Starting phenix.real_space_refine on Mon Nov 18 01:00:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oix_16901/11_2024/8oix_16901.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oix_16901/11_2024/8oix_16901.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oix_16901/11_2024/8oix_16901.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oix_16901/11_2024/8oix_16901.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oix_16901/11_2024/8oix_16901.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oix_16901/11_2024/8oix_16901.cif" } resolution = 2.89 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= 0.001 sd= 0.040 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 256 5.16 5 C 30170 2.51 5 N 8218 2.21 5 O 9142 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 47786 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 1843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1843 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 8, 'TRANS': 230} Chain: "B" Number of atoms: 1770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1770 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain: "C" Number of atoms: 1833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1833 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 5, 'TRANS': 229} Chain breaks: 1 Chain: "D" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1801 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 223} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1785 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 7, 'TRANS': 226} Chain breaks: 1 Chain: "F" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1726 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 214} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 1836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1836 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 11, 'TRANS': 218} Chain: "H" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1536 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 5, 'TRANS': 198} Chain: "I" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1780 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 9, 'TRANS': 220} Chain: "J" Number of atoms: 1605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1605 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 195} Chain: "K" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1499 Classifications: {'peptide': 191} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 185} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "L" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1585 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 4, 'TRANS': 198} Chain: "M" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1656 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 203} Chain: "N" Number of atoms: 1598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1598 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "O" Number of atoms: 1843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1843 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 8, 'TRANS': 230} Chain: "P" Number of atoms: 1770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1770 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain: "Q" Number of atoms: 1833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1833 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 5, 'TRANS': 229} Chain breaks: 1 Chain: "R" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1801 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 223} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1785 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 7, 'TRANS': 226} Chain breaks: 1 Chain: "T" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1726 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 214} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "U" Number of atoms: 1836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1836 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 11, 'TRANS': 218} Chain: "V" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1536 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 5, 'TRANS': 198} Chain: "W" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1780 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 9, 'TRANS': 220} Chain: "X" Number of atoms: 1605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1605 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 195} Chain: "Y" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1499 Classifications: {'peptide': 191} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 185} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "Z" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1585 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 4, 'TRANS': 198} Chain: "a" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1656 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 203} Chain: "b" Number of atoms: 1598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1598 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "H" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'SA1': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'SA1': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'SA1': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'SA1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 24.25, per 1000 atoms: 0.51 Number of scatterers: 47786 At special positions: 0 Unit cell: (179.9, 175.7, 128.8, 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 256 16.00 O 9142 8.00 N 8218 7.00 C 30170 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS J 11 " - pdb=" SG CYS J 143 " distance=2.03 Simple disulfide: pdb=" SG CYS J 167 " - pdb=" SG CYS J 171 " distance=2.06 Simple disulfide: pdb=" SG CYS X 11 " - pdb=" SG CYS X 143 " distance=2.03 Simple disulfide: pdb=" SG CYS X 167 " - pdb=" SG CYS X 171 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.15 Conformation dependent library (CDL) restraints added in 6.3 seconds 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11368 Finding SS restraints... Secondary structure from input PDB file: 170 helices and 74 sheets defined 39.9% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.79 Creating SS restraints... Processing helix chain 'A' and resid 18 through 30 Processing helix chain 'A' and resid 58 through 62 Processing helix chain 'A' and resid 79 through 102 Processing helix chain 'A' and resid 106 through 124 Processing helix chain 'A' and resid 168 through 180 Processing helix chain 'A' and resid 185 through 202 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 226 through 240 removed outlier: 4.201A pdb=" N LYS A 240 " --> pdb=" O ALA A 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 29 Processing helix chain 'B' and resid 57 through 61 removed outlier: 3.836A pdb=" N LEU B 61 " --> pdb=" O VAL B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 100 Processing helix chain 'B' and resid 104 through 122 Processing helix chain 'B' and resid 164 through 176 Processing helix chain 'B' and resid 181 through 196 Processing helix chain 'B' and resid 202 through 204 No H-bonds generated for 'chain 'B' and resid 202 through 204' Processing helix chain 'B' and resid 221 through 231 removed outlier: 3.662A pdb=" N GLU B 231 " --> pdb=" O ASP B 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 30 Processing helix chain 'C' and resid 78 through 101 Processing helix chain 'C' and resid 105 through 123 Processing helix chain 'C' and resid 166 through 178 Processing helix chain 'C' and resid 183 through 199 Processing helix chain 'C' and resid 205 through 207 No H-bonds generated for 'chain 'C' and resid 205 through 207' Processing helix chain 'C' and resid 228 through 238 removed outlier: 3.515A pdb=" N ARG C 238 " --> pdb=" O THR C 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 29 Processing helix chain 'D' and resid 77 through 100 Processing helix chain 'D' and resid 104 through 122 Processing helix chain 'D' and resid 166 through 178 Processing helix chain 'D' and resid 183 through 197 Processing helix chain 'D' and resid 223 through 233 Processing helix chain 'E' and resid 21 through 33 Processing helix chain 'E' and resid 60 through 65 removed outlier: 3.675A pdb=" N GLU E 65 " --> pdb=" O SER E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 104 Processing helix chain 'E' and resid 108 through 121 Processing helix chain 'E' and resid 175 through 185 removed outlier: 4.407A pdb=" N ASP E 185 " --> pdb=" O ALA E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 208 Processing helix chain 'E' and resid 233 through 244 removed outlier: 4.103A pdb=" N ARG E 243 " --> pdb=" O GLU E 239 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU E 244 " --> pdb=" O ILE E 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 31 Processing helix chain 'F' and resid 77 through 99 Processing helix chain 'F' and resid 104 through 122 Processing helix chain 'F' and resid 164 through 175 removed outlier: 4.001A pdb=" N ALA F 168 " --> pdb=" O ARG F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 182 Proline residue: F 180 - end of helix Processing helix chain 'F' and resid 183 through 197 removed outlier: 3.862A pdb=" N ASP F 197 " --> pdb=" O ARG F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 232 removed outlier: 4.266A pdb=" N LYS F 230 " --> pdb=" O GLU F 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 10 removed outlier: 4.027A pdb=" N ASP G 9 " --> pdb=" O SER G 6 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE G 10 " --> pdb=" O GLY G 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 6 through 10' Processing helix chain 'G' and resid 21 through 34 removed outlier: 3.563A pdb=" N ASP G 34 " --> pdb=" O ALA G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 104 Processing helix chain 'G' and resid 108 through 126 removed outlier: 3.675A pdb=" N GLN G 119 " --> pdb=" O GLU G 115 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N HIS G 124 " --> pdb=" O PHE G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 175 Processing helix chain 'G' and resid 176 through 177 No H-bonds generated for 'chain 'G' and resid 176 through 177' Processing helix chain 'G' and resid 178 through 182 Processing helix chain 'G' and resid 183 through 199 Proline residue: G 189 - end of helix Processing helix chain 'H' and resid 48 through 67 Processing helix chain 'H' and resid 76 through 92 Processing helix chain 'H' and resid 130 through 136 removed outlier: 3.842A pdb=" N THR H 134 " --> pdb=" O GLY H 130 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N TYR H 135 " --> pdb=" O SER H 131 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE H 136 " --> pdb=" O GLY H 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 130 through 136' Processing helix chain 'H' and resid 136 through 144 Processing helix chain 'H' and resid 149 through 168 Processing helix chain 'H' and resid 198 through 202 Processing helix chain 'I' and resid 48 through 71 Processing helix chain 'I' and resid 75 through 90 Processing helix chain 'I' and resid 130 through 142 removed outlier: 3.888A pdb=" N VAL I 137 " --> pdb=" O ALA I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 166 Processing helix chain 'I' and resid 201 through 205 Processing helix chain 'J' and resid 4 through 8 removed outlier: 3.736A pdb=" N ASN J 8 " --> pdb=" O SER J 5 " (cutoff:3.500A) Processing helix chain 'J' and resid 57 through 80 Processing helix chain 'J' and resid 84 through 99 removed outlier: 3.717A pdb=" N LYS J 99 " --> pdb=" O THR J 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 143 through 155 removed outlier: 3.642A pdb=" N SER J 153 " --> pdb=" O GLY J 149 " (cutoff:3.500A) Processing helix chain 'J' and resid 160 through 177 Processing helix chain 'K' and resid 49 through 71 Processing helix chain 'K' and resid 76 through 94 removed outlier: 3.778A pdb=" N ARG K 93 " --> pdb=" O ALA K 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 131 through 144 removed outlier: 3.886A pdb=" N PHE K 135 " --> pdb=" O TYR K 131 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N SER K 138 " --> pdb=" O TYR K 134 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL K 139 " --> pdb=" O PHE K 135 " (cutoff:3.500A) Processing helix chain 'K' and resid 149 through 168 Processing helix chain 'L' and resid 48 through 70 Processing helix chain 'L' and resid 75 through 89 Processing helix chain 'L' and resid 131 through 143 Processing helix chain 'L' and resid 148 through 167 Processing helix chain 'L' and resid 192 through 196 Processing helix chain 'M' and resid 68 through 91 Processing helix chain 'M' and resid 95 through 110 removed outlier: 3.777A pdb=" N LYS M 110 " --> pdb=" O THR M 106 " (cutoff:3.500A) Processing helix chain 'M' and resid 152 through 165 Proline residue: M 158 - end of helix Processing helix chain 'M' and resid 178 through 197 Processing helix chain 'N' and resid 56 through 77 Processing helix chain 'N' and resid 83 through 101 Processing helix chain 'N' and resid 140 through 145 removed outlier: 3.647A pdb=" N TYR N 144 " --> pdb=" O GLY N 140 " (cutoff:3.500A) Processing helix chain 'N' and resid 147 through 152 removed outlier: 4.786A pdb=" N ALA N 151 " --> pdb=" O GLY N 147 " (cutoff:3.500A) Processing helix chain 'N' and resid 157 through 176 Processing helix chain 'O' and resid 18 through 30 Processing helix chain 'O' and resid 58 through 62 Processing helix chain 'O' and resid 79 through 102 Processing helix chain 'O' and resid 106 through 124 Processing helix chain 'O' and resid 168 through 180 Processing helix chain 'O' and resid 185 through 202 Processing helix chain 'O' and resid 206 through 208 No H-bonds generated for 'chain 'O' and resid 206 through 208' Processing helix chain 'O' and resid 226 through 240 removed outlier: 4.201A pdb=" N LYS O 240 " --> pdb=" O ALA O 236 " (cutoff:3.500A) Processing helix chain 'P' and resid 17 through 29 Processing helix chain 'P' and resid 57 through 61 removed outlier: 3.838A pdb=" N LEU P 61 " --> pdb=" O VAL P 58 " (cutoff:3.500A) Processing helix chain 'P' and resid 77 through 100 Processing helix chain 'P' and resid 104 through 122 Processing helix chain 'P' and resid 164 through 176 Processing helix chain 'P' and resid 181 through 196 Processing helix chain 'P' and resid 202 through 204 No H-bonds generated for 'chain 'P' and resid 202 through 204' Processing helix chain 'P' and resid 221 through 231 removed outlier: 3.663A pdb=" N GLU P 231 " --> pdb=" O ASP P 227 " (cutoff:3.500A) Processing helix chain 'Q' and resid 18 through 30 Processing helix chain 'Q' and resid 78 through 101 Processing helix chain 'Q' and resid 105 through 123 Processing helix chain 'Q' and resid 166 through 178 Processing helix chain 'Q' and resid 183 through 199 Processing helix chain 'Q' and resid 205 through 207 No H-bonds generated for 'chain 'Q' and resid 205 through 207' Processing helix chain 'Q' and resid 228 through 238 removed outlier: 3.515A pdb=" N ARG Q 238 " --> pdb=" O THR Q 234 " (cutoff:3.500A) Processing helix chain 'R' and resid 17 through 29 Processing helix chain 'R' and resid 77 through 100 Processing helix chain 'R' and resid 104 through 122 Processing helix chain 'R' and resid 166 through 178 Processing helix chain 'R' and resid 183 through 197 Processing helix chain 'R' and resid 223 through 233 Processing helix chain 'S' and resid 21 through 33 Processing helix chain 'S' and resid 60 through 65 removed outlier: 3.675A pdb=" N GLU S 65 " --> pdb=" O SER S 62 " (cutoff:3.500A) Processing helix chain 'S' and resid 81 through 104 Processing helix chain 'S' and resid 108 through 121 Processing helix chain 'S' and resid 175 through 185 removed outlier: 4.408A pdb=" N ASP S 185 " --> pdb=" O ALA S 181 " (cutoff:3.500A) Processing helix chain 'S' and resid 192 through 208 Processing helix chain 'S' and resid 233 through 242 Processing helix chain 'T' and resid 19 through 31 Processing helix chain 'T' and resid 77 through 99 Processing helix chain 'T' and resid 104 through 122 Processing helix chain 'T' and resid 164 through 175 removed outlier: 4.001A pdb=" N ALA T 168 " --> pdb=" O ARG T 164 " (cutoff:3.500A) Processing helix chain 'T' and resid 176 through 182 Proline residue: T 180 - end of helix Processing helix chain 'T' and resid 183 through 197 removed outlier: 3.863A pdb=" N ASP T 197 " --> pdb=" O ARG T 193 " (cutoff:3.500A) Processing helix chain 'T' and resid 226 through 232 removed outlier: 4.265A pdb=" N LYS T 230 " --> pdb=" O GLU T 227 " (cutoff:3.500A) Processing helix chain 'U' and resid 6 through 10 removed outlier: 4.027A pdb=" N ASP U 9 " --> pdb=" O SER U 6 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE U 10 " --> pdb=" O GLY U 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 6 through 10' Processing helix chain 'U' and resid 21 through 34 removed outlier: 3.563A pdb=" N ASP U 34 " --> pdb=" O ALA U 30 " (cutoff:3.500A) Processing helix chain 'U' and resid 81 through 104 Processing helix chain 'U' and resid 108 through 126 removed outlier: 3.675A pdb=" N GLN U 119 " --> pdb=" O GLU U 115 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N HIS U 124 " --> pdb=" O PHE U 120 " (cutoff:3.500A) Processing helix chain 'U' and resid 166 through 175 Processing helix chain 'U' and resid 176 through 177 No H-bonds generated for 'chain 'U' and resid 176 through 177' Processing helix chain 'U' and resid 178 through 182 Processing helix chain 'U' and resid 183 through 199 Proline residue: U 189 - end of helix Processing helix chain 'V' and resid 48 through 67 Processing helix chain 'V' and resid 76 through 92 Processing helix chain 'V' and resid 130 through 136 removed outlier: 3.842A pdb=" N THR V 134 " --> pdb=" O GLY V 130 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N TYR V 135 " --> pdb=" O SER V 131 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE V 136 " --> pdb=" O GLY V 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 130 through 136' Processing helix chain 'V' and resid 136 through 144 Processing helix chain 'V' and resid 149 through 168 Processing helix chain 'V' and resid 198 through 202 Processing helix chain 'W' and resid 48 through 71 Processing helix chain 'W' and resid 75 through 90 Processing helix chain 'W' and resid 130 through 142 removed outlier: 3.888A pdb=" N VAL W 137 " --> pdb=" O ALA W 133 " (cutoff:3.500A) Processing helix chain 'W' and resid 147 through 166 Processing helix chain 'W' and resid 201 through 205 Processing helix chain 'X' and resid 4 through 8 removed outlier: 3.736A pdb=" N ASN X 8 " --> pdb=" O SER X 5 " (cutoff:3.500A) Processing helix chain 'X' and resid 57 through 80 Processing helix chain 'X' and resid 84 through 99 removed outlier: 3.717A pdb=" N LYS X 99 " --> pdb=" O THR X 95 " (cutoff:3.500A) Processing helix chain 'X' and resid 143 through 155 removed outlier: 3.642A pdb=" N SER X 153 " --> pdb=" O GLY X 149 " (cutoff:3.500A) Processing helix chain 'X' and resid 160 through 177 Processing helix chain 'Y' and resid 49 through 71 Processing helix chain 'Y' and resid 76 through 94 removed outlier: 3.777A pdb=" N ARG Y 93 " --> pdb=" O ALA Y 89 " (cutoff:3.500A) Processing helix chain 'Y' and resid 131 through 144 removed outlier: 3.886A pdb=" N PHE Y 135 " --> pdb=" O TYR Y 131 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N SER Y 138 " --> pdb=" O TYR Y 134 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL Y 139 " --> pdb=" O PHE Y 135 " (cutoff:3.500A) Processing helix chain 'Y' and resid 149 through 168 Processing helix chain 'Z' and resid 48 through 70 Processing helix chain 'Z' and resid 75 through 89 Processing helix chain 'Z' and resid 131 through 143 Processing helix chain 'Z' and resid 148 through 167 Processing helix chain 'Z' and resid 192 through 196 Processing helix chain 'a' and resid 68 through 91 Processing helix chain 'a' and resid 95 through 110 removed outlier: 3.777A pdb=" N LYS a 110 " --> pdb=" O THR a 106 " (cutoff:3.500A) Processing helix chain 'a' and resid 152 through 165 Proline residue: a 158 - end of helix Processing helix chain 'a' and resid 178 through 197 Processing helix chain 'b' and resid 56 through 77 Processing helix chain 'b' and resid 83 through 101 Processing helix chain 'b' and resid 140 through 145 removed outlier: 3.648A pdb=" N TYR b 144 " --> pdb=" O GLY b 140 " (cutoff:3.500A) Processing helix chain 'b' and resid 147 through 152 removed outlier: 4.786A pdb=" N ALA b 151 " --> pdb=" O GLY b 147 " (cutoff:3.500A) Processing helix chain 'b' and resid 157 through 176 Processing sheet with id=AA1, first strand: chain 'A' and resid 162 through 166 removed outlier: 5.010A pdb=" N THR A 34 " --> pdb=" O GLN A 49 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 65 through 67 removed outlier: 4.428A pdb=" N LEU A 148 " --> pdb=" O PHE A 160 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLY A 159 " --> pdb=" O GLU B 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 158 through 160 removed outlier: 3.771A pdb=" N GLY B 41 " --> pdb=" O ALA B 38 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 64 through 65 removed outlier: 3.883A pdb=" N LEU B 144 " --> pdb=" O TRP B 156 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 160 through 163 removed outlier: 3.599A pdb=" N GLY C 42 " --> pdb=" O PHE C 39 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N PHE C 211 " --> pdb=" O LEU C 227 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 64 through 68 removed outlier: 6.124A pdb=" N ILE C 71 " --> pdb=" O ILE C 67 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE C 133 " --> pdb=" O THR C 149 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 160 through 163 Processing sheet with id=AA8, first strand: chain 'D' and resid 64 through 65 removed outlier: 3.731A pdb=" N ASP D 138 " --> pdb=" O GLN D 143 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN D 143 " --> pdb=" O ASP D 138 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 169 through 172 Processing sheet with id=AB1, first strand: chain 'E' and resid 67 through 69 Processing sheet with id=AB2, first strand: chain 'F' and resid 158 through 161 Processing sheet with id=AB3, first strand: chain 'F' and resid 63 through 67 removed outlier: 6.379A pdb=" N ILE F 70 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU F 144 " --> pdb=" O TYR F 156 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 160 through 163 Processing sheet with id=AB5, first strand: chain 'G' and resid 160 through 163 removed outlier: 3.547A pdb=" N TRP G 206 " --> pdb=" O PHE G 233 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 67 through 71 removed outlier: 6.090A pdb=" N ILE G 74 " --> pdb=" O ILE G 70 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 126 through 129 Processing sheet with id=AB8, first strand: chain 'H' and resid 20 through 22 removed outlier: 6.937A pdb=" N THR H 20 " --> pdb=" O PRO H 27 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 34 through 38 removed outlier: 6.480A pdb=" N ILE H 41 " --> pdb=" O ILE H 37 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 124 through 127 removed outlier: 5.710A pdb=" N VAL I 173 " --> pdb=" O ASP I 197 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP I 197 " --> pdb=" O VAL I 173 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 20 through 21 Processing sheet with id=AC3, first strand: chain 'I' and resid 34 through 38 removed outlier: 6.394A pdb=" N ILE I 41 " --> pdb=" O ILE I 37 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 221 through 228 removed outlier: 5.645A pdb=" N CYS J 11 " --> pdb=" O ASP J 26 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 29 through 31 removed outlier: 6.573A pdb=" N LEU J 29 " --> pdb=" O VAL J 36 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 43 through 47 removed outlier: 6.290A pdb=" N ILE J 50 " --> pdb=" O ILE J 46 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 126 through 129 removed outlier: 4.059A pdb=" N VAL K 177 " --> pdb=" O ILE K 188 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 21 through 23 removed outlier: 6.724A pdb=" N VAL K 21 " --> pdb=" O MET K 28 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 35 through 37 Processing sheet with id=AD1, first strand: chain 'L' and resid 125 through 129 removed outlier: 5.897A pdb=" N VAL L 174 " --> pdb=" O LYS L 189 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS L 189 " --> pdb=" O VAL L 174 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL L 176 " --> pdb=" O ILE L 187 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 20 through 22 removed outlier: 6.993A pdb=" N GLY L 22 " --> pdb=" O ILE L 26 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ILE L 26 " --> pdb=" O GLY L 22 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 34 through 38 removed outlier: 6.352A pdb=" N MET L 41 " --> pdb=" O LEU L 37 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N MET L 100 " --> pdb=" O THR L 44 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 34 through 38 removed outlier: 6.352A pdb=" N MET L 41 " --> pdb=" O LEU L 37 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N MET L 100 " --> pdb=" O THR L 44 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE L 111 " --> pdb=" O GLY L 123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 146 through 150 removed outlier: 5.346A pdb=" N THR M 22 " --> pdb=" O ASP M 37 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 40 through 42 removed outlier: 7.032A pdb=" N VAL M 42 " --> pdb=" O ILE M 46 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ILE M 46 " --> pdb=" O VAL M 42 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 54 through 56 removed outlier: 3.804A pdb=" N ILE M 119 " --> pdb=" O TYR M 135 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU M 132 " --> pdb=" O LEU M 144 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 32 through 35 removed outlier: 5.638A pdb=" N PHE N 33 " --> pdb=" O TYR N 29 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N TYR N 29 " --> pdb=" O PHE N 33 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE N 48 " --> pdb=" O VAL N 44 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 32 through 35 removed outlier: 5.638A pdb=" N PHE N 33 " --> pdb=" O TYR N 29 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N TYR N 29 " --> pdb=" O PHE N 33 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 136 through 139 removed outlier: 4.860A pdb=" N PHE N 185 " --> pdb=" O ALA N 197 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ALA N 197 " --> pdb=" O PHE N 185 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N THR N 187 " --> pdb=" O HIS N 195 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N HIS N 195 " --> pdb=" O THR N 187 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N THR N 189 " --> pdb=" O ILE N 193 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ILE N 193 " --> pdb=" O THR N 189 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'O' and resid 162 through 166 removed outlier: 5.010A pdb=" N THR O 34 " --> pdb=" O GLN O 49 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'O' and resid 65 through 67 removed outlier: 4.429A pdb=" N LEU O 148 " --> pdb=" O PHE O 160 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY O 159 " --> pdb=" O GLU P 56 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'P' and resid 158 through 160 removed outlier: 3.772A pdb=" N GLY P 41 " --> pdb=" O ALA P 38 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'P' and resid 64 through 65 removed outlier: 3.884A pdb=" N LEU P 144 " --> pdb=" O TRP P 156 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Q' and resid 160 through 