT: j 129 GLU cc_start: 0.8545 (mm-30) cc_final: 0.7915 (mm-30) REVERT: j 196 GLN cc_start: 0.8965 (tt0) cc_final: 0.8723 (tt0) REVERT: j 223 LYS cc_start: 0.9343 (mtmt) cc_final: 0.9092 (mtmm) REVERT: j 264 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.8090 (ptt90) REVERT: k 39 GLU cc_start: 0.8484 (tm-30) cc_final: 0.8129 (tm-30) REVERT: k 41 LYS cc_start: 0.9048 (mttm) cc_final: 0.8778 (mttm) REVERT: k 87 SER cc_start: 0.9190 (t) cc_final: 0.8925 (p) REVERT: k 128 LYS cc_start: 0.8219 (mttm) cc_final: 0.7832 (mtmt) REVERT: k 155 TRP cc_start: 0.8531 (t60) cc_final: 0.7911 (t60) REVERT: k 164 SER cc_start: 0.9334 (m) cc_final: 0.8865 (t) REVERT: k 178 CYS cc_start: 0.8483 (m) cc_final: 0.7809 (m) REVERT: k 194 GLN cc_start: 0.9067 (tp40) cc_final: 0.8844 (mm-40) REVERT: l 49 ASP cc_start: 0.9084 (t70) cc_final: 0.8879 (t0) REVERT: l 53 PHE cc_start: 0.9014 (m-80) cc_final: 0.8787 (m-80) REVERT: m 105 ILE cc_start: 0.9303 (mt) cc_final: 0.9037 (mt) REVERT: m 111 VAL cc_start: 0.9261 (m) cc_final: 0.8879 (p) REVERT: m 166 ASP cc_start: 0.8516 (p0) cc_final: 0.7613 (p0) REVERT: m 216 ASN cc_start: 0.7726 (t0) cc_final: 0.6798 (m-40) REVERT: m 218 ASP cc_start: 0.8199 (m-30) cc_final: 0.7412 (m-30) REVERT: n 13 VAL cc_start: 0.9606 (t) cc_final: 0.9352 (p) REVERT: n 60 SER cc_start: 0.9456 (m) cc_final: 0.9095 (p) REVERT: n 71 TRP cc_start: 0.8681 (t60) cc_final: 0.8464 (t60) REVERT: n 129 GLU cc_start: 0.8571 (tp30) cc_final: 0.7797 (tp30) REVERT: n 249 ILE cc_start: 0.9460 (mt) cc_final: 0.9161 (mt) REVERT: o 65 MET cc_start: 0.9073 (mmm) cc_final: 0.8335 (tpp) REVERT: o 86 LEU cc_start: 0.9339 (tp) cc_final: 0.9135 (tp) REVERT: o 87 SER cc_start: 0.9127 (m) cc_final: 0.8210 (p) REVERT: o 157 LEU cc_start: 0.8307 (mt) cc_final: 0.8003 (mt) REVERT: o 175 TYR cc_start: 0.9046 (m-80) cc_final: 0.8826 (m-10) REVERT: o 207 MET cc_start: 0.8436 (ptp) cc_final: 0.8031 (ptp) REVERT: o 234 LYS cc_start: 0.7962 (tttt) cc_final: 0.7246 (mttt) REVERT: q 105 ILE cc_start: 0.9062 (mt) cc_final: 0.8543 (tt) REVERT: q 111 VAL cc_start: 0.9417 (p) cc_final: 0.9141 (t) REVERT: q 126 ASP cc_start: 0.8417 (m-30) cc_final: 0.8153 (m-30) REVERT: q 165 TRP cc_start: 0.8621 (p-90) cc_final: 0.8096 (p-90) REVERT: q 171 GLN cc_start: 0.8621 (mt0) cc_final: 0.8201 (mt0) REVERT: q 231 ASP cc_start: 0.7366 (t0) cc_final: 0.7066 (t0) REVERT: r 26 GLN cc_start: 0.7348 (mt0) cc_final: 0.6975 (mt0) REVERT: r 48 ASN cc_start: 0.8881 (t0) cc_final: 0.8668 (t0) REVERT: r 116 LYS cc_start: 0.8838 (mttt) cc_final: 0.8607 (mtmt) REVERT: r 221 MET cc_start: 0.8212 (mtt) cc_final: 0.7998 (mtt) REVERT: s 18 ASP cc_start: 0.8265 (t0) cc_final: 0.8000 (t0) REVERT: s 74 ASP cc_start: 0.7750 (p0) cc_final: 0.7397 (p0) REVERT: s 92 LYS cc_start: 0.8757 (mtmm) cc_final: 0.8525 (mtmm) REVERT: s 154 ILE cc_start: 0.8859 (mt) cc_final: 0.8618 (pt) REVERT: s 234 LYS cc_start: 0.8535 (mtmt) cc_final: 0.7985 (mttp) REVERT: t 28 THR cc_start: 0.9301 (m) cc_final: 0.9073 (p) outliers start: 228 outliers final: 187 residues processed: 1222 average time/residue: 0.4581 time to fit residues: 901.0442 Evaluate side-chains 1249 residues out of total 3684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 1054 time to evaluate : 3.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 51 ILE Chi-restraints excluded: chain a residue 54 ASP Chi-restraints excluded: chain a residue 61 VAL Chi-restraints excluded: chain a residue 66 THR Chi-restraints excluded: chain a residue 68 SER Chi-restraints excluded: chain a residue 71 CYS Chi-restraints excluded: chain a residue 130 THR Chi-restraints excluded: chain a residue 134 THR Chi-restraints excluded: chain a residue 190 SER Chi-restraints excluded: chain a residue 198 ASN Chi-restraints excluded: chain a residue 280 ASP Chi-restraints excluded: chain a residue 293 ASP Chi-restraints excluded: chain a residue 295 ILE Chi-restraints excluded: chain b residue 21 SER Chi-restraints excluded: chain b residue 26 GLN Chi-restraints excluded: chain b residue 45 SER Chi-restraints excluded: chain b residue 74 THR Chi-restraints excluded: chain b residue 104 SER Chi-restraints excluded: chain b residue 172 ARG Chi-restraints excluded: chain b residue 173 LYS Chi-restraints excluded: chain b residue 202 THR Chi-restraints excluded: chain b residue 268 VAL Chi-restraints excluded: chain c residue 7 THR Chi-restraints excluded: chain c residue 10 SER Chi-restraints excluded: chain c residue 17 ASP Chi-restraints excluded: chain c residue 62 VAL Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 159 LEU Chi-restraints excluded: chain c residue 177 ARG Chi-restraints excluded: chain c residue 184 THR Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain c residue 213 VAL Chi-restraints excluded: chain c residue 239 THR Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain d residue 60 LEU Chi-restraints excluded: chain e residue 22 THR Chi-restraints excluded: chain e residue 104 ASN Chi-restraints excluded: chain e residue 110 THR Chi-restraints excluded: chain e residue 134 THR Chi-restraints excluded: chain e residue 135 GLU Chi-restraints excluded: chain e residue 163 SER Chi-restraints excluded: chain e residue 175 ASN Chi-restraints excluded: chain e residue 189 MET Chi-restraints excluded: chain e residue 196 ILE Chi-restraints excluded: chain e residue 237 VAL Chi-restraints excluded: chain e residue 252 VAL Chi-restraints excluded: chain e residue 282 ILE Chi-restraints excluded: chain e residue 293 ASP Chi-restraints excluded: chain f residue 37 GLU Chi-restraints excluded: chain f residue 40 THR Chi-restraints excluded: chain f residue 45 SER Chi-restraints excluded: chain f residue 58 VAL Chi-restraints excluded: chain f residue 88 ASP Chi-restraints excluded: chain f residue 140 THR Chi-restraints excluded: chain f residue 263 LEU Chi-restraints excluded: chain f residue 265 ASN Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain g residue 99 LEU Chi-restraints excluded: chain g residue 112 SER Chi-restraints excluded: chain g residue 190 THR Chi-restraints excluded: chain g residue 198 VAL Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain g residue 203 THR Chi-restraints excluded: chain g residue 207 MET Chi-restraints excluded: chain g residue 224 LEU Chi-restraints excluded: chain g residue 227 THR Chi-restraints excluded: chain h residue 7 THR Chi-restraints excluded: chain h residue 10 THR Chi-restraints excluded: chain h residue 23 SER Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 51 SER Chi-restraints excluded: chain h residue 57 VAL Chi-restraints excluded: chain i residue 40 THR Chi-restraints excluded: chain i residue 88 THR Chi-restraints excluded: chain i residue 100 PHE Chi-restraints excluded: chain i residue 128 GLU Chi-restraints excluded: chain i residue 132 VAL Chi-restraints excluded: chain i residue 166 ASP Chi-restraints excluded: chain i residue 190 SER Chi-restraints excluded: chain i residue 229 ILE Chi-restraints excluded: chain i residue 296 THR Chi-restraints excluded: chain j residue 25 THR Chi-restraints excluded: chain j residue 38 TRP Chi-restraints excluded: chain j residue 40 THR Chi-restraints excluded: chain j residue 45 SER Chi-restraints excluded: chain j residue 50 VAL Chi-restraints excluded: chain j residue 58 VAL Chi-restraints excluded: chain j residue 67 GLU Chi-restraints excluded: chain j residue 84 ASP Chi-restraints excluded: chain j residue 126 LEU Chi-restraints excluded: chain j residue 181 LEU Chi-restraints excluded: chain j residue 183 SER Chi-restraints excluded: chain j residue 246 GLN Chi-restraints excluded: chain j residue 247 VAL Chi-restraints excluded: chain j residue 264 ARG Chi-restraints excluded: chain k residue 5 MET Chi-restraints excluded: chain k residue 10 SER Chi-restraints excluded: chain k residue 21 SER Chi-restraints excluded: chain k residue 76 LEU Chi-restraints excluded: chain k residue 81 ILE Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain k residue 103 LEU Chi-restraints excluded: chain k residue 116 THR Chi-restraints excluded: chain k residue 126 THR Chi-restraints excluded: chain k residue 189 ILE Chi-restraints excluded: chain k residue 199 VAL Chi-restraints excluded: chain k residue 203 THR Chi-restraints excluded: chain k residue 218 ASP Chi-restraints excluded: chain k residue 223 LEU Chi-restraints excluded: chain k residue 226 ASP Chi-restraints excluded: chain k residue 227 THR Chi-restraints excluded: chain k residue 233 SER Chi-restraints excluded: chain l residue 26 ASN Chi-restraints excluded: chain l residue 44 GLN Chi-restraints excluded: chain l residue 64 THR Chi-restraints excluded: chain m residue 61 VAL Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain m residue 83 THR Chi-restraints excluded: chain m residue 84 ILE Chi-restraints excluded: chain m residue 95 GLU Chi-restraints excluded: chain m residue 106 THR Chi-restraints excluded: chain m residue 127 LEU Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 173 SER Chi-restraints excluded: chain m residue 177 SER Chi-restraints excluded: chain m residue 196 ILE Chi-restraints excluded: chain m residue 198 ASN Chi-restraints excluded: chain m residue 272 VAL Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 74 THR Chi-restraints excluded: chain n residue 84 ASP Chi-restraints excluded: chain n residue 141 SER Chi-restraints excluded: chain n residue 152 GLU Chi-restraints excluded: chain n residue 183 SER Chi-restraints excluded: chain n residue 186 LEU Chi-restraints excluded: chain n residue 198 ILE Chi-restraints excluded: chain n residue 217 VAL Chi-restraints