163 removed outlier: 3.599A pdb=" N GLY Q 42 " --> pdb=" O PHE Q 39 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N PHE Q 211 " --> pdb=" O LEU Q 227 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG Q 225 " --> pdb=" O VAL Q 213 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Q' and resid 64 through 68 removed outlier: 6.124A pdb=" N ILE Q 71 " --> pdb=" O ILE Q 67 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE Q 133 " --> pdb=" O THR Q 149 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'R' and resid 160 through 163 Processing sheet with id=AE9, first strand: chain 'R' and resid 64 through 65 removed outlier: 3.731A pdb=" N ASP R 138 " --> pdb=" O GLN R 143 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN R 143 " --> pdb=" O ASP R 138 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'S' and resid 169 through 172 Processing sheet with id=AF2, first strand: chain 'S' and resid 67 through 69 Processing sheet with id=AF3, first strand: chain 'T' and resid 158 through 161 Processing sheet with id=AF4, first strand: chain 'T' and resid 63 through 67 removed outlier: 6.378A pdb=" N ILE T 70 " --> pdb=" O ILE T 66 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU T 144 " --> pdb=" O TYR T 156 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'U' and resid 160 through 163 Processing sheet with id=AF6, first strand: chain 'U' and resid 160 through 163 removed outlier: 3.547A pdb=" N TRP U 206 " --> pdb=" O PHE U 233 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'U' and resid 67 through 71 removed outlier: 6.090A pdb=" N ILE U 74 " --> pdb=" O ILE U 70 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'V' and resid 126 through 129 Processing sheet with id=AF9, first strand: chain 'V' and resid 20 through 22 removed outlier: 6.938A pdb=" N THR V 20 " --> pdb=" O PRO V 27 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'V' and resid 34 through 38 removed outlier: 6.480A pdb=" N ILE V 41 " --> pdb=" O ILE V 37 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'W' and resid 124 through 127 removed outlier: 5.711A pdb=" N VAL W 173 " --> pdb=" O ASP W 197 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASP W 197 " --> pdb=" O VAL W 173 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'W' and resid 20 through 21 Processing sheet with id=AG4, first strand: chain 'W' and resid 34 through 38 removed outlier: 6.394A pdb=" N ILE W 41 " --> pdb=" O ILE W 37 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'W' and resid 221 through 228 removed outlier: 5.645A pdb=" N CYS X 11 " --> pdb=" O ASP X 26 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'X' and resid 29 through 31 removed outlier: 6.572A pdb=" N LEU X 29 " --> pdb=" O VAL X 36 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'X' and resid 43 through 47 removed outlier: 6.289A pdb=" N ILE X 50 " --> pdb=" O ILE X 46 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Y' and resid 126 through 129 removed outlier: 4.059A pdb=" N VAL Y 177 " --> pdb=" O ILE Y 188 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Y' and resid 21 through 23 removed outlier: 6.723A pdb=" N VAL Y 21 " --> pdb=" O MET Y 28 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Y' and resid 35 through 37 Processing sheet with id=AH2, first strand: chain 'Z' and resid 125 through 129 removed outlier: 5.897A pdb=" N VAL Z 174 " --> pdb=" O LYS Z 189 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS Z 189 " --> pdb=" O VAL Z 174 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL Z 176 " --> pdb=" O ILE Z 187 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Z' and resid 20 through 22 removed outlier: 6.993A pdb=" N GLY Z 22 " --> pdb=" O ILE Z 26 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ILE Z 26 " --> pdb=" O GLY Z 22 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'Z' and resid 34 through 38 removed outlier: 6.351A pdb=" N MET Z 41 " --> pdb=" O LEU Z 37 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N MET Z 100 " --> pdb=" O THR Z 44 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'Z' and resid 34 through 38 removed outlier: 6.351A pdb=" N MET Z 41 " --> pdb=" O LEU Z 37 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N MET Z 100 " --> pdb=" O THR Z 44 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE Z 111 " --> pdb=" O GLY Z 123 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'a' and resid 146 through 150 removed outlier: 5.346A pdb=" N THR a 22 " --> pdb=" O ASP a 37 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'a' and resid 40 through 42 removed outlier: 7.031A pdb=" N VAL a 42 " --> pdb=" O ILE a 46 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ILE a 46 " --> pdb=" O VAL a 42 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'a' and resid 54 through 56 removed outlier: 3.804A pdb=" N ILE a 119 " --> pdb=" O TYR a 135 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU a 132 " --> pdb=" O LEU a 144 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'b' and resid 32 through 35 removed outlier: 5.638A pdb=" N PHE b 33 " --> pdb=" O TYR b 29 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N TYR b 29 " --> pdb=" O PHE b 33 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE b 48 " --> pdb=" O VAL b 44 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'b' and resid 32 through 35 removed outlier: 5.638A pdb=" N PHE b 33 " --> pdb=" O TYR b 29 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N TYR b 29 " --> pdb=" O PHE b 33 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'b' and resid 136 through 139 removed outlier: 4.859A pdb=" N PHE b 185 " --> pdb=" O ALA b 197 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ALA b 197 " --> pdb=" O PHE b 185 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N THR b 187 " --> pdb=" O HIS b 195 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N HIS b 195 " --> pdb=" O THR b 187 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N THR b 189 " --> pdb=" O ILE b 193 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ILE b 193 " --> pdb=" O THR b 189 " (cutoff:3.500A) 2865 hydrogen bonds defined for protein. 8217 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: 23.80 Time building geometry restraints manager: 13.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 15972 1.35 - 1.49: 11949 1.49 - 1.63: 20369 1.63 - 1.76: 0 1.76 - 1.90: 396 Bond restraints: 48686 Sorted by residual: bond pdb=" CA ALA E 146 " pdb=" CB ALA E 146 " ideal model delta sigma weight residual 1.534 1.476 0.057 1.78e-02 3.16e+03 1.04e+01 bond pdb=" CA ALA S 146 " pdb=" CB ALA S 146 " ideal model delta sigma weight residual 1.535 1.473 0.063 2.09e-02 2.29e+03 8.95e+00 bond pdb=" C3 SA1 I 301 " pdb=" C9 SA1 I 301 " ideal model delta sigma weight residual 1.578 1.520 0.058 2.00e-02 2.50e+03 8.45e+00 bond pdb=" C3 SA1 W 301 " pdb=" C9 SA1 W 301 " ideal model delta sigma weight residual 1.578 1.521 0.057 2.00e-02 2.50e+03 8.21e+00 bond pdb=" CB CYS X 171 " pdb=" SG CYS X 171 " ideal model delta sigma weight residual 1.808 1.897 -0.089 3.30e-02 9.18e+02 7.20e+00 ... (remaining 48681 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 65304 2.53 - 5.07: 531 5.07 - 7.60: 33 7.60 - 10.13: 14 10.13 - 12.66: 2 Bond angle restraints: 65884 Sorted by residual: angle pdb=" CA TRP B 154 " pdb=" CB TRP B 154 " pdb=" CG TRP B 154 " ideal model delta sigma weight residual 113.60 122.74 -9.14 1.90e+00 2.77e-01 2.31e+01 angle pdb=" N ILE J 46 " pdb=" CA ILE J 46 " pdb=" C ILE J 46 " ideal model delta sigma weight residual 111.81 107.68 4.13 8.60e-01 1.35e+00 2.30e+01 angle pdb=" CA TRP P 154 " pdb=" CB TRP P 154 " pdb=" CG TRP P 154 " ideal model delta sigma weight residual 113.60 122.72 -9.12 1.90e+00 2.77e-01 2.30e+01 angle pdb=" N ILE X 46 " pdb=" CA ILE X 46 " pdb=" C ILE X 46 " ideal model delta sigma weight residual 111.81 107.73 4.08 8.60e-01 1.35e+00 2.25e+01 angle pdb=" N GLY L 98 " pdb=" CA GLY L 98 " pdb=" C GLY L 98 " ideal model delta sigma weight residual 113.18 104.58 8.60 2.37e+00 1.78e-01 1.32e+01 ... (remaining 65879 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.16: 28114 24.16 - 48.32: 1024 48.32 - 72.48: 174 72.48 - 96.63: 38 96.63 - 120.79: 12 Dihedral angle restraints: 29362 sinusoidal: 11640 harmonic: 17722 Sorted by residual: dihedral pdb=" CD ARG I 19 " pdb=" NE ARG I 19 " pdb=" CZ ARG I 19 " pdb=" NH1 ARG I 19 " ideal model delta sinusoidal sigma weight residual 0.00 -43.75 43.75 1 1.00e+01 1.00e-02 2.67e+01 dihedral pdb=" CD ARG W 19 " pdb=" NE ARG W 19 " pdb=" CZ ARG W 19 " pdb=" NH1 ARG W 19 " ideal model delta sinusoidal sigma weight residual 0.00 -43.63 43.63 1 1.00e+01 1.00e-02 2.65e+01 dihedral pdb=" CA HIS a 90 " pdb=" C HIS a 90 " pdb=" N PHE a 91 " pdb=" CA PHE a 91 " ideal model delta harmonic sigma weight residual 180.00 158.34 21.66 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 29359 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 6431 0.067 - 0.134: 964 0.134 - 0.201: 28 0.201 - 0.268: 7 0.268 - 0.335: 4 Chirality restraints: 7434 Sorted by residual: chirality pdb=" C3 SA1 H 301 " pdb=" C5 SA1 H 301 " pdb=" C9 SA1 H 301 " pdb=" O2 SA1 H 301 " both_signs ideal model delta sigma weight residual False -2.98 -2.65 -0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" C3 SA1 V 301 " pdb=" C5 SA1 V 301 " pdb=" C9 SA1 V 301 " pdb=" O2 SA1 V 301 " both_signs ideal model delta sigma weight residual False -2.98 -2.65 -0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" C3 SA1 I 301 " pdb=" C5 SA1 I 301 " pdb=" C9 SA1 I 301 " pdb=" O2 SA1 I 301 " both_signs ideal model delta sigma weight residual False -2.98 -2.71 -0.28 2.00e-01 2.50e+01 1.89e+00 ... (remaining 7431 not shown) Planarity restraints: 8518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG I 19 " 0.773 9.50e-02 1.11e+02 3.47e-01 7.31e+01 pdb=" NE ARG I 19 " -0.045 2.00e-02 2.50e+03 pdb=" CZ ARG I 19 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG I 19 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG I 19 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG W 19 " -0.770 9.50e-02 1.11e+02 3.45e-01 7.25e+01 pdb=" NE ARG W 19 " 0.045 2.00e-02 2.50e+03 pdb=" CZ ARG W 19 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG W 19 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG W 19 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5 SA1 W 301 " -0.035 2.00e-02 2.50e+03 6.88e-02 5.92e+01 pdb=" C6 SA1 W 301 " -0.014 2.00e-02 2.50e+03 pdb=" C9 SA1 W 301 " 0.086 2.00e-02 2.50e+03 pdb=" N8 SA1 W 301 " -0.103 2.00e-02 2.50e+03 pdb=" O7 SA1 W 301 " 0.065 2.00e-02 2.50e+03 ... (remaining 8515 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 993 2.66 - 3.22: 47298 3.22 - 3.78: 85792 3.78 - 4.34: 123363 4.34 - 4.90: 197276 Nonbonded interactions: 454722 Sorted by model distance: nonbonded pdb=" OG1 THR R 32 " pdb=" O ARG R 165 " model vdw 2.098 3.040 nonbonded pdb=" OG1 THR D 32 " pdb=" O ARG D 165 " model vdw 2.098 3.040 nonbonded pdb=" OE2 GLU S 105 " pdb=" OH TYR a 86 " model vdw 2.116 3.040 nonbonded pdb=" OG1 THR S 163 " pdb=" OE1 GLN T 60 " model vdw 2.117 3.040 nonbonded pdb=" OE2 GLU E 105 " pdb=" OH TYR M 86 " model vdw 2.118 3.040 ... (remaining 454717 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'P' } ncs_group { reference = chain 'C' selection = chain 'Q' } ncs_group { reference = chain 'D' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'S' } ncs_group { reference = chain 'F' selection = chain 'T' } ncs_group { reference = chain 'G' selection = chain 'U' } ncs_group { reference = chain 'H' selection = chain 'V' } ncs_group { reference = chain 'I' selection = chain 'W' } ncs_group { reference = chain 'J' selection = chain 'X' } ncs_group { reference = chain 'K' selection = chain 'Y' } ncs_group { reference = chain 'L' selection = chain 'Z' } ncs_group { reference = chain 'M' selection = chain 'a' } ncs_group { reference = chain 'N' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.920 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: 0.040 Extract box with map and model: 1.880 Check model and map are aligned: 0.320 Set scattering table: 0.420 Process input model: 105.760 Find NCS groups from input model: 4.780 Set up NCS constraints: 0.600 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:13.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 135.