excluded: chain n residue 265 ASN Chi-restraints excluded: chain o residue 27 ASN Chi-restraints excluded: chain o residue 30 VAL Chi-restraints excluded: chain o residue 51 THR Chi-restraints excluded: chain o residue 118 LEU Chi-restraints excluded: chain o residue 126 THR Chi-restraints excluded: chain o residue 132 SER Chi-restraints excluded: chain o residue 153 ILE Chi-restraints excluded: chain o residue 164 SER Chi-restraints excluded: chain o residue 190 THR Chi-restraints excluded: chain o residue 198 VAL Chi-restraints excluded: chain o residue 199 VAL Chi-restraints excluded: chain o residue 226 ASP Chi-restraints excluded: chain p residue 25 ILE Chi-restraints excluded: chain p residue 32 TYR Chi-restraints excluded: chain p residue 40 SER Chi-restraints excluded: chain p residue 57 VAL Chi-restraints excluded: chain q residue 36 VAL Chi-restraints excluded: chain q residue 62 VAL Chi-restraints excluded: chain q residue 71 CYS Chi-restraints excluded: chain q residue 99 HIS Chi-restraints excluded: chain q residue 100 PHE Chi-restraints excluded: chain q residue 177 SER Chi-restraints excluded: chain q residue 178 ILE Chi-restraints excluded: chain q residue 190 SER Chi-restraints excluded: chain q residue 217 THR Chi-restraints excluded: chain q residue 265 CYS Chi-restraints excluded: chain q residue 296 THR Chi-restraints excluded: chain r residue 18 LEU Chi-restraints excluded: chain r residue 24 THR Chi-restraints excluded: chain r residue 32 ILE Chi-restraints excluded: chain r residue 40 THR Chi-restraints excluded: chain r residue 46 GLU Chi-restraints excluded: chain r residue 50 VAL Chi-restraints excluded: chain r residue 51 ASP Chi-restraints excluded: chain r residue 84 ASP Chi-restraints excluded: chain r residue 86 LEU Chi-restraints excluded: chain r residue 111 GLN Chi-restraints excluded: chain r residue 131 VAL Chi-restraints excluded: chain r residue 192 VAL Chi-restraints excluded: chain r residue 205 SER Chi-restraints excluded: chain s residue 30 VAL Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain s residue 53 ILE Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain s residue 76 LEU Chi-restraints excluded: chain s residue 85 SER Chi-restraints excluded: chain s residue 86 LEU Chi-restraints excluded: chain s residue 97 THR Chi-restraints excluded: chain s residue 103 LEU Chi-restraints excluded: chain s residue 159 LEU Chi-restraints excluded: chain s residue 173 THR Chi-restraints excluded: chain s residue 182 ASP Chi-restraints excluded: chain s residue 189 ILE Chi-restraints excluded: chain s residue 195 THR Chi-restraints excluded: chain s residue 205 THR Chi-restraints excluded: chain t residue 7 THR Chi-restraints excluded: chain t residue 44 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 403 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 238 optimal weight: 9.9990 chunk 305 optimal weight: 10.0000 chunk 237 optimal weight: 5.9990 chunk 352 optimal weight: 5.9990 chunk 233 optimal weight: 20.0000 chunk 417 optimal weight: 0.9990 chunk 261 optimal weight: 10.0000 chunk 254 optimal weight: 5.9990 chunk 192 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 111 GLN e 23 GLN e 151 GLN e 230 ASN f 265 ASN h 21 ASN ** i 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 61 ASN ** j 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 26 ASN ** n 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 26 ASN ** r 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 4 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.4893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 34975 Z= 0.336 Angle : 0.657 10.294 47711 Z= 0.332 Chirality : 0.047 0.311 5363 Planarity : 0.004 0.052 6193 Dihedral : 5.858 58.849 4860 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 6.27 % Allowed : 19.84 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.60 (0.12), residues: 4201 helix: -1.95 (0.24), residues: 361 sheet: 0.50 (0.15), residues: 1073 loop : -0.53 (0.11), residues: 2767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP f 227 HIS 0.009 0.001 HIS j 109 PHE 0.028 0.002 PHE f 191 TYR 0.037 0.002 TYR g 106 ARG 0.013 0.001 ARG f 264 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1336 residues out of total 3684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 1105 time to evaluate : 3.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN n 272 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN r 272 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: a 54 ASP cc_start: 0.8849 (OUTLIER) cc_final: 0.8358 (m-30) REVERT: a 105 ILE cc_start: 0.9534 (mt) cc_final: 0.8966 (tt) REVERT: a 169 THR cc_start: 0.9196 (p) cc_final: 0.8743 (t) REVERT: b 33 VAL cc_start: 0.9551 (t) cc_final: 0.9281 (m) REVERT: b 104 SER cc_start: 0.9372 (OUTLIER) cc_final: 0.9167 (p) REVERT: b 172 ARG cc_start: 0.7198 (OUTLIER) cc_final: 0.6961 (mtm-85) REVERT: b 183 SER cc_start: 0.9273 (p) cc_final: 0.8965 (t) REVERT: c 56 ASN cc_start: 0.9565 (t0) cc_final: 0.9301 (t0) REVERT: c 101 GLU cc_start: 0.8537 (mm-30) cc_final: 0.7807 (mm-30) REVERT: d 21 ASN cc_start: 0.7823 (p0) cc_final: 0.6928 (p0) REVERT: e 151 GLN cc_start: 0.8457 (tt0) cc_final: 0.8133 (tt0) REVERT: e 182 TYR cc_start: 0.8848 (t80) cc_final: 0.8417 (t80) REVERT: e 205 ASP cc_start: 0.8822 (t0) cc_final: 0.8414 (t70) REVERT: f 23 ILE cc_start: 0.9275 (mt) cc_final: 0.9036 (mm) REVERT: f 30 ASN cc_start: 0.8525 (t0) cc_final: 0.8275 (t0) REVERT: f 91 MET cc_start: 0.8202 (mmm) cc_final: 0.7958 (tpp) REVERT: f 101 LEU cc_start: 0.8984 (mt) cc_final: 0.8334 (mp) REVERT: f 116 LYS cc_start: 0.9165 (mttt) cc_final: 0.8794 (mttp) REVERT: f 264 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7772 (ptt-90) REVERT: g 55 MET cc_start: 0.8720 (mmm) cc_final: 0.8396 (tpp) REVERT: g 99 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9076 (tt) REVERT: g 154 ILE cc_start: 0.9325 (mm) cc_final: 0.8954 (mm) REVERT: g 156 ASP cc_start: 0.8391 (t0) cc_final: 0.7892 (p0) REVERT: g 173 THR cc_start: 0.8960 (p) cc_final: 0.8733 (p) REVERT: g 216 CYS cc_start: 0.8858 (m) cc_final: 0.8537 (m) REVERT: g 218 ASP cc_start: 0.8613 (p0) cc_final: 0.8284 (p0) REVERT: h 36 SER cc_start: 0.9037 (p) cc_final: 0.8559 (t) REVERT: i 95 GLU cc_start: 0.7205 (tt0) cc_final: 0.6961 (tt0) REVERT: i 98 LYS cc_start: 0.9041 (mttt) cc_final: 0.8791 (mtpp) REVERT: i 166 ASP cc_start: 0.8032 (p0) cc_final: 0.7015 (p0) REVERT: i 204 TYR cc_start: 0.8418 (t80) cc_final: 0.7769 (t80) REVERT: j 129 GLU cc_start: 0.8629 (mm-30) cc_final: 0.7793 (mm-30) REVERT: j 223 LYS cc_start: 0.9305 (mtmt) cc_final: 0.8859 (mtmm) REVERT: j 264 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.8024 (ptt90) REVERT: k 52 LEU cc_start: 0.9435 (tp) cc_final: 0.9165 (mp) REVERT: k 87 SER cc_start: 0.9199 (t) cc_final: 0.8951 (p) REVERT: k 128 LYS cc_start: 0.8228 (mttm) cc_final: 0.7837 (mtmt) REVERT: k 155 TRP cc_start: 0.8561 (t60) cc_final: 0.7958 (t60) REVERT: k 164 SER cc_start: 0.9336 (m) cc_final: 0.8860 (t) REVERT: k 178 CYS cc_start: 0.8446 (m) cc_final: 0.7813 (m) REVERT: k 194 GLN cc_start: 0.9074 (tp40) cc_final: 0.8844 (mm-40) REVERT: l 53 PHE cc_start: 0.9018 (m-80) cc_final: 0.8787 (m-80) REVERT: m 105 ILE cc_start: 0.9311 (mt) cc_final: 0.9040 (mt) REVERT: m 111 VAL cc_start: 0.9201 (m) cc_final: 0.8980 (p) REVERT: m 166 ASP cc_start: 0.8510 (p0) cc_final: 0.7632 (p0) REVERT: m 216 ASN cc_start: 0.7720 (t0) cc_final: 0.6841 (m-40) REVERT: m 218 ASP cc_start: 0.8189 (m-30) cc_final: 0.7536 (m-30) REVERT: m 240 VAL cc_start: 0.9601 (OUTLIER) cc_final: 0.9233 (t) REVERT: n 13 VAL cc_start: 0.9603 (t) cc_final: 0.9356 (p) REVERT: n 60 SER cc_start: 0.9449 (m) cc_final: 0.9087 (p) REVERT: n 129 GLU cc_start: 0.8587 (tp30) cc_final: 0.7753 (tp30) REVERT: n 249 ILE cc_start: 0.9458 (mt) cc_final: 0.9134 (mt) REVERT: o 65 MET cc_start: 0.9046 (mmm) cc_final: 0.8318 (tpp) REVERT: o 87 SER cc_start: 0.9125 (m) cc_final: 0.8217 (p) REVERT: o 101 GLU cc_start: 0.8507 (tp30) cc_final: 0.8276 (tp30) REVERT: o 146 ASP cc_start: 0.7929 (t0) cc_final: 0.7716 (t0) REVERT: o 157 LEU cc_start: 0.8294 (mt) cc_final: 0.8001 (mt) REVERT: o 175 TYR cc_start: 0.9034 (m-80) cc_final: 0.8774 (m-10) REVERT: o 207 MET cc_start: 0.8420 (ptp) cc_final: 0.8034 (ptp) REVERT: o 218 ASP cc_start: 0.8799 (p0) cc_final: 0.8584 (p0) REVERT: o 234 LYS cc_start: 0.7986 (tttt) cc_final: 0.7165 (mttt) REVERT: q 105 ILE cc_start: 0.9037 (mt) cc_final: 0.8517 (tt) REVERT: q 126 ASP cc_start: 0.8440 (m-30) cc_final: 0.8132 (m-30) REVERT: q 171 GLN cc_start: 0.8616 (mt0) cc_final: 0.8178 (mt0) REVERT: r 26 GLN cc_start: 0.7360 (mt0) cc_final: 0.6980 (mt0) REVERT: r 48 ASN cc_start: 0.8849 (t0) cc_final: 0.8625 (t0) REVERT: r 212 TYR cc_start: 0.8441 (t80) cc_final: 0.8237 (t80) REVERT: s 18 ASP cc_start: 0.8265 (t0) cc_final: 0.7970 (t0) REVERT: s 20 GLN cc_start: 0.9083 (mt0) cc_final: 0.8799 (mt0) REVERT: s 74 ASP cc_start: 0.7707 (p0) cc_final: 0.7406 (p0) REVERT: s 234 LYS cc_start: 0.8474 (mtmt) cc_final: 0.7962 (mttp) REVERT: t 28 THR cc_start: 0.9318 (m) cc_final: 0.9075 (p) outliers start: 231 outliers final: 189 residues processed: 1222 average time/residue: 0.5025 time to fit residues: 1009.9851 Evaluate side-chains 1266 residues out of total 3684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 1070 time to evaluate : 3.