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 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 : 0.004 0.089 48686 Z= 0.250 Angle : 0.612 12.664 65884 Z= 0.333 Chirality : 0.046 0.335 7434 Planarity : 0.010 0.347 8518 Dihedral : 13.464 120.793 17982 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.91 % Allowed : 6.45 % Favored : 92.64 % 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: -0.02 (0.11), residues: 6082 helix: 0.79 (0.11), residues: 2232 sheet: -0.70 (0.12), residues: 1518 loop : -0.11 (0.13), residues: 2332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 154 HIS 0.009 0.001 HIS a 224 PHE 0.020 0.002 PHE B 153 TYR 0.020 0.002 TYR M 115 ARG 0.026 0.002 ARG a 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1273 residues out of total 5152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 1226 time to evaluate : 5.668 Fit side-chains REVERT: A 178 LYS cc_start: 0.6934 (mttt) cc_final: 0.6723 (mmmt) REVERT: C 22 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8580 (mm-30) REVERT: C 189 ASP cc_start: 0.7212 (m-30) cc_final: 0.6998 (m-30) REVERT: C 233 ASP cc_start: 0.6681 (t70) cc_final: 0.6419 (t70) REVERT: D 40 ASP cc_start: 0.6536 (p0) cc_final: 0.5229 (p0) REVERT: D 86 GLN cc_start: 0.7430 (tt0) cc_final: 0.7185 (tt0) REVERT: D 159 LYS cc_start: 0.7854 (mttt) cc_final: 0.7618 (mttm) REVERT: D 210 TYR cc_start: 0.7452 (p90) cc_final: 0.7142 (p90) REVERT: E 149 GLU cc_start: 0.7971 (tt0) cc_final: 0.7297 (tp30) REVERT: E 213 ASN cc_start: 0.6951 (t0) cc_final: 0.6685 (t0) REVERT: E 232 TYR cc_start: 0.8349 (m-10) cc_final: 0.8087 (m-10) REVERT: F 18 ARG cc_start: 0.7923 (mtp180) cc_final: 0.7363 (mtm110) REVERT: F 55 GLU cc_start: 0.6719 (tp30) cc_final: 0.6511 (tp30) REVERT: F 224 GLU cc_start: 0.7361 (mt-10) cc_final: 0.7108 (mt-10) REVERT: G 216 GLU cc_start: 0.6946 (tm-30) cc_final: 0.6585 (tp30) REVERT: H 106 ASP cc_start: 0.7947 (p0) cc_final: 0.7550 (p0) REVERT: I 77 ASP cc_start: 0.8684 (p0) cc_final: 0.8416 (p0) REVERT: I 80 THR cc_start: 0.9106 (m) cc_final: 0.8874 (m) REVERT: K 33 ASP cc_start: 0.8197 (t0) cc_final: 0.7864 (t70) REVERT: K 52 ASP cc_start: 0.8431 (m-30) cc_final: 0.8220 (m-30) REVERT: L 45 MET cc_start: 0.8374 (ttt) cc_final: 0.7901 (tmt) REVERT: M 29 ASP cc_start: 0.7597 (t70) cc_final: 0.7274 (t0) REVERT: M 30 ASP cc_start: 0.8222 (p0) cc_final: 0.8015 (p0) REVERT: M 78 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.8430 (ttt90) REVERT: N 64 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8636 (mt-10) REVERT: O 178 LYS cc_start: 0.6935 (mttt) cc_final: 0.6717 (mmmt) REVERT: Q 22 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8579 (mm-30) REVERT: Q 189 ASP cc_start: 0.7211 (m-30) cc_final: 0.6996 (m-30) REVERT: Q 233 ASP cc_start: 0.6670 (t70) cc_final: 0.6409 (t70) REVERT: R 40 ASP cc_start: 0.6539 (p0) cc_final: 0.5242 (p0) REVERT: R 86 GLN cc_start: 0.7427 (tt0) cc_final: 0.7182 (tt0) REVERT: R 159 LYS cc_start: 0.7855 (mttt) cc_final: 0.7616 (mttm) REVERT: R 210 TYR cc_start: 0.7449 (p90) cc_final: 0.7140 (p90) REVERT: S 149 GLU cc_start: 0.7910 (tt0) cc_final: 0.7551 (tp30) REVERT: S 213 ASN cc_start: 0.6954 (t0) cc_final: 0.6688 (t0) REVERT: S 232 TYR cc_start: 0.8348 (m-10) cc_final: 0.8085 (m-10) REVERT: T 18 ARG cc_start: 0.7924 (mtp180) cc_final: 0.7363 (mtm110) REVERT: T 55 GLU cc_start: 0.6719 (tp30) cc_final: 0.6509 (tp30) REVERT: T 224 GLU cc_start: 0.7359 (mt-10) cc_final: 0.7105 (mt-10) REVERT: U 216 GLU cc_start: 0.6945 (tm-30) cc_final: 0.6584 (tp30) REVERT: V 106 ASP cc_start: 0.7941 (p0) cc_final: 0.7549 (p0) REVERT: W 77 ASP cc_start: 0.8688 (p0) cc_final: 0.8426 (p0) REVERT: W 80 THR cc_start: 0.9106 (m) cc_final: 0.8875 (m) REVERT: W 203 GLU cc_start: 0.8546 (pm20) cc_final: 0.8336 (pm20) REVERT: Y 33 ASP cc_start: 0.8200 (t0) cc_final: 0.7866 (t70) REVERT: Y 52 ASP cc_start: 0.8432 (m-30) cc_final: 0.8219 (m-30) REVERT: Z 45 MET cc_start: 0.8371 (ttt) cc_final: 0.7897 (tmt) REVERT: a 29 ASP cc_start: 0.7600 (t70) cc_final: 0.7280 (t0) REVERT: a 30 ASP cc_start: 0.8230 (p0) cc_final: 0.8020 (p0) REVERT: a 78 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.8424 (ttt90) REVERT: b 64 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8635 (mt-10) outliers start: 47 outliers final: 11 residues processed: 1257 average time/residue: 1.6664 time to fit residues: 2591.5253 Evaluate side-chains 914 residues out of total 5152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 901 time to evaluate : 5.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain F residue 122 LYS Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 136 TYR Chi-restraints excluded: chain M residue 78 ARG Chi-restraints excluded: chain P residue 122 ILE Chi-restraints excluded: chain T residue 122 LYS Chi-restraints excluded: chain Y residue 139 VAL Chi-restraints excluded: chain Z residue 84 VAL Chi-restraints excluded: chain Z residue 136 TYR Chi-restraints excluded: chain a residue 78 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 510 optimal weight: 0.7980 chunk 457 optimal weight: 0.9980 chunk 254 optimal weight: 3.9990 chunk 156 optimal weight: 9.9990 chunk 308 optimal weight: 0.0870 chunk 244 optimal weight: 2.9990 chunk 473 optimal weight: 10.0000 chunk 183 optimal weight: 0.8980 chunk 287 optimal weight: 3.9990 chunk 352 optimal weight: 0.0370 chunk 548 optimal weight: 1.9990 overall best weight: 0.5636 ------------------------------------------------------------------------------- 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 219 ASN B 69 ASN B 146 GLN C 29 ASN C 30 GLN C 51 ASN C 215 GLN D 55 GLN E 97 GLN E 157 HIS ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN G 91 GLN G 175 GLN H 176 ASN ** I 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 8 ASN K 61 GLN L 181 GLN ** M 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 GLN M 149 ASN M 224 HIS N 47 ASN ** N 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 219 ASN P 69 ASN P 146 GLN Q 29 ASN Q 30 GLN Q 51 ASN Q 215 GLN R 55 GLN S 97 GLN S 157 HIS ** T 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 53 ASN U 91 GLN U 175 GLN V 176 ASN ** W 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 8 ASN Y 61 GLN Z 181 GLN ** a 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 89 GLN a 149 ASN ** a 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 47 ASN ** b 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 48686 Z= 0.224 Angle : 0.573 12.701 65884 Z= 0.306 Chirality : 0.045 0.187 7434 Planarity : 0.005 0.067 8518 Dihedral : 7.417 135.076 6889 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.57 % Allowed : 13.14 % Favored : 84.30 % 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: 0.39 (0.11), residues: 6082 helix: 1.16 (0.10), residues: 2266 sheet: -0.51 (0.13), residues: 1510 loop : 0.08 (0.13), residues: 2306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 154 HIS 0.006 0.001 HIS K 143 PHE 0.019 0.002 PHE X 70 TYR 0.016 0.002 TYR G 86 ARG 0.007 0.001 ARG b 99 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1181 residues out of total 5152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 1049 time to evaluate : 5.177 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8100 (mtmm) cc_final: 0.7880 (mtmt) REVERT: A 49 GLN cc_start: 0.7798 (pt0) cc_final: 0.7414 (pm20) REVERT: A 169 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.7067 (tt0) REVERT: A 178 LYS cc_start: 0.6905 (mttt) cc_final: 0.6671 (mmmt) REVERT: B 107 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7807 (mm-30) REVERT: B 213 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7212 (pp20) REVERT: C 22 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8565 (mm-30) REVERT: C 189 ASP cc_start: 0.7220 (m-30) cc_final: 0.7019 (m-30) REVERT: D 58 HIS cc_start: 0.5344 (OUTLIER) cc_final: 0.4445 (m90) REVERT: D 86 GLN cc_start: 0.7477 (tt0) cc_final: 0.7176 (tt0) REVERT: D 210 TYR cc_start: 0.7358 (p90) cc_final: 0.6942 (p90) REVERT: E 213 ASN cc_start: 0.6989 (t0) cc_final: 0.6730 (t0) REVERT: F 18 ARG cc_start: 0.7920 (mtp180) cc_final: 0.7663 (mtm110) REVERT: F 224 GLU cc_start: 0.7327 (mt-10) cc_final: 0.7103 (mt-10) REVERT: H 106 ASP cc_start: 0.8074 (p0) cc_final: 0.7719 (p0) REVERT: H 200 ASP cc_start: 0.8306 (m-30) cc_final: 0.8014 (m-30) REVERT: J 66 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7787 (mt-10) REVERT: J 119 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7337 (tp30) REVERT: J 160 ASN cc_start: 0.8880 (p0) cc_final: 0.8608 (p0) REVERT: K 33 ASP cc_start: 0.8104 (t0) cc_final: 0.7766 (t70) REVERT: K 52 ASP cc_start: 0.8495 (m-30) cc_final: 0.8231 (m-30) REVERT: L 45 MET cc_start: 0.8238 (ttt) cc_final: 0.7894 (tmt) REVERT: L 53 GLN cc_start: 0.8879 (mt0) cc_final: 0.8645 (mt0) REVERT: L 86 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7853 (mm-30) REVERT: M 29 ASP cc_start: 0.7539 (t70) cc_final: 0.7170 (t0) REVERT: N 58 ASP cc_start: 0.8719 (m-30) cc_final: 0.8468 (m-30) REVERT: N 64 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8610 (mt-10) REVERT: O 41 LYS cc_start: 0.8101 (mtmm) cc_final: 0.7880 (mtmt) REVERT: O 49 GLN cc_start: 0.7808 (pt0) cc_final: 0.7435 (pm20) REVERT: O 169 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.7063 (tt0) REVERT: O 178 LYS cc_start: 0.6904 (mttt) cc_final: 0.6665 (mmmt) REVERT: P 107 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7806 (mm-30) REVERT: P 213 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7211 (pp20) REVERT: Q 22 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8566 (mm-30) REVERT: Q 189 ASP cc_start: 0.7225 (m-30) cc_final: 0.7016 (m-30) REVERT: Q 233 ASP cc_start: 0.6633 (t70) cc_final: 0.6432 (t70) REVERT: R 58 HIS cc_start: 0.5348 (OUTLIER) cc_final: 0.4449 (m90) REVERT: R 86 GLN cc_start: 0.7481 (tt0) cc_final: 0.7178 (tt0) REVERT: R 210 TYR cc_start: 0.7356 (p90) cc_final: 0.6968 (p90) REVERT: S 213 ASN cc_start: 0.6989 (t0) cc_final: 0.6730 (t0) REVERT: T 18 ARG cc_start: 0.7916 (mtp180) cc_final: 0.7659 (mtm110) REVERT: T 224 GLU cc_start: 0.7324 (mt-10) cc_final: 0.7098 (mt-10) REVERT: V 106 ASP cc_start: 0.8078 (p0) cc_final: 0.7721 (p0) REVERT: V 200 ASP cc_start: 0.8308 (m-30) cc_final: 0.8015 (m-30) REVERT: W 203 GLU cc_start: 0.8531 (pm20) cc_final: 0.8266 (pm20) REVERT: X 66 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7792 (mt-10) REVERT: X 119 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7336 (tp30) REVERT: X 160 ASN cc_start: 0.8881 (p0) cc_final: 0.8608 (p0) REVERT: Y 33 ASP cc_start: 0.8109 (t0) cc_final: 0.7776 (t70) REVERT: Y 52 ASP cc_start: 0.8496 (m-30) cc_final: 0.8233 (m-30) REVERT: Z 45 MET cc_start: 0.8239 (ttt) cc_final: 0.7892 (tmt) REVERT: Z 53 GLN cc_start: 0.8876 (mt0) cc_final: 0.8641 (mt0) REVERT: Z 86 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7850 (mm-30) REVERT: a 29 ASP cc_start: 0.7542 (t70) cc_final: 0.7175 (t0) REVERT: a 69 ASP cc_start: 0.8877 (t0) cc_final: 0.8306 (t70) REVERT: b 58 ASP cc_start: 0.8715 (m-30) cc_final: 0.8470 (m-30) REVERT: b 64 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8610 (mt-10) outliers start: 132 outliers final: 52 residues processed: 1119 average time/residue: 1.5700 time to fit residues: 2188.9394 Evaluate side-chains 944 residues out of total 5152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 886 time to evaluate : 5.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 220 TYR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 58 HIS Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 217 ASP Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 71 ASN Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 136 TYR Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain M residue 17 GLU Chi-restraints excluded: chain M residue 167 ILE Chi-restraints excluded: chain M residue 209 PHE Chi-restraints excluded: chain O residue 32 GLU Chi-restraints excluded: chain O residue 33 VAL Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain O residue 167 VAL Chi-restraints excluded: chain O residue 169 GLU Chi-restraints excluded: chain O residue 185 THR Chi-restraints excluded: chain P residue 152 THR Chi-restraints excluded: chain Q residue 79 THR Chi-restraints excluded: chain Q residue 220 TYR Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 58 HIS Chi-restraints excluded: chain R residue 182 MET Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 158 THR Chi-restraints excluded: chain T residue 35 THR Chi-restraints excluded: chain T residue 217 ASP Chi-restraints excluded: chain T residue 223 LEU Chi-restraints excluded: chain W residue 28 VAL Chi-restraints excluded: chain X residue 66 GLU Chi-restraints excluded: chain Y residue 21 VAL Chi-restraints excluded: chain Y residue 71 ASN Chi-restraints excluded: chain Y residue 139 VAL Chi-restraints excluded: chain Z residue 84 VAL Chi-restraints excluded: chain Z residue 136 TYR Chi-restraints excluded: chain Z residue 190 THR Chi-restraints excluded: chain a residue 17 GLU Chi-restraints excluded: chain a residue 167 ILE Chi-restraints excluded: chain a residue 209 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 304 optimal weight: 3.9990 chunk 170 optimal weight: 0.9990 chunk 456 optimal weight: 0.9990 chunk 373 optimal weight: 7.9990 chunk 151 optimal weight: 7.9990 chunk 549 optimal weight: 2.9990 chunk 593 optimal weight: 0.6980 chunk 489 optimal weight: 5.9990 chunk 544 optimal weight: 0.9990 chunk 187 optimal weight: 5.9990 chunk 440 optimal weight: 0.8980 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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 198 GLN A 219 ASN B 146 GLN C 29 ASN C 30 GLN D 116 GLN E 150 ASN F 68 GLN ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 GLN I 69 ASN I 89 GLN ** I 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 144 ASN I 174 ASN J 8 ASN ** L 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 110 HIS L 181 GLN M 60 ASN N 47 ASN N 77 HIS ** N 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 155 ASN ** O 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 198 GLN O 219 ASN P 146 GLN Q 29 ASN Q 30 GLN Q 215 GLN R 116 GLN S 150 ASN S 238 GLN ** T 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 91 GLN W 69 ASN W 89 GLN W 109 GLN ** W 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 144 ASN W 174 ASN X 8 ASN ** Z 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 110 HIS Z 181 GLN a 60 ASN ** a 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 47 ASN b 77 HIS ** b 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 155 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 48686 Z= 0.235 Angle : 0.553 14.498 65884 Z= 0.294 Chirality : 0.045 0.187 7434 Planarity : 0.004 0.056 8518 Dihedral : 7.147 129.956 6869 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.93 % Allowed : 15.02 % Favored : 82.04 % 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: 0.58 (0.11), residues: 6082 helix: 1.37 (0.10), residues: 2266 sheet: -0.44 (0.13), residues: 1506 loop : 0.16 (0.13), residues: 2310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 154 HIS 0.005 0.001 HIS b 88 PHE 0.018 0.002 PHE X 70 TYR 0.016 0.002 TYR G 86 ARG 0.006 0.001 ARG P 169 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1145 residues out of total 5152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 994 time to evaluate : 5.