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 51 ILE Chi-restraints excluded: chain a residue 54 ASP Chi-restraints excluded: chain a residue 66 THR Chi-restraints excluded: chain a residue 68 SER Chi-restraints excluded: chain a residue 71 CYS Chi-restraints excluded: chain a residue 130 THR Chi-restraints excluded: chain a residue 134 THR Chi-restraints excluded: chain a residue 190 SER Chi-restraints excluded: chain a residue 250 THR Chi-restraints excluded: chain a residue 280 ASP Chi-restraints excluded: chain a residue 293 ASP Chi-restraints excluded: chain a residue 295 ILE Chi-restraints excluded: chain a residue 296 THR Chi-restraints excluded: chain b residue 21 SER Chi-restraints excluded: chain b residue 45 SER Chi-restraints excluded: chain b residue 74 THR Chi-restraints excluded: chain b residue 104 SER Chi-restraints excluded: chain b residue 172 ARG Chi-restraints excluded: chain b residue 202 THR Chi-restraints excluded: chain b residue 268 VAL Chi-restraints excluded: chain c residue 7 THR Chi-restraints excluded: chain c residue 10 SER Chi-restraints excluded: chain c residue 17 ASP Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 159 LEU Chi-restraints excluded: chain c residue 184 THR Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain c residue 213 VAL Chi-restraints excluded: chain c residue 239 THR Chi-restraints excluded: chain d residue 60 LEU Chi-restraints excluded: chain e residue 22 THR Chi-restraints excluded: chain e residue 66 THR Chi-restraints excluded: chain e residue 104 ASN Chi-restraints excluded: chain e residue 110 THR Chi-restraints excluded: chain e residue 134 THR Chi-restraints excluded: chain e residue 135 GLU Chi-restraints excluded: chain e residue 163 SER Chi-restraints excluded: chain e residue 175 ASN Chi-restraints excluded: chain e residue 189 MET Chi-restraints excluded: chain e residue 196 ILE Chi-restraints excluded: chain e residue 227 VAL Chi-restraints excluded: chain e residue 237 VAL Chi-restraints excluded: chain e residue 252 VAL Chi-restraints excluded: chain e residue 282 ILE Chi-restraints excluded: chain f residue 37 GLU Chi-restraints excluded: chain f residue 40 THR Chi-restraints excluded: chain f residue 45 SER Chi-restraints excluded: chain f residue 58 VAL Chi-restraints excluded: chain f residue 88 ASP Chi-restraints excluded: chain f residue 140 THR Chi-restraints excluded: chain f residue 146 ILE Chi-restraints excluded: chain f residue 264 ARG Chi-restraints excluded: chain f residue 265 ASN Chi-restraints excluded: chain g residue 43 MET Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain g residue 99 LEU Chi-restraints excluded: chain g residue 107 THR Chi-restraints excluded: chain g residue 112 SER Chi-restraints excluded: chain g residue 132 SER Chi-restraints excluded: chain g residue 190 THR Chi-restraints excluded: chain g residue 198 VAL Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain g residue 203 THR Chi-restraints excluded: chain g residue 207 MET Chi-restraints excluded: chain g residue 224 LEU Chi-restraints excluded: chain g residue 227 THR Chi-restraints excluded: chain h residue 7 THR Chi-restraints excluded: chain h residue 10 THR Chi-restraints excluded: chain h residue 23 SER Chi-restraints excluded: chain h residue 26 ASN Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 51 SER Chi-restraints excluded: chain h residue 55 GLU Chi-restraints excluded: chain h residue 57 VAL Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain i residue 25 THR Chi-restraints excluded: chain i residue 40 THR Chi-restraints excluded: chain i residue 83 THR Chi-restraints excluded: chain i residue 88 THR Chi-restraints excluded: chain i residue 100 PHE Chi-restraints excluded: chain i residue 128 GLU Chi-restraints excluded: chain i residue 132 VAL Chi-restraints excluded: chain i residue 190 SER Chi-restraints excluded: chain i residue 229 ILE Chi-restraints excluded: chain i residue 296 THR Chi-restraints excluded: chain j residue 25 THR Chi-restraints excluded: chain j residue 38 TRP Chi-restraints excluded: chain j residue 40 THR Chi-restraints excluded: chain j residue 45 SER Chi-restraints excluded: chain j residue 50 VAL Chi-restraints excluded: chain j residue 58 VAL Chi-restraints excluded: chain j residue 69 VAL Chi-restraints excluded: chain j residue 84 ASP Chi-restraints excluded: chain j residue 85 CYS Chi-restraints excluded: chain j residue 126 LEU Chi-restraints excluded: chain j residue 181 LEU Chi-restraints excluded: chain j residue 183 SER Chi-restraints excluded: chain j residue 246 GLN Chi-restraints excluded: chain j residue 247 VAL Chi-restraints excluded: chain j residue 264 ARG Chi-restraints excluded: chain k residue 5 MET Chi-restraints excluded: chain k residue 10 SER Chi-restraints excluded: chain k residue 21 SER Chi-restraints excluded: chain k residue 81 ILE Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain k residue 103 LEU Chi-restraints excluded: chain k residue 116 THR Chi-restraints excluded: chain k residue 126 THR Chi-restraints excluded: chain k residue 189 ILE Chi-restraints excluded: chain k residue 199 VAL Chi-restraints excluded: chain k residue 203 THR Chi-restraints excluded: chain k residue 218 ASP Chi-restraints excluded: chain k residue 219 PHE Chi-restraints excluded: chain k residue 223 LEU Chi-restraints excluded: chain k residue 226 ASP Chi-restraints excluded: chain k residue 227 THR Chi-restraints excluded: chain k residue 233 SER Chi-restraints excluded: chain l residue 26 ASN Chi-restraints excluded: chain l residue 44 GLN Chi-restraints excluded: chain l residue 64 THR Chi-restraints excluded: chain m residue 61 VAL Chi-restraints excluded: chain m residue 63 ASN Chi-restraints excluded: chain m residue 68 SER Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain m residue 83 THR Chi-restraints excluded: chain m residue 84 ILE Chi-restraints excluded: chain m residue 95 GLU Chi-restraints excluded: chain m residue 106 THR Chi-restraints excluded: chain m residue 127 LEU Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 173 SER Chi-restraints excluded: chain m residue 177 SER Chi-restraints excluded: chain m residue 196 ILE Chi-restraints excluded: chain m residue 240 VAL Chi-restraints excluded: chain m residue 272 VAL Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 69 VAL Chi-restraints excluded: chain n residue 74 THR Chi-restraints excluded: chain n residue 84 ASP Chi-restraints excluded: chain n residue 152 GLU Chi-restraints excluded: chain n residue 183 SER Chi-restraints excluded: chain n residue 198 ILE Chi-restraints excluded: chain n residue 217 VAL Chi-restraints excluded: chain n residue 252 THR Chi-restraints excluded: chain n residue 259 GLU Chi-restraints excluded: chain n residue 265 ASN Chi-restraints excluded: chain o residue 30 VAL Chi-restraints excluded: chain o residue 51 THR Chi-restraints excluded: chain o residue 118 LEU Chi-restraints excluded: chain o residue 126 THR Chi-restraints excluded: chain o residue 132 SER Chi-restraints excluded: chain o residue 198 VAL Chi-restraints excluded: chain o residue 199 VAL Chi-restraints excluded: chain o residue 226 ASP Chi-restraints excluded: chain p residue 25 ILE Chi-restraints excluded: chain p residue 32 TYR Chi-restraints excluded: chain p residue 40 SER Chi-restraints excluded: chain p residue 57 VAL Chi-restraints excluded: chain q residue 22 THR Chi-restraints excluded: chain q residue 36 VAL Chi-restraints excluded: chain q residue 47 SER Chi-restraints excluded: chain q residue 62 VAL Chi-restraints excluded: chain q residue 71 CYS Chi-restraints excluded: chain q residue 99 HIS Chi-restraints excluded: chain q residue 100 PHE Chi-restraints excluded: chain q residue 177 SER Chi-restraints excluded: chain q residue 178 ILE Chi-restraints excluded: chain q residue 190 SER Chi-restraints excluded: chain q residue 217 THR Chi-restraints excluded: chain q residue 296 THR Chi-restraints excluded: chain r residue 18 LEU Chi-restraints excluded: chain r residue 32 ILE Chi-restraints excluded: chain r residue 46 GLU Chi-restraints excluded: chain r residue 50 VAL Chi-restraints excluded: chain r residue 51 ASP Chi-restraints excluded: chain r residue 84 ASP Chi-restraints excluded: chain r residue 111 GLN Chi-restraints excluded: chain r residue 131 VAL Chi-restraints excluded: chain r residue 192 VAL Chi-restraints excluded: chain r residue 205 SER Chi-restraints excluded: chain s residue 30 VAL Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain s residue 53 ILE Chi-restraints excluded: chain s residue 76 LEU Chi-restraints excluded: chain s residue 86 LEU Chi-restraints excluded: chain s residue 97 THR Chi-restraints excluded: chain s residue 103 LEU Chi-restraints excluded: chain s residue 159 LEU Chi-restraints excluded: chain s residue 173 THR Chi-restraints excluded: chain s residue 182 ASP Chi-restraints excluded: chain s residue 189 ILE Chi-restraints excluded: chain s residue 195 THR Chi-restraints excluded: chain s residue 205 THR Chi-restraints excluded: chain t residue 7 THR Chi-restraints excluded: chain t residue 44 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 258 optimal weight: 9.9990 chunk 166 optimal weight: 6.9990 chunk 249 optimal weight: 9.9990 chunk 125 optimal weight: 20.0000 chunk 82 optimal weight: 10.0000 chunk 80 optimal weight: 0.6980 chunk 265 optimal weight: 9.9990 chunk 284 optimal weight: 10.0000 chunk 206 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 chunk 328 optimal weight: 10.0000 overall best weight: 7.