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 GLN cc_start: 0.7812 (pt0) cc_final: 0.7503 (pt0) REVERT: A 169 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.7087 (tt0) REVERT: A 178 LYS cc_start: 0.6929 (mttt) cc_final: 0.6668 (mmmt) REVERT: B 154 TRP cc_start: 0.6457 (OUTLIER) cc_final: 0.4887 (m-90) REVERT: C 22 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8554 (mm-30) REVERT: C 48 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7485 (tt0) REVERT: C 107 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7436 (tm-30) REVERT: C 189 ASP cc_start: 0.7177 (m-30) cc_final: 0.6952 (m-30) REVERT: D 58 HIS cc_start: 0.5368 (OUTLIER) cc_final: 0.4492 (m90) REVERT: D 86 GLN cc_start: 0.7432 (tt0) cc_final: 0.7162 (tt0) REVERT: D 210 TYR cc_start: 0.7338 (p90) cc_final: 0.6897 (p90) REVERT: E 213 ASN cc_start: 0.7052 (t0) cc_final: 0.6748 (t0) REVERT: F 27 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7565 (mttm) REVERT: G 232 ARG cc_start: 0.7501 (mpt-90) cc_final: 0.7296 (mmt90) REVERT: H 200 ASP cc_start: 0.8299 (m-30) cc_final: 0.8031 (m-30) REVERT: J 66 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7809 (mt-10) REVERT: J 86 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8487 (mttt) REVERT: J 105 PHE cc_start: 0.7893 (m-80) cc_final: 0.7637 (m-80) REVERT: J 119 GLU cc_start: 0.7520 (mm-30) cc_final: 0.7286 (tp30) REVERT: J 160 ASN cc_start: 0.8836 (p0) cc_final: 0.8582 (p0) REVERT: K 33 ASP cc_start: 0.8115 (t0) cc_final: 0.7797 (t70) REVERT: K 52 ASP cc_start: 0.8480 (m-30) cc_final: 0.8228 (m-30) REVERT: L 45 MET cc_start: 0.8208 (ttt) cc_final: 0.7921 (tmt) REVERT: L 86 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7938 (mm-30) REVERT: N 64 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8627 (mt-10) REVERT: O 49 GLN cc_start: 0.7811 (pt0) cc_final: 0.7508 (pt0) REVERT: O 169 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.7084 (tt0) REVERT: O 178 LYS cc_start: 0.6927 (mttt) cc_final: 0.6664 (mmmt) REVERT: P 154 TRP cc_start: 0.6426 (OUTLIER) cc_final: 0.4862 (m-90) REVERT: Q 22 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8551 (mm-30) REVERT: Q 48 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7527 (tt0) REVERT: Q 107 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7432 (tm-30) REVERT: Q 189 ASP cc_start: 0.7174 (m-30) cc_final: 0.6974 (m-30) REVERT: R 58 HIS cc_start: 0.5354 (OUTLIER) cc_final: 0.4478 (m90) REVERT: R 86 GLN cc_start: 0.7420 (tt0) cc_final: 0.7157 (tt0) REVERT: R 210 TYR cc_start: 0.7332 (p90) cc_final: 0.6912 (p90) REVERT: S 213 ASN cc_start: 0.7081 (t0) cc_final: 0.6769 (t0) REVERT: T 18 ARG cc_start: 0.7936 (mtp180) cc_final: 0.7640 (mtm110) REVERT: T 27 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7579 (mttm) REVERT: U 232 ARG cc_start: 0.7502 (mpt-90) cc_final: 0.7295 (mmt90) REVERT: V 200 ASP cc_start: 0.8303 (m-30) cc_final: 0.8021 (m-30) REVERT: W 203 GLU cc_start: 0.8539 (pm20) cc_final: 0.8332 (pm20) REVERT: X 66 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.7812 (mt-10) REVERT: X 86 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8490 (mttt) REVERT: X 105 PHE cc_start: 0.7897 (m-80) cc_final: 0.7640 (m-80) REVERT: X 119 GLU cc_start: 0.7516 (mm-30) cc_final: 0.7284 (tp30) REVERT: X 160 ASN cc_start: 0.8836 (p0) cc_final: 0.8579 (p0) REVERT: Y 33 ASP cc_start: 0.8116 (t0) cc_final: 0.7798 (t70) REVERT: Y 52 ASP cc_start: 0.8481 (m-30) cc_final: 0.8224 (m-30) REVERT: Z 45 MET cc_start: 0.8209 (ttt) cc_final: 0.7917 (tmt) REVERT: Z 86 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7945 (mm-30) REVERT: b 64 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8625 (mt-10) outliers start: 151 outliers final: 60 residues processed: 1079 average time/residue: 1.5385 time to fit residues: 2086.6643 Evaluate side-chains 947 residues out of total 5152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 873 time to evaluate : 5.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 154 TRP Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 220 TYR Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 58 HIS Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain F residue 27 LYS Chi-restraints excluded: chain F residue 217 ASP Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 188 MET Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 86 LYS Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 71 ASN Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 124 LYS Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 136 TYR Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain M residue 209 PHE Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain O residue 33 VAL Chi-restraints excluded: chain O residue 92 SER Chi-restraints excluded: chain O residue 167 VAL Chi-restraints excluded: chain O residue 169 GLU Chi-restraints excluded: chain O residue 185 THR Chi-restraints excluded: chain P residue 152 THR Chi-restraints excluded: chain P residue 154 TRP Chi-restraints excluded: chain Q residue 48 GLU Chi-restraints excluded: chain Q residue 79 THR Chi-restraints excluded: chain Q residue 188 MET Chi-restraints excluded: chain Q residue 214 LEU Chi-restraints excluded: chain Q residue 220 TYR Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 58 HIS Chi-restraints excluded: chain R residue 182 MET Chi-restraints excluded: chain S residue 24 VAL Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 158 THR Chi-restraints excluded: chain T residue 27 LYS Chi-restraints excluded: chain T residue 217 ASP Chi-restraints excluded: chain T residue 223 LEU Chi-restraints excluded: chain V residue 131 SER Chi-restraints excluded: chain V residue 188 MET Chi-restraints excluded: chain W residue 28 VAL Chi-restraints excluded: chain X residue 66 GLU Chi-restraints excluded: chain X residue 86 LYS Chi-restraints excluded: chain Y residue 21 VAL Chi-restraints excluded: chain Y residue 71 ASN Chi-restraints excluded: chain Y residue 139 VAL Chi-restraints excluded: chain Z residue 84 VAL Chi-restraints excluded: chain Z residue 124 LYS Chi-restraints excluded: chain Z residue 128 VAL Chi-restraints excluded: chain Z residue 136 TYR Chi-restraints excluded: chain Z residue 190 THR Chi-restraints excluded: chain a residue 209 PHE Chi-restraints excluded: chain b residue 117 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 542 optimal weight: 4.9990 chunk 413 optimal weight: 8.9990 chunk 285 optimal weight: 4.9990 chunk 60 optimal weight: 9.9990 chunk 262 optimal weight: 0.9990 chunk 368 optimal weight: 7.9990 chunk 551 optimal weight: 0.9980 chunk 583 optimal weight: 0.4980 chunk 288 optimal weight: 0.9990 chunk 522 optimal weight: 1.9990 chunk 157 optimal weight: 10.0000 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 198 GLN A 219 ASN B 146 GLN C 29 ASN C 30 GLN E 150 ASN G 91 GLN I 89 GLN I 109 GLN ** I 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 144 ASN I 149 HIS J 8 ASN K 31 ASN ** L 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 GLN N 47 ASN N 89 ASN ** N 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 198 GLN O 219 ASN P 146 GLN Q 29 ASN Q 30 GLN Q 215 GLN S 150 ASN T 68 GLN U 91 GLN ** V 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 89 GLN ** W 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 144 ASN W 149 HIS X 8 ASN ** Z 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 53 GLN ** a 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 47 ASN ** b 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 48686 Z= 0.243 Angle : 0.549 14.835 65884 Z= 0.291 Chirality : 0.045 0.188 7434 Planarity : 0.004 0.053 8518 Dihedral : 7.077 128.612 6868 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.01 % Allowed : 16.19 % Favored : 80.80 % 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: 0.65 (0.11), residues: 6082 helix: 1.44 (0.11), residues: 2268 sheet: -0.42 (0.13), residues: 1500 loop : 0.20 (0.13), residues: 2314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP P 154 HIS 0.006 0.001 HIS a 224 PHE 0.018 0.002 PHE J 70 TYR 0.016 0.002 TYR G 86 ARG 0.009 0.001 ARG D 10 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1075 residues out of total 5152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 920 time to evaluate : 5.275 Fit side-chains revert: symmetry clash REVERT: A 49 GLN cc_start: 0.7799 (pt0) cc_final: 0.7512 (pt0) REVERT: A 169 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.7084 (tt0) REVERT: A 178 LYS cc_start: 0.6904 (mttt) cc_final: 0.6641 (mmmt) REVERT: B 107 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7755 (mm-30) REVERT: B 154 TRP cc_start: 0.6433 (OUTLIER) cc_final: 0.4891 (m-90) REVERT: B 213 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7309 (pp20) REVERT: C 54 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.6960 (ttt180) REVERT: C 107 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7386 (tm-30) REVERT: D 58 HIS cc_start: 0.5378 (OUTLIER) cc_final: 0.4470 (m90) REVERT: D 86 GLN cc_start: 0.7449 (tt0) cc_final: 0.7196 (tt0) REVERT: D 210 TYR cc_start: 0.7325 (p90) cc_final: 0.6898 (p90) REVERT: E 213 ASN cc_start: 0.7145 (t0) cc_final: 0.6839 (t0) REVERT: E 232 TYR cc_start: 0.8512 (m-10) cc_final: 0.8290 (m-10) REVERT: F 18 ARG cc_start: 0.8346 (mtm110) cc_final: 0.7814 (mtm110) REVERT: F 27 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7580 (mttm) REVERT: G 67 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8733 (mm) REVERT: H 131 SER cc_start: 0.9034 (OUTLIER) cc_final: 0.8818 (m) REVERT: H 200 ASP cc_start: 0.8294 (m-30) cc_final: 0.8019 (m-30) REVERT: J 66 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7795 (mt-10) REVERT: J 86 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8478 (mttt) REVERT: J 105 PHE cc_start: 0.7900 (m-80) cc_final: 0.7662 (m-80) REVERT: J 119 GLU cc_start: 0.7533 (mm-30) cc_final: 0.7257 (tp30) REVERT: J 160 ASN cc_start: 0.8808 (p0) cc_final: 0.8547 (p0) REVERT: J 200 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7934 (tt0) REVERT: K 33 ASP cc_start: 0.8130 (t0) cc_final: 0.7823 (t70) REVERT: K 52 ASP cc_start: 0.8502 (m-30) cc_final: 0.8264 (m-30) REVERT: L 45 MET cc_start: 0.8139 (ttt) cc_final: 0.7883 (tmt) REVERT: L 86 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7928 (mm-30) REVERT: M 69 ASP cc_start: 0.8835 (t0) cc_final: 0.8259 (t70) REVERT: N 64 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8613 (mt-10) REVERT: N 163 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.7866 (tttp) REVERT: O 49 GLN cc_start: 0.7794 (pt0) cc_final: 0.7513 (pt0) REVERT: O 169 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.7081 (tt0) REVERT: O 178 LYS cc_start: 0.6901 (mttt) cc_final: 0.6638 (mmmt) REVERT: P 107 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7751 (mm-30) REVERT: P 154 TRP cc_start: 0.6403 (OUTLIER) cc_final: 0.4863 (m-90) REVERT: P 213 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7305 (pp20) REVERT: Q 48 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7505 (tt0) REVERT: Q 54 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.6985 (ttt180) REVERT: Q 107 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7380 (tm-30) REVERT: Q 189 ASP cc_start: 0.7205 (m-30) cc_final: 0.7000 (m-30) REVERT: R 58 HIS cc_start: 0.5379 (OUTLIER) cc_final: 0.4467 (m90) REVERT: R 86 GLN cc_start: 0.7456 (tt0) cc_final: 0.7199 (tt0) REVERT: R 210 TYR cc_start: 0.7325 (p90) cc_final: 0.6919 (p90) REVERT: S 213 ASN cc_start: 0.7154 (t0) cc_final: 0.6840 (t0) REVERT: S 232 TYR cc_start: 0.8526 (m-10) cc_final: 0.8317 (m-10) REVERT: T 18 ARG cc_start: 0.7960 (mtp180) cc_final: 0.7670 (mtm110) REVERT: T 27 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7581 (mttm) REVERT: U 67 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8732 (mm) REVERT: V 131 SER cc_start: 0.9037 (OUTLIER) cc_final: 0.8824 (m) REVERT: V 200 ASP cc_start: 0.8298 (m-30) cc_final: 0.8000 (m-30) REVERT: X 66 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7800 (mt-10) REVERT: X 86 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8468 (mttt) REVERT: X 105 PHE cc_start: 0.7905 (m-80) cc_final: 0.7666 (m-80) REVERT: X 119 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7253 (tp30) REVERT: X 160 ASN cc_start: 0.8809 (p0) cc_final: 0.8578 (p0) REVERT: X 200 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7936 (tt0) REVERT: Y 33 ASP cc_start: 0.8130 (t0) cc_final: 0.7819 (t70) REVERT: Y 52 ASP cc_start: 0.8491 (m-30) cc_final: 0.8250 (m-30) REVERT: Z 45 MET cc_start: 0.8138 (ttt) cc_final: 0.7879 (tmt) REVERT: Z 86 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7943 (mm-30) REVERT: b 64 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8615 (mt-10) REVERT: b 163 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.7892 (tttp) outliers start: 155 outliers final: 75 residues processed: 1015 average time/residue: 1.5440 time to fit residues: 1968.5782 Evaluate side-chains 960 residues out of total 5152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 864 time to evaluate : 5.