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 48 ASN b 111 GLN e 230 ASN f 265 ASN h 21 ASN ** i 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 30 ASN j 196 GLN ** l 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 26 ASN ** m 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 26 ASN q 18 GLN ** r 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 4 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.5065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 34975 Z= 0.460 Angle : 0.714 11.174 47711 Z= 0.363 Chirality : 0.049 0.321 5363 Planarity : 0.005 0.082 6193 Dihedral : 6.042 56.983 4860 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 6.60 % Allowed : 19.92 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.80 (0.12), residues: 4201 helix: -2.02 (0.24), residues: 361 sheet: 0.33 (0.15), residues: 1070 loop : -0.67 (0.11), residues: 2770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP f 227 HIS 0.010 0.002 HIS j 109 PHE 0.047 0.002 PHE k 19 TYR 0.033 0.002 TYR i 154 ARG 0.015 0.001 ARG f 264 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1321 residues out of total 3684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 243 poor density : 1078 time to evaluate : 3.861 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 TARDY: cannot create tardy model for: "GLN n 272 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLN r 272 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: a 54 ASP cc_start: 0.8856 (OUTLIER) cc_final: 0.8324 (m-30) REVERT: a 105 ILE cc_start: 0.9560 (mt) cc_final: 0.8999 (tt) REVERT: a 169 THR cc_start: 0.9216 (p) cc_final: 0.8776 (t) REVERT: b 33 VAL cc_start: 0.9533 (t) cc_final: 0.9252 (m) REVERT: b 104 SER cc_start: 0.9359 (OUTLIER) cc_final: 0.9095 (p) REVERT: b 172 ARG cc_start: 0.7145 (OUTLIER) cc_final: 0.6561 (mtt90) REVERT: b 183 SER cc_start: 0.9307 (p) cc_final: 0.8956 (t) REVERT: c 56 ASN cc_start: 0.9540 (t0) cc_final: 0.9303 (t0) REVERT: c 101 GLU cc_start: 0.8570 (mm-30) cc_final: 0.7855 (mm-30) REVERT: c 177 ARG cc_start: 0.8985 (OUTLIER) cc_final: 0.8179 (mpt-90) REVERT: d 21 ASN cc_start: 0.7897 (p0) cc_final: 0.6995 (p0) REVERT: e 182 TYR cc_start: 0.8910 (t80) cc_final: 0.8521 (t80) REVERT: e 204 TYR cc_start: 0.8655 (t80) cc_final: 0.7955 (t80) REVERT: e 205 ASP cc_start: 0.8801 (t0) cc_final: 0.8438 (t70) REVERT: e 221 ASP cc_start: 0.7178 (p0) cc_final: 0.6933 (p0) REVERT: f 23 ILE cc_start: 0.9314 (mt) cc_final: 0.9057 (mm) REVERT: f 91 MET cc_start: 0.8259 (mmm) cc_final: 0.7991 (tpp) REVERT: f 103 ARG cc_start: 0.9036 (ttt-90) cc_final: 0.8688 (ttt-90) REVERT: f 116 LYS cc_start: 0.9203 (mttt) cc_final: 0.8821 (mttp) REVERT: g 55 MET cc_start: 0.8804 (mmm) cc_final: 0.8461 (tpp) REVERT: g 99 LEU cc_start: 0.9461 (OUTLIER) cc_final: 0.9034 (tt) REVERT: g 154 ILE cc_start: 0.9339 (mm) cc_final: 0.8908 (mm) REVERT: g 173 THR cc_start: 0.9026 (p) cc_final: 0.8817 (p) REVERT: g 194 GLN cc_start: 0.9038 (tp40) cc_final: 0.8654 (tp40) REVERT: g 216 CYS cc_start: 0.8889 (m) cc_final: 0.8541 (m) REVERT: g 218 ASP cc_start: 0.8598 (p0) cc_final: 0.8203 (p0) REVERT: g 225 ARG cc_start: 0.8406 (ptt90) cc_final: 0.8155 (ptt90) REVERT: h 36 SER cc_start: 0.8981 (p) cc_final: 0.8535 (t) REVERT: i 95 GLU cc_start: 0.7214 (tt0) cc_final: 0.6965 (tt0) REVERT: i 98 LYS cc_start: 0.9084 (mttt) cc_final: 0.8812 (mtpp) REVERT: i 166 ASP cc_start: 0.8159 (p0) cc_final: 0.7169 (p0) REVERT: i 204 TYR cc_start: 0.8509 (t80) cc_final: 0.7472 (t80) REVERT: i 205 ASP cc_start: 0.8260 (t70) cc_final: 0.7993 (t0) REVERT: j 129 GLU cc_start: 0.8605 (mm-30) cc_final: 0.7828 (mm-30) REVERT: j 223 LYS cc_start: 0.9369 (mtmt) cc_final: 0.9104 (mtmm) REVERT: j 264 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.7921 (ptt90) REVERT: k 39 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8093 (tm-30) REVERT: k 52 LEU cc_start: 0.9447 (tp) cc_final: 0.9168 (mp) REVERT: k 67 MET cc_start: 0.9029 (ptp) cc_final: 0.8815 (ptp) REVERT: k 87 SER cc_start: 0.9193 (t) cc_final: 0.8961 (p) REVERT: k 128 LYS cc_start: 0.8278 (mttm) cc_final: 0.7906 (mtmt) REVERT: k 155 TRP cc_start: 0.8611 (t60) cc_final: 0.8025 (t60) REVERT: k 178 CYS cc_start: 0.8479 (m) cc_final: 0.7834 (m) REVERT: k 194 GLN cc_start: 0.9035 (tp40) cc_final: 0.8826 (mm-40) REVERT: l 53 PHE cc_start: 0.9086 (m-80) cc_final: 0.8880 (m-80) REVERT: m 105 ILE cc_start: 0.9345 (mt) cc_final: 0.9118 (mt) REVERT: m 166 ASP cc_start: 0.8531 (p0) cc_final: 0.7725 (p0) REVERT: m 216 ASN cc_start: 0.7776 (t0) cc_final: 0.6783 (m-40) REVERT: m 218 ASP cc_start: 0.8242 (m-30) cc_final: 0.7605 (m-30) REVERT: m 240 VAL cc_start: 0.9615 (OUTLIER) cc_final: 0.9254 (t) REVERT: n 13 VAL cc_start: 0.9623 (t) cc_final: 0.9378 (p) REVERT: n 60 SER cc_start: 0.9447 (m) cc_final: 0.9097 (p) REVERT: n 249 ILE cc_start: 0.9471 (mt) cc_final: 0.9134 (mt) REVERT: o 43 MET cc_start: 0.8443 (ttm) cc_final: 0.8157 (ttm) REVERT: o 101 GLU cc_start: 0.8510 (tp30) cc_final: 0.8284 (tp30) REVERT: o 146 ASP cc_start: 0.7963 (OUTLIER) cc_final: 0.7693 (t0) REVERT: o 157 LEU cc_start: 0.8304 (mt) cc_final: 0.7974 (mt) REVERT: o 207 MET cc_start: 0.8477 (ptp) cc_final: 0.8104 (ptp) REVERT: o 218 ASP cc_start: 0.8796 (p0) cc_final: 0.8551 (p0) REVERT: o 234 LYS cc_start: 0.8097 (tttt) cc_final: 0.7242 (mttt) REVERT: q 105 ILE cc_start: 0.9025 (mt) cc_final: 0.8524 (tt) REVERT: q 126 ASP cc_start: 0.8472 (m-30) cc_final: 0.8169 (m-30) REVERT: q 171 GLN cc_start: 0.8656 (mt0) cc_final: 0.8220 (mt0) REVERT: r 26 GLN cc_start: 0.7373 (mt0) cc_final: 0.6974 (mt0) REVERT: r 48 ASN cc_start: 0.8904 (t0) cc_final: 0.8580 (t0) REVERT: r 170 GLU cc_start: 0.5470 (tp30) cc_final: 0.5069 (tp30) REVERT: s 18 ASP cc_start: 0.8206 (t0) cc_final: 0.7964 (t0) REVERT: s 20 GLN cc_start: 0.9138 (mt0) cc_final: 0.8854 (mt0) REVERT: s 74 ASP cc_start: 0.7771 (p0) cc_final: 0.7479 (p0) REVERT: s 146 ASP cc_start: 0.8335 (m-30) cc_final: 0.8120 (m-30) REVERT: s 154 ILE cc_start: 0.8960 (mt) cc_final: 0.8521 (pt) REVERT: s 234 LYS cc_start: 0.8507 (mtmt) cc_final: 0.8052 (mttp) REVERT: t 28 THR cc_start: 0.9327 (m) cc_final: 0.9068 (p) outliers start: 243 outliers final: 209 residues processed: 1198 average time/residue: 0.4740 time to fit residues: 915.2574 Evaluate side-chains 1265 residues out of total 3684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 1048 time to evaluate : 3.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 51 ILE Chi-restraints excluded: chain a residue 54 ASP Chi-restraints excluded: chain a residue 66 THR Chi-restraints excluded: chain a residue 68 SER Chi-restraints excluded: chain a residue 71 CYS Chi-restraints excluded: chain a residue 130 THR Chi-restraints excluded: chain a residue 134 THR Chi-restraints excluded: chain a residue 190 SER Chi-restraints excluded: chain a residue 250 THR Chi-restraints excluded: chain a residue 280 ASP Chi-restraints excluded: chain a residue 293 ASP Chi-restraints excluded: chain a residue 295 ILE Chi-restraints excluded: chain a residue 296 THR Chi-restraints excluded: chain b residue 11 ASP Chi-restraints excluded: chain b residue 21 SER Chi-restraints excluded: chain b residue 26 GLN Chi-restraints excluded: chain b residue 45 SER Chi-restraints excluded: chain b residue 74 THR Chi-restraints excluded: chain b residue 104 SER Chi-restraints excluded: chain b residue 172 ARG Chi-restraints excluded: chain b residue 202 THR Chi-restraints excluded: chain b residue 234 LEU Chi-restraints excluded: chain b residue 268 VAL Chi-restraints excluded: chain c residue 7 THR Chi-restraints excluded: chain c residue 10 SER Chi-restraints excluded: chain c residue 12 GLN Chi-restraints excluded: chain c residue 17 ASP Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 159 LEU Chi-restraints excluded: chain c residue 177 ARG Chi-restraints excluded: chain c residue 184 THR Chi-restraints excluded: chain c residue 198 VAL Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain c residue 213 VAL Chi-restraints excluded: chain c residue 239 THR Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain d residue 60 LEU Chi-restraints excluded: chain e residue 22 THR Chi-restraints excluded: chain e residue 51 ILE Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 66 THR Chi-restraints excluded: chain e residue 104 ASN Chi-restraints excluded: chain e residue 110 THR Chi-restraints excluded: chain e residue 134 THR Chi-restraints excluded: chain e residue 135 GLU Chi-restraints excluded: chain e residue 163 SER Chi-restraints excluded: chain e residue 175 ASN Chi-restraints excluded: chain e residue 189 MET Chi-restraints excluded: chain e residue 196 ILE Chi-restraints excluded: chain e residue 227 VAL Chi-restraints excluded: chain e residue 237 VAL Chi-restraints excluded: chain e residue 252 VAL Chi-restraints excluded: chain e residue 282 ILE Chi-restraints excluded: chain f residue 37 GLU Chi-restraints excluded: chain f residue 40 THR Chi-restraints excluded: chain f residue 45 SER Chi-restraints excluded: chain f residue 58 VAL Chi-restraints excluded: chain f residue 88 ASP Chi-restraints excluded: chain f residue 146 ILE Chi-restraints excluded: chain g residue 43 MET Chi-restraints excluded: chain g residue 67 MET Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain g residue 99 LEU Chi-restraints excluded: chain g residue 107 THR Chi-restraints excluded: chain g residue 112 SER Chi-restraints excluded: chain g residue 132 SER Chi-restraints excluded: chain g residue 153 ILE Chi-restraints excluded: chain g residue 190 THR Chi-restraints excluded: chain g residue 198 VAL Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain g residue 203 THR Chi-restraints excluded: chain g residue 205 THR Chi-restraints excluded: chain g residue 207 MET Chi-restraints excluded: chain g residue 224 LEU Chi-restraints excluded: chain g residue 227 THR Chi-restraints excluded: chain h residue 7 THR Chi-restraints excluded: chain h residue 10 THR Chi-restraints excluded: chain h residue 23 SER Chi-restraints excluded: chain h residue 26 ASN Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 40 SER Chi-restraints excluded: chain h residue 51 SER Chi-restraints excluded: chain h residue 55 GLU Chi-restraints excluded: chain h residue 57 VAL Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain i residue 25 THR Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 40 THR Chi-restraints excluded: chain i residue 54 ASP Chi-restraints excluded: chain i residue 84 ILE Chi-restraints excluded: chain i residue 88 THR Chi-restraints excluded: chain i residue 100 PHE Chi-restraints excluded: chain i residue 128 GLU Chi-restraints excluded: chain i residue 132 VAL Chi-restraints excluded: chain i residue 190 SER Chi-restraints excluded: chain i residue 229 ILE Chi-restraints excluded: chain i residue 296 THR Chi-restraints excluded: chain j residue 25 THR Chi-restraints excluded: chain j residue 38 TRP Chi-restraints excluded: chain j residue 40 THR Chi-restraints excluded: chain j residue 45 SER Chi-restraints excluded: chain j residue 58 VAL Chi-restraints excluded: chain j residue 67 GLU Chi-restraints excluded: chain j residue 69 VAL Chi-restraints excluded: chain j residue 84 ASP Chi-restraints excluded: chain j residue 85 CYS Chi-restraints excluded: chain j residue 126 LEU Chi-restraints excluded: chain j residue 181 LEU Chi-restraints excluded: chain j residue 183 SER Chi-restraints excluded: chain j residue 246 GLN Chi-restraints excluded: chain j residue 247 VAL Chi-restraints excluded: chain j residue 264 ARG Chi-restraints excluded: chain k residue 5 MET Chi-restraints excluded: chain k residue 10 SER Chi-restraints excluded: chain k residue 21 SER Chi-restraints excluded: chain k residue 76 LEU Chi-restraints excluded: chain k residue 81 ILE Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain k residue 103 LEU Chi-restraints excluded: chain k residue 116 THR Chi-restraints excluded: chain k residue 126 THR Chi-restraints excluded: chain k residue 189 ILE Chi-restraints excluded: chain k residue 199 VAL Chi-restraints excluded: chain k residue 203 THR Chi-restraints excluded: chain k residue 218 ASP Chi-restraints excluded: chain k residue 219 PHE Chi-restraints excluded: chain k residue 223 LEU Chi-restraints excluded: chain k residue 227 THR Chi-restraints excluded: chain k residue 233 SER Chi-restraints excluded: chain l residue 44 GLN Chi-restraints excluded: chain l residue 64 THR Chi-restraints excluded: chain m residue 61 VAL Chi-restraints excluded: chain m residue 63 ASN Chi-restraints excluded: chain m residue 68 SER Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain m residue 83 THR Chi-restraints excluded: chain m residue 84 ILE Chi-restraints excluded: chain m residue 95 GLU Chi-restraints excluded: chain m residue 106 THR Chi-restraints excluded: chain m residue 110 THR Chi-restraints excluded: chain m residue 127 LEU Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 173 SER Chi-restraints excluded: chain m residue 177 SER Chi-restraints excluded: chain m residue 196 ILE Chi-restraints excluded: chain m residue 198 ASN Chi-restraints excluded: chain m residue 240 VAL Chi-restraints excluded: chain m residue 272 VAL Chi-restraints excluded: chain n residue 45 SER Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 69 VAL Chi-restraints excluded: chain n residue 74 THR Chi-restraints excluded: chain n residue 84 ASP Chi-restraints excluded: chain n residue 152 GLU Chi-restraints excluded: chain n residue 183 SER Chi-restraints excluded: chain n residue 198 ILE Chi-restraints excluded: chain n residue 252 THR Chi-restraints excluded: chain n residue 259 GLU Chi-restraints excluded: chain n residue 265 ASN Chi-restraints excluded: chain o residue 27 ASN Chi-restraints excluded: chain o residue 30 VAL Chi-restraints excluded: chain o residue 51 THR Chi-restraints excluded: chain o residue 118 LEU Chi-restraints excluded: chain o residue 126 THR Chi-restraints excluded: chain o residue 132 SER Chi-restraints excluded: chain o residue 146 ASP Chi-restraints excluded: chain o residue 153 ILE Chi-restraints excluded: chain o residue 198 VAL Chi-restraints excluded: chain o residue 199 VAL Chi-restraints excluded: chain o residue 226 ASP Chi-restraints excluded: chain p residue 25 ILE Chi-restraints excluded: chain p residue 40 SER Chi-restraints excluded: chain p residue 57 VAL Chi-restraints excluded: chain q residue 22 THR Chi-restraints excluded: chain q residue 36 VAL Chi-restraints excluded: chain q residue 99 HIS Chi-restraints excluded: chain q residue 100 PHE Chi-restraints excluded: chain q residue 177 SER Chi-restraints excluded: chain q residue 178 ILE Chi-restraints excluded: chain q residue 190 SER Chi-restraints excluded: chain q residue 217 THR Chi-restraints excluded: chain q residue 248 ILE Chi-restraints excluded: chain q residue 296 THR Chi-restraints excluded: chain r residue 18 LEU Chi-restraints excluded: chain r residue 24 THR Chi-restraints excluded: chain r residue 32 ILE Chi-restraints excluded: chain r residue 40 THR Chi-restraints excluded: chain r residue 46 GLU Chi-restraints excluded: chain r residue 50 VAL Chi-restraints excluded: chain r residue 51 ASP Chi-restraints excluded: chain r residue 84 ASP Chi-restraints excluded: chain r residue 111 GLN Chi-restraints excluded: chain r residue 131 VAL Chi-restraints excluded: chain r residue 185 VAL Chi-restraints excluded: chain r residue 192 VAL Chi-restraints excluded: chain r residue 205 SER Chi-restraints excluded: chain r residue 224 HIS Chi-restraints excluded: chain r residue 252 THR Chi-restraints excluded: chain s residue 10 SER Chi-restraints excluded: chain s residue 30 VAL Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain s residue 53 ILE Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain s residue 76 LEU Chi-restraints excluded: chain s residue 85 SER Chi-restraints excluded: chain s residue 86 LEU Chi-restraints excluded: chain s residue 97 THR Chi-restraints excluded: chain s residue 103 LEU Chi-restraints excluded: chain s residue 159 LEU Chi-restraints excluded: chain s residue 173 THR Chi-restraints excluded: chain s residue 182 ASP Chi-restraints excluded: chain s residue 189 ILE Chi-restraints excluded: chain s residue 195 THR Chi-restraints excluded: chain s residue 205 THR Chi-restraints excluded: chain t residue 7 THR Chi-restraints excluded: chain t residue 44 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 379 optimal weight: 20.0000 chunk 399 optimal weight: 0.9990 chunk 364 optimal weight: 4.9990 chunk 388 optimal weight: 6.9990 chunk 234 optimal weight: 9.9990 chunk 169 optimal weight: 9.9990 chunk 305 optimal weight: 8.9990 chunk 119 optimal weight: 6.9990 chunk 351 optimal weight: 3.9990 chunk 367 optimal weight: 7.9990 chunk 387 optimal weight: 1.9990 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 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 151 GLN e 230 ASN ** f 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 21 ASN ** i 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 265 ASN ** l 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 26 ASN ** n 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 12 GLN ** s 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.5169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 34975 Z= 0.293 Angle : 0.656 11.450 47711 Z= 0.330 Chirality : 0.047 0.323 5363 Planarity : 0.004 0.050 6193 Dihedral : 5.938 58.275 4860 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 5.65 % Allowed : 21.17 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.73 (0.12), residues: 4201 helix: -1.87 (0.25), residues: 355 sheet: 0.32 (0.15), residues: 1092 loop : -0.61 (0.12), residues: 2754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP n 71 HIS 0.009 0.001 HIS j 109 PHE 0.042 0.002 PHE k 19 TYR 0.027 0.002 TYR i 154 ARG 0.010 0.001 ARG f 264 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1309 residues out of total 3684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 1101 time to evaluate : 4.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN n 272 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN r 272 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: a 54 ASP cc_start: 0.8848 (OUTLIER) cc_final: 0.8269 (m-30) REVERT: a 105 ILE cc_start: 0.9530 (mt) cc_final: 0.8958 (tt) REVERT: a 169 THR cc_start: 0.9182 (p) cc_final: 0.8745 (t) REVERT: b 33 VAL cc_start: 0.9554 (t) cc_final: 0.9265 (m) REVERT: b 84 ASP cc_start: 0.8279 (t0) cc_final: 0.8014 (t0) REVERT: b 183 SER cc_start: 0.9254 (p) cc_final: 0.8913 (t) REVERT: b 227 TRP cc_start: 0.9136 (m100) cc_final: 0.8906 (m100) REVERT: c 76 LEU cc_start: 0.8487 (tp) cc_final: 0.8257 (tp) REVERT: c 177 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8154 (mpt-90) REVERT: d 21 ASN cc_start: 0.7800 (p0) cc_final: 0.6866 (p0) REVERT: e 182 TYR cc_start: 0.8855 (t80) cc_final: 0.8417 (t80) REVERT: e 204 TYR cc_start: 0.8651 (t80) cc_final: 0.7950 (t80) REVERT: e 205 ASP cc_start: 0.8989 (t0) cc_final: 0.8419 (t70) REVERT: e 221 ASP cc_start: 0.7124 (p0) cc_final: 0.6849 (p0) REVERT: f 23 ILE cc_start: 0.9267 (mt) cc_final: 0.9032 (mm) REVERT: f 91 MET cc_start: 0.8205 (mmm) cc_final: 0.7939 (tpp) REVERT: f 101 LEU cc_start: 0.8959 (mt) cc_final: 0.8359 (mp) REVERT: f 116 LYS cc_start: 0.9185 (mttt) cc_final: 0.8834 (mttp) REVERT: f 178 ASP cc_start: 0.8859 (p0) cc_final: 0.8341 (p0) REVERT: f 264 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.8131 (ptt-90) REVERT: g 55 MET cc_start: 0.8728 (mmm) cc_final: 0.8469 (tpp) REVERT: g 99 LEU cc_start: 0.9477 (OUTLIER) cc_final: 0.9090 (tt) REVERT: g 154 ILE cc_start: 0.9317 (mm) cc_final: 0.8963 (mm) REVERT: g 156 ASP cc_start: 0.8383 (t0) cc_final: 0.7862 (p0) REVERT: g 173 THR cc_start: 0.8953 (p) cc_final: 0.8748 (p) REVERT: g 177 ARG cc_start: 0.9053 (ttm110) cc_final: 0.8586 (mtm110) REVERT: g 216 CYS cc_start: 0.8930 (m) cc_final: 0.8598 (m) REVERT: g 218 ASP cc_start: 0.8576 (p0) cc_final: 0.8168 (p0) REVERT: h 36 SER cc_start: 0.9007 (p) cc_final: 0.8543 (t) REVERT: i 95 GLU cc_start: 0.7278 (tt0) cc_final: 0.7021 (tt0) REVERT: i 98 LYS cc_start: 0.9073 (mttt) cc_final: 0.8802 (mtpp) REVERT: i 166 ASP cc_start: 0.8135 (p0) cc_final: 0.7158 (p0) REVERT: i 205 ASP cc_start: 0.8324 (t70) cc_final: 0.8092 (t0) REVERT: j 196 GLN cc_start: 0.8932 (tt0) cc_final: 0.8729 (mt0) REVERT: j 223 LYS cc_start: 0.9357 (mtmt) cc_final: 0.8805 (mttp) REVERT: j 264 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.7982 (ptt90) REVERT: k 39 GLU cc_start: 0.8400 (tm-30) cc_final: 0.7997 (tm-30) REVERT: k 52 LEU cc_start: 0.9438 (tp) cc_final: 0.9202 (mp) REVERT: k 67 MET cc_start: 0.9055 (ptp) cc_final: 0.8809 (ptp) REVERT: k 87 SER cc_start: 0.9133 (t) cc_final: 0.8911 (p) REVERT: k 148 MET cc_start: 0.4533 (ttt) cc_final: 0.4297 (ttt) REVERT: k 155 TRP cc_start: 0.8592 (t60) cc_final: 0.8029 (t60) REVERT: k 178 CYS cc_start: 0.8443 (m) cc_final: 0.7718 (m) REVERT: k 183 PHE cc_start: 0.7512 (t80) cc_final: 0.7160 (t80) REVERT: k 194 GLN cc_start: 0.9026 (tp40) cc_final: 0.8812 (mm-40) REVERT: l 53 PHE cc_start: 0.9034 (m-80) cc_final: 0.8813 (m-80) REVERT: m 105 ILE cc_start: 0.9349 (mt) cc_final: 0.9077 (mt) REVERT: m 166 ASP cc_start: 0.8550 (p0) cc_final: 0.7565 (p0) REVERT: m 216 ASN cc_start: 0.7722 (t0) cc_final: 0.6718 (m-40) REVERT: m 218 ASP cc_start: 0.8199 (m-30) cc_final: 0.7577 (m-30) REVERT: m 240 VAL cc_start: 0.9575 (OUTLIER) cc_final: 0.9197 (t) REVERT: n 13 VAL cc_start: 0.9611 (t) cc_final: 0.9374 (p) REVERT: n 60 SER cc_start: 0.9401 (m) cc_final: 0.9100 (p) REVERT: n 249 ILE cc_start: 0.9441 (mt) cc_final: 0.9140 (mt) REVERT: o 43 MET cc_start: 0.8489 (ttm) cc_final: 0.8131 (ttm) REVERT: o 65 MET cc_start: 0.9072 (mmm) cc_final: 0.8417 (mmm) REVERT: o 101 GLU cc_start: 0.8450 (tp30) cc_final: 0.8242 (tp30) REVERT: o 157 LEU cc_start: 0.8258 (mt) cc_final: 0.7938 (mt) REVERT: o 207 MET cc_start: 0.8399 (ptp) cc_final: 0.8055 (ptp) REVERT: o 218 ASP cc_start: 0.8786 (p0) cc_final: 0.8530 (p0) REVERT: o 234 LYS cc_start: 0.7978 (tttt) cc_final: 0.7089 (mttt) REVERT: q 85 LEU cc_start: 0.8770 (mt) cc_final: 0.8502 (mt) REVERT: q 105 ILE cc_start: 0.9042 (mt) cc_final: 0.8512 (tt) REVERT: q 126 ASP cc_start: 0.8475 (m-30) cc_final: 0.8033 (m-30) REVERT: q 165 TRP cc_start: 0.8660 (p-90) cc_final: 0.8232 (p-90) REVERT: q 171 GLN cc_start: 0.8617 (mt0) cc_final: 0.8221 (mt0) REVERT: r 26 GLN cc_start: 0.7348 (mt0) cc_final: 0.6953 (mt0) REVERT: r 48 ASN cc_start: 0.8853 (t0) cc_final: 0.8544 (t0) REVERT: r 116 LYS cc_start: 0.7702 (mtmt) cc_final: 0.7478 (mtmm) REVERT: s 18 ASP cc_start: 0.8255 (t0) cc_final: 0.8003 (t0) REVERT: s 20 GLN cc_start: 0.9125 (mt0) cc_final: 0.8818 (mt0) REVERT: s 43 MET cc_start: 0.8539 (ttm) cc_final: 0.8201 (tpp) REVERT: s 74 ASP cc_start: 0.7675 (p0) cc_final: 0.7402 (p0) REVERT: s 176 ARG cc_start: 0.8574 (mtt-85) cc_final: 0.8344 (mtt-85) REVERT: t 28 THR cc_start: 0.9306 (m) cc_final: 0.9081 (p) outliers start: 208 outliers final: 177 residues processed: 1202 average time/residue: 0.4637 time to fit residues: 903.9060 Evaluate side-chains 1242 residues out of total 3684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 1059 time to evaluate : 3.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 51 ILE Chi-restraints excluded: chain a residue 54 ASP Chi-restraints excluded: chain a residue 66 THR Chi-restraints excluded: chain a residue 68 SER Chi-restraints excluded: chain a residue 71 CYS Chi-restraints excluded: chain a residue 134 THR Chi-restraints excluded: chain a residue 190 SER Chi-restraints excluded: chain a residue 198 ASN Chi-restraints excluded: chain a residue 280 ASP Chi-restraints excluded: chain a residue 293 ASP Chi-restraints excluded: chain a residue 295 ILE Chi-restraints excluded: chain a residue 296 THR Chi-restraints excluded: chain b residue 21 SER Chi-restraints excluded: chain b residue 26 GLN Chi-restraints excluded: chain b residue 45 SER Chi-restraints excluded: chain b residue 74 THR Chi-restraints excluded: chain b residue 202 THR Chi-restraints excluded: chain b residue 234 LEU Chi-restraints excluded: chain b residue 242 THR Chi-restraints excluded: chain b residue 268 VAL Chi-restraints excluded: chain c residue 7 THR Chi-restraints excluded: chain c residue 10 SER Chi-restraints excluded: chain c residue 74 ASP Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 159 LEU Chi-restraints excluded: chain c residue 177 ARG Chi-restraints excluded: chain c residue 184 THR Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain c residue 213 VAL Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain d residue 60 LEU Chi-restraints excluded: chain e residue 51 ILE Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 66 THR Chi-restraints excluded: chain e residue 104 ASN Chi-restraints excluded: chain e residue 110 THR Chi-restraints excluded: chain e residue 135 GLU Chi-restraints excluded: chain e residue 163 SER Chi-restraints excluded: chain e residue 175 ASN Chi-restraints excluded: chain e residue 189 MET Chi-restraints excluded: chain e residue 196 ILE Chi-restraints excluded: chain e residue 227 VAL Chi-restraints excluded: chain e residue 237 VAL Chi-restraints excluded: chain e residue 282 ILE Chi-restraints excluded: chain e residue 293 ASP Chi-restraints excluded: chain f residue 37 GLU Chi-restraints excluded: chain f residue 40 THR Chi-restraints excluded: chain f residue 45 SER Chi-restraints excluded: chain f residue 88 ASP Chi-restraints excluded: chain f residue 140 THR Chi-restraints excluded: chain f residue 146 ILE Chi-restraints excluded: chain f residue 264 ARG Chi-restraints excluded: chain g residue 67 MET Chi-restraints excluded: chain g residue 99 LEU Chi-restraints excluded: chain g residue 107 THR Chi-restraints excluded: chain g residue 112 SER Chi-restraints excluded: chain g residue 132 SER Chi-restraints excluded: chain g residue 190 THR Chi-restraints excluded: chain g residue 198 VAL Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain g residue 203 THR Chi-restraints excluded: chain g residue 205 THR Chi-restraints excluded: chain g residue 207 MET Chi-restraints excluded: chain g residue 224 LEU Chi-restraints excluded: chain g residue 227 THR Chi-restraints excluded: chain h residue 7 THR Chi-restraints excluded: chain h residue 10 THR Chi-restraints excluded: chain h residue 15 ASN Chi-restraints excluded: chain h residue 23 SER Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 40 SER Chi-restraints excluded: chain h residue 57 VAL Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain i residue 25 THR Chi-restraints excluded: chain i residue 40 THR Chi-restraints excluded: chain i residue 54 ASP Chi-restraints excluded: chain i residue 88 THR Chi-restraints excluded: chain i residue 100 PHE Chi-restraints excluded: chain i residue 128 GLU Chi-restraints excluded: chain i residue 132 VAL Chi-restraints excluded: chain i residue 229 ILE Chi-restraints excluded: chain j residue 25 THR Chi-restraints excluded: chain j residue 38 TRP Chi-restraints excluded: chain j residue 40 THR Chi-restraints excluded: chain j residue 45 SER Chi-restraints excluded: chain j residue 58 VAL Chi-restraints excluded: chain j residue 84 ASP Chi-restraints excluded: chain j residue 85 CYS Chi-restraints excluded: chain j residue 126 LEU Chi-restraints excluded: chain j residue 181 LEU Chi-restraints excluded: chain j residue 183 SER Chi-restraints excluded: chain j residue 246 GLN Chi-restraints excluded: chain j residue 247 VAL Chi-restraints excluded: chain j residue 264 ARG Chi-restraints excluded: chain k residue 5 MET Chi-restraints excluded: chain k residue 10 SER Chi-restraints excluded: chain k residue 21 SER Chi-restraints excluded: chain k residue 81 ILE Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain k residue 103 LEU Chi-restraints excluded: chain k residue 116 THR Chi-restraints excluded: chain k residue 126 THR Chi-restraints excluded: chain k residue 199 VAL Chi-restraints excluded: chain k residue 203 THR Chi-restraints excluded: chain k residue 218 ASP Chi-restraints excluded: chain k residue 219 PHE Chi-restraints excluded: chain k residue 223 LEU Chi-restraints excluded: chain k residue 227 THR Chi-restraints excluded: chain k residue 233 SER Chi-restraints excluded: chain l residue 64 THR Chi-restraints excluded: chain m residue 61 VAL Chi-restraints excluded: chain m residue 63 ASN Chi-restraints excluded: chain m residue 68 SER Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain m residue 83 THR Chi-restraints excluded: chain m residue 84 ILE Chi-restraints excluded: chain m residue 95 GLU Chi-restraints excluded: chain m residue 106 THR Chi-restraints excluded: chain m residue 127 LEU Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 173 SER Chi-restraints excluded: chain m residue 177 SER Chi-restraints excluded: chain m residue 181 MET Chi-restraints excluded: chain m residue 196 ILE Chi-restraints excluded: chain m residue 240 VAL Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 69 VAL Chi-restraints excluded: chain n residue 84 ASP Chi-restraints excluded: chain n residue 126 