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 154 TRP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 220 TYR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 58 HIS Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 194 HIS Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain F residue 27 LYS Chi-restraints excluded: chain F residue 217 ASP Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain G residue 67 ILE Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 146 GLU Chi-restraints excluded: chain H residue 186 LYS Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 86 LYS Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 71 ASN Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 136 TYR Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain M residue 209 PHE Chi-restraints excluded: chain N residue 78 ASN Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain N residue 163 LYS Chi-restraints excluded: chain O residue 33 VAL Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain O residue 92 SER Chi-restraints excluded: chain O residue 167 VAL Chi-restraints excluded: chain O residue 169 GLU Chi-restraints excluded: chain O residue 185 THR Chi-restraints excluded: chain O residue 195 SER Chi-restraints excluded: chain P residue 152 THR Chi-restraints excluded: chain P residue 154 TRP Chi-restraints excluded: chain P residue 182 VAL Chi-restraints excluded: chain Q residue 48 GLU Chi-restraints excluded: chain Q residue 54 ARG Chi-restraints excluded: chain Q residue 79 THR Chi-restraints excluded: chain Q residue 214 LEU Chi-restraints excluded: chain Q residue 220 TYR Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 58 HIS Chi-restraints excluded: chain R residue 87 SER Chi-restraints excluded: chain R residue 182 MET Chi-restraints excluded: chain S residue 13 ASN Chi-restraints excluded: chain S residue 24 VAL Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 158 THR Chi-restraints excluded: chain S residue 194 HIS Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 233 THR Chi-restraints excluded: chain T residue 27 LYS Chi-restraints excluded: chain T residue 217 ASP Chi-restraints excluded: chain T residue 223 LEU Chi-restraints excluded: chain U residue 67 ILE Chi-restraints excluded: chain V residue 131 SER Chi-restraints excluded: chain V residue 146 GLU Chi-restraints excluded: chain V residue 186 LYS Chi-restraints excluded: chain W residue 28 VAL Chi-restraints excluded: chain X residue 66 GLU Chi-restraints excluded: chain X residue 86 LYS Chi-restraints excluded: chain Y residue 21 VAL Chi-restraints excluded: chain Y residue 71 ASN Chi-restraints excluded: chain Y residue 139 VAL Chi-restraints excluded: chain Z residue 84 VAL Chi-restraints excluded: chain Z residue 136 TYR Chi-restraints excluded: chain Z residue 190 THR Chi-restraints excluded: chain a residue 167 ILE Chi-restraints excluded: chain a residue 209 PHE Chi-restraints excluded: chain a residue 224 HIS Chi-restraints excluded: chain b residue 78 ASN Chi-restraints excluded: chain b residue 117 ASP Chi-restraints excluded: chain b residue 163 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 486 optimal weight: 0.8980 chunk 331 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 chunk 434 optimal weight: 0.9980 chunk 240 optimal weight: 4.9990 chunk 498 optimal weight: 9.9990 chunk 403 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 298 optimal weight: 2.9990 chunk 524 optimal weight: 0.9990 chunk 147 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 198 GLN A 219 ASN B 180 GLN C 30 GLN E 150 ASN G 91 GLN I 89 GLN ** I 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 144 ASN I 149 HIS I 174 ASN J 8 ASN K 31 ASN K 61 GLN ** L 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 GLN N 47 ASN ** N 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 198 GLN O 219 ASN P 180 GLN Q 30 GLN Q 215 GLN S 150 ASN U 91 GLN W 89 GLN ** W 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 144 ASN W 149 HIS W 174 ASN X 8 ASN Y 61 GLN ** Z 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 89 GLN ** a 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 47 ASN b 89 ASN ** b 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 48686 Z= 0.245 Angle : 0.548 15.125 65884 Z= 0.291 Chirality : 0.044 0.192 7434 Planarity : 0.004 0.071 8518 Dihedral : 7.026 127.653 6868 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.05 % Allowed : 16.91 % Favored : 80.04 % 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: 0.69 (0.11), residues: 6082 helix: 1.48 (0.11), residues: 2268 sheet: -0.38 (0.13), residues: 1490 loop : 0.19 (0.14), residues: 2324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 154 HIS 0.007 0.001 HIS a 224 PHE 0.019 0.002 PHE J 70 TYR 0.017 0.002 TYR U 86 ARG 0.007 0.001 ARG D 10 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1082 residues out of total 5152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 925 time to evaluate : 5.527 Fit side-chains REVERT: A 49 GLN cc_start: 0.7773 (pt0) cc_final: 0.7513 (pt0) REVERT: A 84 ASN cc_start: 0.8139 (m-40) cc_final: 0.7921 (m-40) REVERT: A 169 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7084 (tt0) REVERT: A 178 LYS cc_start: 0.6906 (mttt) cc_final: 0.6638 (mmmt) REVERT: B 213 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7280 (pp20) REVERT: C 17 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.7803 (ptp90) REVERT: C 107 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7440 (tm-30) REVERT: C 165 GLU cc_start: 0.7661 (pt0) cc_final: 0.7356 (pt0) REVERT: D 58 HIS cc_start: 0.5373 (OUTLIER) cc_final: 0.4396 (m90) REVERT: D 86 GLN cc_start: 0.7452 (tt0) cc_final: 0.7178 (tt0) REVERT: D 210 TYR cc_start: 0.7299 (p90) cc_final: 0.6901 (p90) REVERT: E 78 MET cc_start: 0.8457 (mtm) cc_final: 0.8183 (mtm) REVERT: E 213 ASN cc_start: 0.7146 (t0) cc_final: 0.6806 (t0) REVERT: F 18 ARG cc_start: 0.8339 (mtm110) cc_final: 0.7802 (mtm110) REVERT: F 27 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7613 (mttm) REVERT: G 67 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8718 (mm) REVERT: G 217 THR cc_start: 0.8368 (p) cc_final: 0.7971 (t) REVERT: H 131 SER cc_start: 0.9039 (p) cc_final: 0.8824 (m) REVERT: H 200 ASP cc_start: 0.8304 (m-30) cc_final: 0.8019 (m-30) REVERT: J 66 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.7797 (mt-10) REVERT: J 119 GLU cc_start: 0.7528 (mm-30) cc_final: 0.7254 (tp30) REVERT: J 160 ASN cc_start: 0.8793 (p0) cc_final: 0.8555 (p0) REVERT: J 200 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7933 (tt0) REVERT: K 33 ASP cc_start: 0.8137 (t0) cc_final: 0.7845 (t70) REVERT: K 52 ASP cc_start: 0.8489 (m-30) cc_final: 0.8269 (m-30) REVERT: L 86 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7981 (mm-30) REVERT: M 69 ASP cc_start: 0.8897 (t0) cc_final: 0.8284 (t70) REVERT: N 64 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8618 (mt-10) REVERT: N 163 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.7891 (tttp) REVERT: O 49 GLN cc_start: 0.7762 (pt0) cc_final: 0.7512 (pt0) REVERT: O 84 ASN cc_start: 0.8142 (m-40) cc_final: 0.7926 (m-40) REVERT: O 169 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.7078 (tt0) REVERT: O 178 LYS cc_start: 0.6905 (mttt) cc_final: 0.6635 (mmmt) REVERT: P 213 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7298 (pp20) REVERT: Q 17 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.7787 (ptp90) REVERT: Q 48 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7431 (tt0) REVERT: Q 107 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7441 (tm-30) REVERT: Q 189 ASP cc_start: 0.7221 (m-30) cc_final: 0.6996 (m-30) REVERT: R 58 HIS cc_start: 0.5373 (OUTLIER) cc_final: 0.4413 (m90) REVERT: R 86 GLN cc_start: 0.7456 (tt0) cc_final: 0.7181 (tt0) REVERT: R 210 TYR cc_start: 0.7304 (p90) cc_final: 0.6895 (p90) REVERT: S 78 MET cc_start: 0.8505 (mtm) cc_final: 0.8190 (mtm) REVERT: S 213 ASN cc_start: 0.7144 (t0) cc_final: 0.6808 (t0) REVERT: T 27 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7588 (mttm) REVERT: U 217 THR cc_start: 0.8369 (p) cc_final: 0.7965 (t) REVERT: V 131 SER cc_start: 0.9039 (p) cc_final: 0.8828 (m) REVERT: V 200 ASP cc_start: 0.8290 (m-30) cc_final: 0.8002 (m-30) REVERT: X 66 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7798 (mt-10) REVERT: X 119 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7256 (tp30) REVERT: X 160 ASN cc_start: 0.8778 (p0) cc_final: 0.8561 (p0) REVERT: X 200 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7934 (tt0) REVERT: Y 33 ASP cc_start: 0.8136 (t0) cc_final: 0.7830 (t70) REVERT: Y 52 ASP cc_start: 0.8491 (m-30) cc_final: 0.8269 (m-30) REVERT: Z 86 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7977 (mm-30) REVERT: b 64 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8617 (mt-10) REVERT: b 163 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.7899 (tttp) outliers start: 157 outliers final: 87 residues processed: 1010 average time/residue: 1.5608 time to fit residues: 1976.3874 Evaluate side-chains 950 residues out of total 5152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 849 time to evaluate : 5.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain C residue 17 ARG Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 220 TYR Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 58 HIS Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 194 HIS Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain F residue 27 LYS Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 217 ASP Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain G residue 67 ILE Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain H residue 146 GLU Chi-restraints excluded: chain H residue 186 LYS Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 71 ASN Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 124 LYS Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 136 TYR Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain M residue 97 GLU Chi-restraints excluded: chain M residue 167 ILE Chi-restraints excluded: chain M residue 209 PHE Chi-restraints excluded: chain N residue 78 ASN Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain N residue 163 LYS Chi-restraints excluded: chain O residue 33 VAL Chi-restraints excluded: chain O residue 92 SER Chi-restraints excluded: chain O residue 167 VAL Chi-restraints excluded: chain O residue 169 GLU Chi-restraints excluded: chain O residue 185 THR Chi-restraints excluded: chain O residue 195 SER Chi-restraints excluded: chain P residue 152 THR Chi-restraints excluded: chain P residue 182 VAL Chi-restraints excluded: chain Q residue 17 ARG Chi-restraints excluded: chain Q residue 48 GLU Chi-restraints excluded: chain Q residue 79 THR Chi-restraints excluded: chain Q residue 214 LEU Chi-restraints excluded: chain Q residue 220 TYR Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 58 HIS Chi-restraints excluded: chain R residue 87 SER Chi-restraints excluded: chain R residue 182 MET Chi-restraints excluded: chain S residue 13 ASN Chi-restraints excluded: chain S residue 24 VAL Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 158 THR Chi-restraints excluded: chain S residue 194 HIS Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 233 THR Chi-restraints excluded: chain T residue 27 LYS Chi-restraints excluded: chain T residue 123 VAL Chi-restraints excluded: chain T residue 217 ASP Chi-restraints excluded: chain T residue 223 LEU Chi-restraints excluded: chain U residue 210 MET Chi-restraints excluded: chain U residue 213 LEU Chi-restraints excluded: chain V residue 146 GLU Chi-restraints excluded: chain V residue 186 LYS Chi-restraints excluded: chain W residue 28 VAL Chi-restraints excluded: chain X residue 66 GLU Chi-restraints excluded: chain Y residue 21 VAL Chi-restraints excluded: chain Y residue 71 ASN Chi-restraints excluded: chain Y residue 139 VAL Chi-restraints excluded: chain Z residue 84 VAL Chi-restraints excluded: chain Z residue 124 LYS Chi-restraints excluded: chain Z residue 128 VAL Chi-restraints excluded: chain Z residue 136 TYR Chi-restraints excluded: chain Z residue 190 THR Chi-restraints excluded: chain a residue 167 ILE Chi-restraints excluded: chain a residue 209 PHE Chi-restraints excluded: chain a residue 224 HIS Chi-restraints excluded: chain b residue 78 ASN Chi-restraints excluded: chain b residue 117 ASP Chi-restraints excluded: chain b residue 163 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 196 optimal weight: 5.9990 chunk 525 optimal weight: 3.9990 chunk 115 optimal weight: 7.9990 chunk 342 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 584 optimal weight: 0.3980 chunk 485 optimal weight: 0.6980 chunk 270 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 193 optimal weight: 4.9990 chunk 306 optimal weight: 2.