LEU Chi-restraints excluded: chain n residue 152 GLU Chi-restraints excluded: chain n residue 183 SER Chi-restraints excluded: chain n residue 198 ILE Chi-restraints excluded: chain n residue 252 THR Chi-restraints excluded: chain n residue 265 ASN Chi-restraints excluded: chain o residue 30 VAL Chi-restraints excluded: chain o residue 126 THR Chi-restraints excluded: chain o residue 132 SER Chi-restraints excluded: chain o residue 153 ILE Chi-restraints excluded: chain o residue 198 VAL Chi-restraints excluded: chain o residue 199 VAL Chi-restraints excluded: chain o residue 226 ASP Chi-restraints excluded: chain p residue 25 ILE Chi-restraints excluded: chain p residue 32 TYR Chi-restraints excluded: chain p residue 57 VAL Chi-restraints excluded: chain q residue 22 THR Chi-restraints excluded: chain q residue 36 VAL Chi-restraints excluded: chain q residue 100 PHE Chi-restraints excluded: chain q residue 175 ASN Chi-restraints excluded: chain q residue 177 SER Chi-restraints excluded: chain q residue 178 ILE Chi-restraints excluded: chain q residue 190 SER Chi-restraints excluded: chain q residue 217 THR Chi-restraints excluded: chain q residue 248 ILE Chi-restraints excluded: chain q residue 296 THR Chi-restraints excluded: chain r residue 18 LEU Chi-restraints excluded: chain r residue 24 THR Chi-restraints excluded: chain r residue 32 ILE Chi-restraints excluded: chain r residue 40 THR Chi-restraints excluded: chain r residue 46 GLU Chi-restraints excluded: chain r residue 51 ASP Chi-restraints excluded: chain r residue 84 ASP Chi-restraints excluded: chain r residue 111 GLN Chi-restraints excluded: chain r residue 131 VAL Chi-restraints excluded: chain r residue 173 LYS Chi-restraints excluded: chain r residue 185 VAL Chi-restraints excluded: chain r residue 205 SER Chi-restraints excluded: chain r residue 252 THR Chi-restraints excluded: chain s residue 4 THR Chi-restraints excluded: chain s residue 10 SER Chi-restraints excluded: chain s residue 12 GLN Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain s residue 53 ILE Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain s residue 76 LEU Chi-restraints excluded: chain s residue 86 LEU Chi-restraints excluded: chain s residue 97 THR Chi-restraints excluded: chain s residue 103 LEU Chi-restraints excluded: chain s residue 173 THR Chi-restraints excluded: chain s residue 182 ASP Chi-restraints excluded: chain s residue 189 ILE Chi-restraints excluded: chain s residue 205 THR Chi-restraints excluded: chain t residue 7 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 255 optimal weight: 0.9980 chunk 411 optimal weight: 8.9990 chunk 251 optimal weight: 9.9990 chunk 195 optimal weight: 7.9990 chunk 285 optimal weight: 10.0000 chunk 431 optimal weight: 20.0000 chunk 397 optimal weight: 8.9990 chunk 343 optimal weight: 0.1980 chunk 35 optimal weight: 0.5980 chunk 265 optimal weight: 7.9990 chunk 210 optimal weight: 6.9990 overall best weight: 3.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 56 ASN e 230 ASN ** f 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 21 ASN ** i 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 26 ASN ** r 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 12 GLN ** s 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.5261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 34975 Z= 0.267 Angle : 0.660 15.938 47711 Z= 0.329 Chirality : 0.047 0.341 5363 Planarity : 0.004 0.050 6193 Dihedral : 5.825 59.058 4860 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.99 % Allowed : 21.96 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.68 (0.13), residues: 4201 helix: -1.76 (0.25), residues: 355 sheet: 0.33 (0.15), residues: 1102 loop : -0.59 (0.12), residues: 2744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP n 71 HIS 0.009 0.001 HIS j 109 PHE 0.039 0.002 PHE k 19 TYR 0.045 0.002 TYR o 175 ARG 0.010 0.001 ARG f 264 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1306 residues out of total 3684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 1122 time to evaluate : 3.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN n 272 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN r 272 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: a 54 ASP cc_start: 0.8827 (OUTLIER) cc_final: 0.8234 (m-30) REVERT: a 105 ILE cc_start: 0.9522 (mt) cc_final: 0.8948 (tt) REVERT: a 169 THR cc_start: 0.9177 (p) cc_final: 0.8735 (t) REVERT: b 33 VAL cc_start: 0.9567 (t) cc_final: 0.9265 (m) REVERT: b 111 GLN cc_start: 0.8434 (mp10) cc_final: 0.8229 (mp10) REVERT: b 183 SER cc_start: 0.9216 (p) cc_final: 0.8950 (t) REVERT: b 227 TRP cc_start: 0.9092 (m100) cc_final: 0.8872 (m100) REVERT: c 177 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.8196 (mpt-90) REVERT: d 21 ASN cc_start: 0.7774 (p0) cc_final: 0.7233 (p0) REVERT: e 182 TYR cc_start: 0.8765 (t80) cc_final: 0.8364 (t80) REVERT: e 204 TYR cc_start: 0.8628 (t80) cc_final: 0.7924 (t80) REVERT: e 205 ASP cc_start: 0.9009 (t0) cc_final: 0.8432 (t70) REVERT: e 221 ASP cc_start: 0.7129 (p0) cc_final: 0.6866 (p0) REVERT: f 23 ILE cc_start: 0.9251 (mt) cc_final: 0.9011 (mm) REVERT: f 91 MET cc_start: 0.8221 (mmm) cc_final: 0.7952 (tpp) REVERT: f 101 LEU cc_start: 0.8921 (mt) cc_final: 0.8333 (mp) REVERT: f 116 LYS cc_start: 0.9180 (mttt) cc_final: 0.8835 (mttp) REVERT: f 178 ASP cc_start: 0.8830 (p0) cc_final: 0.8310 (p0) REVERT: f 225 ASN cc_start: 0.8506 (m-40) cc_final: 0.7973 (m-40) REVERT: f 264 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.8080 (ptt-90) REVERT: g 99 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9105 (tt) REVERT: g 112 SER cc_start: 0.9068 (OUTLIER) cc_final: 0.8155 (p) REVERT: g 154 ILE cc_start: 0.9306 (mm) cc_final: 0.8957 (mm) REVERT: g 156 ASP cc_start: 0.8375 (t0) cc_final: 0.7849 (p0) REVERT: g 177 ARG cc_start: 0.9046 (ttm110) cc_final: 0.8525 (mtm110) REVERT: g 216 CYS cc_start: 0.8894 (m) cc_final: 0.7711 (m) REVERT: g 218 ASP cc_start: 0.8521 (p0) cc_final: 0.8073 (p0) REVERT: h 36 SER cc_start: 0.9087 (p) cc_final: 0.8534 (t) REVERT: i 95 GLU cc_start: 0.7296 (tt0) cc_final: 0.7038 (tt0) REVERT: i 98 LYS cc_start: 0.9060 (mttt) cc_final: 0.8793 (mtpp) REVERT: i 166 ASP cc_start: 0.8132 (p0) cc_final: 0.7177 (p0) REVERT: j 129 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8017 (mm-30) REVERT: j 196 GLN cc_start: 0.8941 (tt0) cc_final: 0.8730 (mt0) REVERT: j 223 LYS cc_start: 0.9384 (mtmt) cc_final: 0.8780 (mtmp) REVERT: j 264 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.8011 (ptt90) REVERT: k 17 ASP cc_start: 0.7539 (t0) cc_final: 0.6998 (t0) REVERT: k 39 GLU cc_start: 0.8392 (tm-30) cc_final: 0.7963 (tm-30) REVERT: k 52 LEU cc_start: 0.9422 (tp) cc_final: 0.9207 (mp) REVERT: k 67 MET cc_start: 0.9046 (ptp) cc_final: 0.8798 (ptp) REVERT: k 87 SER cc_start: 0.9091 (t) cc_final: 0.8878 (p) REVERT: k 155 TRP cc_start: 0.8556 (t60) cc_final: 0.8027 (t60) REVERT: k 178 CYS cc_start: 0.8420 (m) cc_final: 0.7706 (m) REVERT: k 183 PHE cc_start: 0.7434 (t80) cc_final: 0.7071 (t80) REVERT: l 53 PHE cc_start: 0.8990 (m-80) cc_final: 0.8784 (m-80) REVERT: m 105 ILE cc_start: 0.9332 (mt) cc_final: 0.9040 (mt) REVERT: m 122 TYR cc_start: 0.8878 (m-80) cc_final: 0.8223 (m-80) REVERT: m 166 ASP cc_start: 0.8564 (p0) cc_final: 0.7577 (p0) REVERT: m 216 ASN cc_start: 0.7775 (t0) cc_final: 0.6745 (m-40) REVERT: m 218 ASP cc_start: 0.8217 (m-30) cc_final: 0.7582 (m-30) REVERT: m 240 VAL cc_start: 0.9575 (OUTLIER) cc_final: 0.9214 (t) REVERT: n 13 VAL cc_start: 0.9603 (t) cc_final: 0.9363 (p) REVERT: n 60 SER cc_start: 0.9286 (m) cc_final: 0.9076 (p) REVERT: n 129 GLU cc_start: 0.8441 (tp30) cc_final: 0.7584 (tp30) REVERT: n 249 ILE cc_start: 0.9431 (mt) cc_final: 0.9139 (mt) REVERT: o 43 MET cc_start: 0.8555 (ttm) cc_final: 0.8264 (ttm) REVERT: o 52 LEU cc_start: 0.9353 (tp) cc_final: 0.9060 (mp) REVERT: o 65 MET cc_start: 0.9064 (mmm) cc_final: 0.8392 (tpp) REVERT: o 155 TRP cc_start: 0.8852 (t60) cc_final: 0.7856 (t60) REVERT: o 157 LEU cc_start: 0.8248 (mt) cc_final: 0.7928 (mt) REVERT: o 207 MET cc_start: 0.8381 (ptp) cc_final: 0.8009 (ptp) REVERT: o 218 ASP cc_start: 0.8772 (p0) cc_final: 0.8506 (p0) REVERT: o 234 LYS cc_start: 0.7987 (tttt) cc_final: 0.7106 (mttt) REVERT: q 88 THR cc_start: 0.8504 (p) cc_final: 0.8148 (p) REVERT: q 105 ILE cc_start: 0.9029 (mt) cc_final: 0.8489 (tt) REVERT: q 126 ASP cc_start: 0.8432 (m-30) cc_final: 0.8215 (m-30) REVERT: q 165 TRP cc_start: 0.8641 (p-90) cc_final: 0.8141 (p-90) REVERT: q 231 ASP cc_start: 0.7262 (t0) cc_final: 0.6895 (t0) REVERT: r 26 GLN cc_start: 0.7332 (mt0) cc_final: 0.6935 (mt0) REVERT: r 48 ASN cc_start: 0.8731 (t0) cc_final: 0.8465 (t0) REVERT: s 18 ASP cc_start: 0.8254 (t0) cc_final: 0.7976 (t0) REVERT: s 20 GLN cc_start: 0.9110 (mt0) cc_final: 0.8804 (mt0) REVERT: s 154 ILE cc_start: 0.8985 (mt) cc_final: 0.8619 (pt) REVERT: t 28 THR cc_start: 0.9304 (m) cc_final: 0.9102 (p) outliers start: 184 outliers final: 169 residues processed: 1206 average time/residue: 0.4600 time to fit residues: 901.3737 Evaluate side-chains 1257 residues out of total 3684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 1081 time to evaluate : 3.