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- 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 198 GLN A 219 ASN C 30 GLN E 150 ASN ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 GLN I 122 GLN ** I 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 8 ASN K 61 GLN ** L 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 GLN N 73 GLN N 77 HIS ** N 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 200 GLN ** O 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 198 GLN O 219 ASN Q 30 GLN Q 215 GLN S 150 ASN ** T 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 91 GLN W 122 GLN ** W 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 8 ASN Y 61 GLN ** Z 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 89 GLN ** a 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 73 GLN b 77 HIS ** b 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 200 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 48686 Z= 0.331 Angle : 0.586 14.430 65884 Z= 0.311 Chirality : 0.046 0.198 7434 Planarity : 0.005 0.062 8518 Dihedral : 7.171 129.270 6868 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.13 % Allowed : 17.94 % Favored : 78.94 % 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 (0.11), residues: 6082 helix: 1.39 (0.10), residues: 2264 sheet: -0.51 (0.13), residues: 1528 loop : 0.24 (0.14), residues: 2290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 154 HIS 0.007 0.001 HIS a 224 PHE 0.017 0.002 PHE J 70 TYR 0.019 0.002 TYR U 86 ARG 0.010 0.001 ARG D 10 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1059 residues out of total 5152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 898 time to evaluate : 5.245 Fit side-chains REVERT: A 49 GLN cc_start: 0.7822 (pt0) cc_final: 0.7492 (pm20) REVERT: A 88 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7102 (tmt) REVERT: A 169 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.7056 (tt0) REVERT: A 178 LYS cc_start: 0.6949 (mttt) cc_final: 0.6668 (mmmt) REVERT: B 154 TRP cc_start: 0.6558 (OUTLIER) cc_final: 0.5018 (m-90) REVERT: D 58 HIS cc_start: 0.5287 (OUTLIER) cc_final: 0.4360 (m90) REVERT: D 86 GLN cc_start: 0.7460 (tt0) cc_final: 0.7168 (tt0) REVERT: D 176 LYS cc_start: 0.6973 (OUTLIER) cc_final: 0.6658 (ttpp) REVERT: D 210 TYR cc_start: 0.7404 (p90) cc_final: 0.7016 (p90) REVERT: E 213 ASN cc_start: 0.7235 (t0) cc_final: 0.6860 (t0) REVERT: F 18 ARG cc_start: 0.8398 (mtm110) cc_final: 0.7861 (mtm110) REVERT: F 27 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7759 (mttt) REVERT: F 169 LYS cc_start: 0.8400 (mtpp) cc_final: 0.7905 (mtmm) REVERT: F 185 ASP cc_start: 0.7835 (t70) cc_final: 0.7578 (t0) REVERT: F 189 ARG cc_start: 0.8061 (tpp80) cc_final: 0.7841 (ttm-80) REVERT: G 67 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8712 (mm) REVERT: G 217 THR cc_start: 0.8470 (p) cc_final: 0.8037 (t) REVERT: H 131 SER cc_start: 0.9063 (OUTLIER) cc_final: 0.8852 (m) REVERT: J 66 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.7822 (mt-10) REVERT: J 105 PHE cc_start: 0.7845 (m-80) cc_final: 0.7639 (m-80) REVERT: J 119 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7305 (tp30) REVERT: J 160 ASN cc_start: 0.8789 (p0) cc_final: 0.8546 (p0) REVERT: J 200 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7936 (tt0) REVERT: K 52 ASP cc_start: 0.8517 (m-30) cc_final: 0.8293 (m-30) REVERT: M 69 ASP cc_start: 0.8881 (t0) cc_final: 0.8311 (t70) REVERT: N 64 GLU cc_start: 0.8927 (mt-10) cc_final: 0.8686 (mt-10) REVERT: N 163 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8020 (tttp) REVERT: O 49 GLN cc_start: 0.7807 (pt0) cc_final: 0.7493 (pm20) REVERT: O 84 ASN cc_start: 0.8168 (m-40) cc_final: 0.7959 (m-40) REVERT: O 88 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7100 (tmt) REVERT: O 169 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.7060 (tt0) REVERT: O 178 LYS cc_start: 0.6949 (mttt) cc_final: 0.6667 (mmmt) REVERT: P 154 TRP cc_start: 0.6562 (OUTLIER) cc_final: 0.5031 (m-90) REVERT: Q 17 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.7790 (ptp90) REVERT: Q 189 ASP cc_start: 0.7222 (m-30) cc_final: 0.6999 (m-30) REVERT: R 58 HIS cc_start: 0.5291 (OUTLIER) cc_final: 0.4363 (m90) REVERT: R 86 GLN cc_start: 0.7460 (tt0) cc_final: 0.7169 (tt0) REVERT: R 176 LYS cc_start: 0.6976 (OUTLIER) cc_final: 0.6659 (ttpp) REVERT: R 210 TYR cc_start: 0.7400 (p90) cc_final: 0.7004 (p90) REVERT: S 213 ASN cc_start: 0.7235 (t0) cc_final: 0.6861 (t0) REVERT: T 27 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7715 (mttm) REVERT: T 169 LYS cc_start: 0.8395 (mtpp) cc_final: 0.7903 (mtmm) REVERT: T 185 ASP cc_start: 0.7833 (t70) cc_final: 0.7580 (t0) REVERT: T 189 ARG cc_start: 0.8070 (tpp80) cc_final: 0.7848 (ttm-80) REVERT: U 67 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8704 (mm) REVERT: U 217 THR cc_start: 0.8471 (p) cc_final: 0.8034 (t) REVERT: V 131 SER cc_start: 0.9064 (OUTLIER) cc_final: 0.8852 (m) REVERT: X 66 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.7821 (mt-10) REVERT: X 105 PHE cc_start: 0.7849 (m-80) cc_final: 0.7639 (m-80) REVERT: X 119 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7308 (tp30) REVERT: X 160 ASN cc_start: 0.8786 (p0) cc_final: 0.8550 (p0) REVERT: X 200 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7934 (tt0) REVERT: Y 52 ASP cc_start: 0.8517 (m-30) cc_final: 0.8287 (m-30) REVERT: b 64 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8683 (mt-10) REVERT: b 163 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8138 (tttp) outliers start: 161 outliers final: 91 residues processed: 986 average time/residue: 1.6239 time to fit residues: 2008.1934 Evaluate side-chains 944 residues out of total 5152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 832 time to evaluate : 5.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 154 TRP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 220 TYR Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 58 HIS Chi-restraints excluded: chain D residue 71 MET Chi-restraints excluded: chain D residue 176 LYS Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 194 HIS Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain F residue 27 LYS Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 217 ASP Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain G residue 67 ILE Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 146 GLU Chi-restraints excluded: chain H residue 186 LYS Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain K residue 149 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 72 GLN Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 124 LYS Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 136 TYR Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain M residue 97 GLU Chi-restraints excluded: chain M residue 167 ILE Chi-restraints excluded: chain M residue 209 PHE Chi-restraints excluded: chain N residue 78 ASN Chi-restraints excluded: chain N residue 110 ILE Chi-restraints excluded: chain N residue 163 LYS Chi-restraints excluded: chain O residue 33 VAL Chi-restraints excluded: chain O residue 88 MET Chi-restraints excluded: chain O residue 92 SER Chi-restraints excluded: chain O residue 167 VAL Chi-restraints excluded: chain O residue 169 GLU Chi-restraints excluded: chain O residue 185 THR Chi-restraints excluded: chain O residue 195 SER Chi-restraints excluded: chain P residue 152 THR Chi-restraints excluded: chain P residue 154 TRP Chi-restraints excluded: chain P residue 182 VAL Chi-restraints excluded: chain Q residue 17 ARG Chi-restraints excluded: chain Q residue 79 THR Chi-restraints excluded: chain Q residue 185 THR Chi-restraints excluded: chain Q residue 214 LEU Chi-restraints excluded: chain Q residue 220 TYR Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 58 HIS Chi-restraints excluded: chain R residue 176 LYS Chi-restraints excluded: chain R residue 182 MET Chi-restraints excluded: chain S residue 13 ASN Chi-restraints excluded: chain S residue 24 VAL Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 158 THR Chi-restraints excluded: chain S residue 194 HIS Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 233 THR Chi-restraints excluded: chain T residue 27 LYS Chi-restraints excluded: chain T residue 123 VAL Chi-restraints excluded: chain T residue 217 ASP Chi-restraints excluded: chain T residue 223 LEU Chi-restraints excluded: chain U residue 67 ILE Chi-restraints excluded: chain U residue 210 MET Chi-restraints excluded: chain U residue 213 LEU Chi-restraints excluded: chain V residue 131 SER Chi-restraints excluded: chain V residue 146 GLU Chi-restraints excluded: chain V residue 186 LYS Chi-restraints excluded: chain W residue 28 VAL Chi-restraints excluded: chain X residue 66 GLU Chi-restraints excluded: chain Y residue 21 VAL Chi-restraints excluded: chain Y residue 139 VAL Chi-restraints excluded: chain Y residue 149 THR Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain Z residue 72 GLN Chi-restraints excluded: chain Z residue 84 VAL Chi-restraints excluded: chain Z residue 124 LYS Chi-restraints excluded: chain Z residue 128 VAL Chi-restraints excluded: chain Z residue 136 TYR Chi-restraints excluded: chain Z residue 190 THR Chi-restraints excluded: chain a residue 97 GLU Chi-restraints excluded: chain a residue 167 ILE Chi-restraints excluded: chain a residue 209 PHE Chi-restraints excluded: chain b residue 163 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 563 optimal weight: 0.0970 chunk 65 optimal weight: 5.9990 chunk 332 optimal weight: 2.9990 chunk 426 optimal weight: 0.5980 chunk 330 optimal weight: 0.0870 chunk 491 optimal weight: 0.8980 chunk 326 optimal weight: 2.9990 chunk 582 optimal weight: 3.9990 chunk 364 optimal weight: 2.9990 chunk 354 optimal weight: 0.9980 chunk 268 optimal weight: 0.8980 overall best weight: 0.5156 ------------------------------------------------------------------------------- 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 198 GLN A 219 ASN C 20 GLN C 29 ASN C 30 GLN D 55 GLN D 121 GLN E 150 ASN G 91 GLN ** H 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 GLN ** I 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 216 ASN J 8 ASN K 61 GLN K 71 ASN L 29 GLN M 89 GLN N 77 HIS ** N 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 198 GLN O 219 ASN Q 20 GLN Q 30 GLN Q 215 GLN S 150 ASN U 91 GLN ** V 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 122 GLN ** W 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 8 ASN Y 61 GLN Y 71 ASN Z 29 GLN a 89 GLN b 77 HIS ** b 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 48686 Z= 0.193 Angle : 0.541 16.535 65884 Z= 0.287 Chirality : 0.044 0.195 7434 Planarity : 0.004 0.049 8518 Dihedral : 6.929 124.857 6868 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.74 % Allowed : 19.02 % Favored : 78.24 % 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: 0.75 (0.11), residues: 6082 helix: 1.52 (0.11), residues: 2276 sheet: -0.34 (0.13), residues: 1472 loop : 0.22 (0.14), residues: 2334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 158 HIS 0.005 0.001 HIS D 145 PHE 0.020 0.002 PHE X 70 TYR 0.016 0.001 TYR C 239 ARG 0.011 0.001 ARG D 10 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1114 residues out of total 5152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 973 time to evaluate : 5.806 Fit side-chains REVERT: A 49 GLN cc_start: 0.7734 (pt0) cc_final: 0.7475 (pm20) REVERT: A 88 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7111 (tmt) REVERT: A 169 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.7068 (tt0) REVERT: A 178 LYS cc_start: 0.6872 (mttt) cc_final: 0.6639 (mmmt) REVERT: B 213 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7270 (pp20) REVERT: C 107 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7478 (tm-30) REVERT: C 165 GLU cc_start: 0.7658 (pt0) cc_final: 0.7148 (mt-10) REVERT: C 197 LYS cc_start: 0.7230 (mtpt) cc_final: 0.6923 (mttt) REVERT: D 58 HIS cc_start: 0.5160 (OUTLIER) cc_final: 0.4194 (m90) REVERT: D 86 GLN cc_start: 0.7436 (tt0) cc_final: 0.7200 (tt0) REVERT: D 143 GLN cc_start: 0.7565 (OUTLIER) cc_final: 0.5763 (tm-30) REVERT: D 210 TYR cc_start: 0.7058 (p90) cc_final: 0.6765 (p90) REVERT: E 84 ASP cc_start: 0.8786 (m-30) cc_final: 0.8524 (m-30) REVERT: E 213 ASN cc_start: 0.7214 (t0) cc_final: 0.6860 (t0) REVERT: F 80 ASP cc_start: 0.8263 (m-30) cc_final: 0.7982 (m-30) REVERT: F 185 ASP cc_start: 0.7839 (t70) cc_final: 0.7619 (t0) REVERT: G 217 THR cc_start: 0.8359 (p) cc_final: 0.8015 (t) REVERT: H 131 SER cc_start: 0.8997 (OUTLIER) cc_final: 0.8790 (m) REVERT: J 66 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7740 (mt-10) REVERT: J 105 PHE cc_start: 0.7641 (m-80) cc_final: 0.7389 (m-80) REVERT: J 119 GLU cc_start: 0.7511 (mm-30) cc_final: 0.7276 (tp30) REVERT: K 33 ASP cc_start: 0.8072 (t0) cc_final: 0.7784 (t70) REVERT: M 69 ASP cc_start: 0.8800 (t0) cc_final: 0.8296 (t70) REVERT: N 64 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8607 (mt-10) REVERT: O 49 GLN cc_start: 0.7729 (pt0) cc_final: 0.7451 (pm20) REVERT: O 84 ASN cc_start: 0.8133 (m-40) cc_final: 0.7929 (m-40) REVERT: O 88 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.7101 (tmt) REVERT: O 169 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.7059 (tt0) REVERT: O 178 LYS cc_start: 0.6869 (mttt) cc_final: 0.6631 (mmmt) REVERT: P 213 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7268 (pp20) REVERT: Q 107 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7486 (tm-30) REVERT: Q 197 LYS cc_start: 0.7199 (mtpt) cc_final: 0.6897 (mttt) REVERT: R 58 HIS cc_start: 0.5210 (OUTLIER) cc_final: 0.4238 (m90) REVERT: R 86 GLN cc_start: 0.7432 (tt0) cc_final: 0.7187 (tt0) REVERT: R 143 GLN cc_start: 0.7565 (OUTLIER) cc_final: 0.5772 (tm-30) REVERT: R 210 TYR cc_start: 0.7036 (p90) cc_final: 0.6737 (p90) REVERT: S 213 ASN cc_start: 0.7210 (t0) cc_final: 0.6860 (t0) REVERT: T 80 ASP cc_start: 0.8258 (m-30) cc_final: 0.7977 (m-30) REVERT: T 185 ASP cc_start: 0.7844 (t70) cc_final: 0.7624 (t0) REVERT: U 67 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8665 (mm) REVERT: U 217 THR cc_start: 0.8360 (p) cc_final: 0.8015 (t) REVERT: V 131 SER cc_start: 0.8996 (OUTLIER) cc_final: 0.8791 (m) REVERT: X 66 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7739 (mt-10) REVERT: X 105 PHE cc_start: 0.7643 (m-80) cc_final: 0.7394 (m-80) REVERT: X 119 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7279 (tp30) REVERT: X 200 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7871 (tt0) REVERT: Y 33 ASP cc_start: 0.8082 (t0) cc_final: 0.7794 (t70) REVERT: a 69 ASP cc_start: 0.8774 (t0) cc_final: 0.8253 (t70) REVERT: b 64 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8606 (mt-10) outliers start: 141 outliers final: 69 residues processed: 1043 average time/residue: 1.6259 time to fit residues: 2182.1075 Evaluate side-chains 931 residues out of total 5152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 849 time to evaluate : 5.