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 51 ILE Chi-restraints excluded: chain a residue 54 ASP Chi-restraints excluded: chain a residue 66 THR Chi-restraints excluded: chain a residue 68 SER Chi-restraints excluded: chain a residue 134 THR Chi-restraints excluded: chain a residue 190 SER Chi-restraints excluded: chain a residue 198 ASN Chi-restraints excluded: chain a residue 280 ASP Chi-restraints excluded: chain a residue 293 ASP Chi-restraints excluded: chain a residue 295 ILE Chi-restraints excluded: chain b residue 21 SER Chi-restraints excluded: chain b residue 26 GLN Chi-restraints excluded: chain b residue 44 ASP Chi-restraints excluded: chain b residue 45 SER Chi-restraints excluded: chain b residue 74 THR Chi-restraints excluded: chain b residue 202 THR Chi-restraints excluded: chain b residue 234 LEU Chi-restraints excluded: chain b residue 242 THR Chi-restraints excluded: chain b residue 268 VAL Chi-restraints excluded: chain c residue 7 THR Chi-restraints excluded: chain c residue 10 SER Chi-restraints excluded: chain c residue 17 ASP Chi-restraints excluded: chain c residue 56 ASN Chi-restraints excluded: chain c residue 67 MET Chi-restraints excluded: chain c residue 74 ASP Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 159 LEU Chi-restraints excluded: chain c residue 177 ARG Chi-restraints excluded: chain c residue 184 THR Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain c residue 213 VAL Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain d residue 60 LEU Chi-restraints excluded: chain e residue 51 ILE Chi-restraints excluded: chain e residue 66 THR Chi-restraints excluded: chain e residue 104 ASN Chi-restraints excluded: chain e residue 110 THR Chi-restraints excluded: chain e residue 134 THR Chi-restraints excluded: chain e residue 135 GLU Chi-restraints excluded: chain e residue 163 SER Chi-restraints excluded: chain e residue 175 ASN Chi-restraints excluded: chain e residue 189 MET Chi-restraints excluded: chain e residue 196 ILE Chi-restraints excluded: chain e residue 227 VAL Chi-restraints excluded: chain e residue 237 VAL Chi-restraints excluded: chain e residue 281 MET Chi-restraints excluded: chain e residue 282 ILE Chi-restraints excluded: chain f residue 37 GLU Chi-restraints excluded: chain f residue 40 THR Chi-restraints excluded: chain f residue 45 SER Chi-restraints excluded: chain f residue 58 VAL Chi-restraints excluded: chain f residue 88 ASP Chi-restraints excluded: chain f residue 146 ILE Chi-restraints excluded: chain f residue 264 ARG Chi-restraints excluded: chain g residue 67 MET Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain g residue 99 LEU Chi-restraints excluded: chain g residue 107 THR Chi-restraints excluded: chain g residue 112 SER Chi-restraints excluded: chain g residue 132 SER Chi-restraints excluded: chain g residue 190 THR Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain g residue 203 THR Chi-restraints excluded: chain g residue 207 MET Chi-restraints excluded: chain g residue 224 LEU Chi-restraints excluded: chain g residue 227 THR Chi-restraints excluded: chain h residue 7 THR Chi-restraints excluded: chain h residue 10 THR Chi-restraints excluded: chain h residue 23 SER Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 40 SER Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain i residue 25 THR Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 40 THR Chi-restraints excluded: chain i residue 54 ASP Chi-restraints excluded: chain i residue 88 THR Chi-restraints excluded: chain i residue 100 PHE Chi-restraints excluded: chain i residue 128 GLU Chi-restraints excluded: chain i residue 132 VAL Chi-restraints excluded: chain i residue 229 ILE Chi-restraints excluded: chain j residue 25 THR Chi-restraints excluded: chain j residue 38 TRP Chi-restraints excluded: chain j residue 40 THR Chi-restraints excluded: chain j residue 45 SER Chi-restraints excluded: chain j residue 58 VAL Chi-restraints excluded: chain j residue 69 VAL Chi-restraints excluded: chain j residue 84 ASP Chi-restraints excluded: chain j residue 85 CYS Chi-restraints excluded: chain j residue 126 LEU Chi-restraints excluded: chain j residue 181 LEU Chi-restraints excluded: chain j residue 183 SER Chi-restraints excluded: chain j residue 246 GLN Chi-restraints excluded: chain j residue 247 VAL Chi-restraints excluded: chain j residue 264 ARG Chi-restraints excluded: chain k residue 5 MET Chi-restraints excluded: chain k residue 10 SER Chi-restraints excluded: chain k residue 21 SER Chi-restraints excluded: chain k residue 81 ILE Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain k residue 103 LEU Chi-restraints excluded: chain k residue 116 THR Chi-restraints excluded: chain k residue 126 THR Chi-restraints excluded: chain k residue 199 VAL Chi-restraints excluded: chain k residue 203 THR Chi-restraints excluded: chain k residue 218 ASP Chi-restraints excluded: chain k residue 219 PHE Chi-restraints excluded: chain k residue 223 LEU Chi-restraints excluded: chain k residue 227 THR Chi-restraints excluded: chain k residue 233 SER Chi-restraints excluded: chain l residue 26 ASN Chi-restraints excluded: chain l residue 64 THR Chi-restraints excluded: chain m residue 61 VAL Chi-restraints excluded: chain m residue 68 SER Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain m residue 83 THR Chi-restraints excluded: chain m residue 84 ILE Chi-restraints excluded: chain m residue 95 GLU Chi-restraints excluded: chain m residue 106 THR Chi-restraints excluded: chain m residue 134 THR Chi-restraints excluded: chain m residue 173 SER Chi-restraints excluded: chain m residue 177 SER Chi-restraints excluded: chain m residue 196 ILE Chi-restraints excluded: chain m residue 240 VAL Chi-restraints excluded: chain n residue 84 ASP Chi-restraints excluded: chain n residue 126 LEU Chi-restraints excluded: chain n residue 152 GLU Chi-restraints excluded: chain n residue 183 SER Chi-restraints excluded: chain n residue 198 ILE Chi-restraints excluded: chain n residue 252 THR Chi-restraints excluded: chain n residue 265 ASN Chi-restraints excluded: chain o residue 30 VAL Chi-restraints excluded: chain o residue 118 LEU Chi-restraints excluded: chain o residue 126 THR Chi-restraints excluded: chain o residue 132 SER Chi-restraints excluded: chain o residue 153 ILE Chi-restraints excluded: chain o residue 198 VAL Chi-restraints excluded: chain o residue 199 VAL Chi-restraints excluded: chain o residue 226 ASP Chi-restraints excluded: chain p residue 25 ILE Chi-restraints excluded: chain p residue 32 TYR Chi-restraints excluded: chain p residue 57 VAL Chi-restraints excluded: chain q residue 36 VAL Chi-restraints excluded: chain q residue 62 VAL Chi-restraints excluded: chain q residue 71 CYS Chi-restraints excluded: chain q residue 100 PHE Chi-restraints excluded: chain q residue 175 ASN Chi-restraints excluded: chain q residue 177 SER Chi-restraints excluded: chain q residue 178 ILE Chi-restraints excluded: chain q residue 190 SER Chi-restraints excluded: chain q residue 217 THR Chi-restraints excluded: chain q residue 296 THR Chi-restraints excluded: chain r residue 18 LEU Chi-restraints excluded: chain r residue 32 ILE Chi-restraints excluded: chain r residue 46 GLU Chi-restraints excluded: chain r residue 51 ASP Chi-restraints excluded: chain r residue 84 ASP Chi-restraints excluded: chain r residue 111 GLN Chi-restraints excluded: chain r residue 131 VAL Chi-restraints excluded: chain r residue 173 LYS Chi-restraints excluded: chain r residue 185 VAL Chi-restraints excluded: chain r residue 205 SER Chi-restraints excluded: chain s residue 4 THR Chi-restraints excluded: chain s residue 10 SER Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain s residue 53 ILE Chi-restraints excluded: chain s residue 76 LEU Chi-restraints excluded: chain s residue 86 LEU Chi-restraints excluded: chain s residue 97 THR Chi-restraints excluded: chain s residue 103 LEU Chi-restraints excluded: chain s residue 173 THR Chi-restraints excluded: chain s residue 189 ILE Chi-restraints excluded: chain s residue 205 THR Chi-restraints excluded: chain t residue 7 THR Chi-restraints excluded: chain t residue 44 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 272 optimal weight: 0.0970 chunk 365 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 chunk 316 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 344 optimal weight: 7.9990 chunk 143 optimal weight: 0.0980 chunk 353 optimal weight: 0.0770 chunk 43 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 overall best weight: 1.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 203 ASN c 56 ASN ** d 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 21 ASN ** i 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 196 GLN ** p 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.111386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.099198 restraints weight = 66855.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.102084 restraints weight = 31810.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.103968 restraints weight = 18507.344| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.5277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.242 34975 Z= 0.353 Angle : 0.776 59.198 47711 Z= 0.417 Chirality : 0.046 0.312 5363 Planarity : 0.005 0.060 6193 Dihedral : 5.830 59.076 4860 Min Nonbonded Distance : 1.716 Molprobity Statistics. All-atom Clashscore : 20.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 5.27 % Allowed : 22.45 % Favored : 72.29 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % 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: -0.68 (0.13), residues: 4201 helix: -1.76 (0.25), residues: 355 sheet: 0.33 (0.15), residues: 1102 loop : -0.58 (0.12), residues: 2744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP n 71 HIS 0.024 0.001 HIS k 96 PHE 0.048 0.002 PHE a 75 TYR 0.052 0.002 TYR o 175 ARG 0.013 0.001 ARG s 238 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12895.76 seconds wall clock time: 231 minutes 11.70 seconds (13871.70 seconds total)