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 220 TYR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 58 HIS Chi-restraints excluded: chain D residue 143 GLN Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 194 HIS Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 186 LYS Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 136 TYR Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain M residue 167 ILE Chi-restraints excluded: chain M residue 209 PHE Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain N residue 78 ASN Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain O residue 32 GLU Chi-restraints excluded: chain O residue 33 VAL Chi-restraints excluded: chain O residue 88 MET Chi-restraints excluded: chain O residue 92 SER Chi-restraints excluded: chain O residue 167 VAL Chi-restraints excluded: chain O residue 169 GLU Chi-restraints excluded: chain O residue 185 THR Chi-restraints excluded: chain O residue 195 SER Chi-restraints excluded: chain P residue 152 THR Chi-restraints excluded: chain Q residue 214 LEU Chi-restraints excluded: chain Q residue 220 TYR Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 58 HIS Chi-restraints excluded: chain R residue 143 GLN Chi-restraints excluded: chain S residue 13 ASN Chi-restraints excluded: chain S residue 24 VAL Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 158 THR Chi-restraints excluded: chain S residue 194 HIS Chi-restraints excluded: chain S residue 233 THR Chi-restraints excluded: chain T residue 123 VAL Chi-restraints excluded: chain T residue 223 LEU Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 67 ILE Chi-restraints excluded: chain U residue 210 MET Chi-restraints excluded: chain U residue 213 LEU Chi-restraints excluded: chain V residue 131 SER Chi-restraints excluded: chain V residue 186 LYS Chi-restraints excluded: chain W residue 28 VAL Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 66 GLU Chi-restraints excluded: chain Y residue 139 VAL Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain Z residue 84 VAL Chi-restraints excluded: chain Z residue 136 TYR Chi-restraints excluded: chain Z residue 190 THR Chi-restraints excluded: chain a residue 97 GLU Chi-restraints excluded: chain a residue 167 ILE Chi-restraints excluded: chain a residue 209 PHE Chi-restraints excluded: chain b residue 49 ILE Chi-restraints excluded: chain b residue 78 ASN Chi-restraints excluded: chain b residue 117 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 360 optimal weight: 5.9990 chunk 232 optimal weight: 7.9990 chunk 347 optimal weight: 9.9990 chunk 175 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 370 optimal weight: 7.9990 chunk 396 optimal weight: 4.9990 chunk 287 optimal weight: 0.0870 chunk 54 optimal weight: 4.9990 chunk 457 optimal weight: 1.9990 overall best weight: 3.6166 ------------------------------------------------------------------------------- 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 198 GLN A 219 ASN C 30 GLN C 177 GLN D 28 GLN D 78 HIS E 150 ASN ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 GLN G 181 ASN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 111 GLN ** I 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 174 ASN I 216 ASN J 8 ASN ** J 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 111 HIS N 47 ASN N 146 GLN N 149 GLN ** O 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 198 GLN O 219 ASN Q 30 GLN Q 177 GLN Q 215 GLN R 28 GLN R 78 HIS R 116 GLN R 188 GLN S 150 ASN ** T 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 91 GLN U 181 ASN ** V 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 111 GLN W 122 GLN ** W 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 140 ASN W 174 ASN ** X 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 111 HIS b 47 ASN ** b 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.115 48686 Z= 0.496 Angle : 0.661 12.971 65884 Z= 0.352 Chirality : 0.049 0.235 7434 Planarity : 0.005 0.056 8518 Dihedral : 7.422 135.131 6868 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.05 % Allowed : 19.39 % Favored : 77.56 % 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: 0.39 (0.11), residues: 6082 helix: 1.17 (0.10), residues: 2254 sheet: -0.57 (0.12), residues: 1572 loop : 0.16 (0.14), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 158 HIS 0.007 0.001 HIS Q 118 PHE 0.021 0.002 PHE Q 39 TYR 0.022 0.002 TYR G 86 ARG 0.012 0.001 ARG F 189 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1001 residues out of total 5152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 844 time to evaluate : 5.415 Fit side-chains REVERT: A 88 MET cc_start: 0.8059 (OUTLIER) cc_final: 0.7099 (tmt) REVERT: A 169 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.7051 (tt0) REVERT: A 178 LYS cc_start: 0.7016 (mttt) cc_final: 0.6746 (mmmt) REVERT: C 138 TYR cc_start: 0.8707 (t80) cc_final: 0.8472 (t80) REVERT: C 177 GLN cc_start: 0.6647 (OUTLIER) cc_final: 0.6119 (mt0) REVERT: D 58 HIS cc_start: 0.5280 (OUTLIER) cc_final: 0.4381 (m90) REVERT: D 86 GLN cc_start: 0.7456 (tt0) cc_final: 0.7199 (tt0) REVERT: D 143 GLN cc_start: 0.7600 (OUTLIER) cc_final: 0.6544 (tm-30) REVERT: D 210 TYR cc_start: 0.7414 (p90) cc_final: 0.7009 (p90) REVERT: E 84 ASP cc_start: 0.8844 (m-30) cc_final: 0.8509 (m-30) REVERT: E 213 ASN cc_start: 0.7342 (t0) cc_final: 0.6924 (t0) REVERT: F 27 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7920 (mttt) REVERT: F 169 LYS cc_start: 0.8425 (mtpp) cc_final: 0.7899 (mtmm) REVERT: F 185 ASP cc_start: 0.8003 (t70) cc_final: 0.7712 (t0) REVERT: G 217 THR cc_start: 0.8566 (p) cc_final: 0.8076 (t) REVERT: I 80 THR cc_start: 0.9239 (m) cc_final: 0.9013 (m) REVERT: J 66 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7852 (mt-10) REVERT: M 142 GLU cc_start: 0.8157 (pt0) cc_final: 0.7953 (tt0) REVERT: N 58 ASP cc_start: 0.8903 (m-30) cc_final: 0.8597 (m-30) REVERT: N 64 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8758 (mt-10) REVERT: N 163 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8292 (tttp) REVERT: O 84 ASN cc_start: 0.8183 (m-40) cc_final: 0.7965 (m-40) REVERT: O 88 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7094 (tmt) REVERT: O 169 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7048 (tt0) REVERT: O 178 LYS cc_start: 0.7015 (mttt) cc_final: 0.6743 (mmmt) REVERT: Q 138 TYR cc_start: 0.8697 (t80) cc_final: 0.8459 (t80) REVERT: Q 177 GLN cc_start: 0.6655 (OUTLIER) cc_final: 0.6116 (mt0) REVERT: R 58 HIS cc_start: 0.5257 (OUTLIER) cc_final: 0.4366 (m90) REVERT: R 86 GLN cc_start: 0.7454 (tt0) cc_final: 0.7196 (tt0) REVERT: R 143 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.6550 (tm-30) REVERT: R 210 TYR cc_start: 0.7413 (p90) cc_final: 0.7010 (p90) REVERT: S 213 ASN cc_start: 0.7298 (t0) cc_final: 0.6883 (t0) REVERT: T 27 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7927 (mttt) REVERT: T 169 LYS cc_start: 0.8426 (mtpp) cc_final: 0.7905 (mtmm) REVERT: T 185 ASP cc_start: 0.8004 (t70) cc_final: 0.7718 (t0) REVERT: U 217 THR cc_start: 0.8555 (p) cc_final: 0.8060 (t) REVERT: W 80 THR cc_start: 0.9240 (m) cc_final: 0.9013 (m) REVERT: X 66 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7850 (mt-10) REVERT: X 200 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7959 (tt0) REVERT: a 142 GLU cc_start: 0.8172 (pt0) cc_final: 0.7957 (tt0) REVERT: b 58 ASP cc_start: 0.8897 (m-30) cc_final: 0.8590 (m-30) REVERT: b 64 GLU cc_start: 0.8966 (mt-10) cc_final: 0.8757 (mt-10) REVERT: b 163 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8302 (tttp) outliers start: 157 outliers final: 83 residues processed: 946 average time/residue: 1.6057 time to fit residues: 1893.3683 Evaluate side-chains 929 residues out of total 5152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 830 time to evaluate : 5.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 220 TYR Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 58 HIS Chi-restraints excluded: chain D residue 64 CYS Chi-restraints excluded: chain D residue 143 GLN Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 194 HIS Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain F residue 27 LYS Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 217 ASP Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 186 LYS Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 71 ASN Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 72 GLN Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 136 TYR Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain M residue 97 GLU Chi-restraints excluded: chain N residue 78 ASN Chi-restraints excluded: chain N residue 163 LYS Chi-restraints excluded: chain O residue 33 VAL Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain O residue 88 MET Chi-restraints excluded: chain O residue 92 SER Chi-restraints excluded: chain O residue 167 VAL Chi-restraints excluded: chain O residue 169 GLU Chi-restraints excluded: chain O residue 185 THR Chi-restraints excluded: chain O residue 195 SER Chi-restraints excluded: chain P residue 152 THR Chi-restraints excluded: chain Q residue 177 GLN Chi-restraints excluded: chain Q residue 180 ASP Chi-restraints excluded: chain Q residue 214 LEU Chi-restraints excluded: chain Q residue 220 TYR Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 58 HIS Chi-restraints excluded: chain R residue 71 MET Chi-restraints excluded: chain R residue 143 GLN Chi-restraints excluded: chain R residue 182 MET Chi-restraints excluded: chain S residue 13 ASN Chi-restraints excluded: chain S residue 24 VAL Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 158 THR Chi-restraints excluded: chain S residue 194 HIS Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 233 THR Chi-restraints excluded: chain T residue 27 LYS Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 123 VAL Chi-restraints excluded: chain T residue 217 ASP Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 210 MET Chi-restraints excluded: chain U residue 213 LEU Chi-restraints excluded: chain V residue 131 SER Chi-restraints excluded: chain V residue 186 LYS Chi-restraints excluded: chain W residue 28 VAL Chi-restraints excluded: chain W residue 104 ASP Chi-restraints excluded: chain X residue 66 GLU Chi-restraints excluded: chain Y residue 21 VAL Chi-restraints excluded: chain Y residue 71 ASN Chi-restraints excluded: chain Y residue 139 VAL Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain Z residue 72 GLN Chi-restraints excluded: chain Z residue 84 VAL Chi-restraints excluded: chain Z residue 136 TYR Chi-restraints excluded: chain Z residue 190 THR Chi-restraints excluded: chain a residue 97 GLU Chi-restraints excluded: chain b residue 78 ASN Chi-restraints excluded: chain b residue 110 ILE Chi-restraints excluded: chain b residue 163 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 529 optimal weight: 1.9990 chunk 557 optimal weight: 0.6980 chunk 508 optimal weight: 0.8980 chunk 542 optimal weight: 0.8980 chunk 326 optimal weight: 1.9990 chunk 236 optimal weight: 3.9990 chunk 425 optimal weight: 0.7980 chunk 166 optimal weight: 0.3980 chunk 490 optimal weight: 0.6980 chunk 513 optimal weight: 0.0570 chunk 540 optimal weight: 0.8980 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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 198 GLN A 219 ASN C 29 ASN C 30 GLN E 150 ASN ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 GLN H 32 ASN ** H 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 54 ASN I 122 GLN ** I 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 140 ASN J 8 ASN K 61 GLN K 71 ASN ** L 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 72 GLN L 110 HIS N 149 GLN ** O 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 198 GLN O 219 ASN Q 30 GLN Q 215 GLN R 116 GLN S 150 ASN ** T 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 91 GLN V 32 ASN ** V 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 54 ASN ** W 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 216 ASN X 8 ASN Y 61 GLN Y 71 ASN Z 110 HIS b 149 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 48686 Z= 0.213 Angle : 0.573 15.697 65884 Z= 0.305 Chirality : 0.044 0.197 7434 Planarity : 0.004 0.057 8518 Dihedral : 7.070 126.156 6868 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.20 % Allowed : 20.97 % Favored : 76.84 % 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: 0.54 (0.11), residues: 6082 helix: 1.27 (0.11), residues: 2284 sheet: -0.50 (0.13), residues: 1476 loop : 0.21 (0.14), residues: 2322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP Z 55 HIS 0.005 0.001 HIS D 145 PHE 0.024 0.002 PHE W 119 TYR 0.019 0.002 TYR E 232 ARG 0.013 0.001 ARG D 10 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1021 residues out of total 5152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 908 time to evaluate : 5.495 Fit side-chains REVERT: A 88 MET cc_start: 0.8053 (OUTLIER) cc_final: 0.7097 (tmt) REVERT: A 169 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.7044 (tt0) REVERT: A 178 LYS cc_start: 0.6911 (mttt) cc_final: 0.6676 (mmmt) REVERT: B 213 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7309 (pp20) REVERT: C 107 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7635 (tm-30) REVERT: C 236 MET cc_start: 0.7260 (mmm) cc_final: 0.6576 (tmm) REVERT: D 58 HIS cc_start: 0.5188 (OUTLIER) cc_final: 0.4277 (m90) REVERT: D 86 GLN cc_start: 0.7417 (tt0) cc_final: 0.7171 (tt0) REVERT: E 84 ASP cc_start: 0.8822 (m-30) cc_final: 0.8540 (m-30) REVERT: E 213 ASN cc_start: 0.7186 (t0) cc_final: 0.6833 (t0) REVERT: F 169 LYS cc_start: 0.8365 (mtpp) cc_final: 0.7945 (mtmm) REVERT: F 185 ASP cc_start: 0.8037 (t70) cc_final: 0.7742 (t0) REVERT: G 217 THR cc_start: 0.8451 (p) cc_final: 0.8048 (t) REVERT: I 80 THR cc_start: 0.9135 (m) cc_final: 0.8895 (m) REVERT: J 66 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.7747 (mt-10) REVERT: J 105 PHE cc_start: 0.7849 (m-80) cc_final: 0.7544 (m-80) REVERT: M 69 ASP cc_start: 0.8750 (t0) cc_final: 0.8210 (t70) REVERT: N 64 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8615 (mt-10) REVERT: O 84 ASN cc_start: 0.8128 (m-40) cc_final: 0.7925 (m-40) REVERT: O 88 MET cc_start: 0.8059 (OUTLIER) cc_final: 0.7100 (tmt) REVERT: O 169 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.7044 (tt0) REVERT: O 178 LYS cc_start: 0.6918 (mttt) cc_final: 0.6677 (mmmt) REVERT: P 213 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7305 (pp20) REVERT: Q 107 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7637 (tm-30) REVERT: Q 197 LYS cc_start: 0.7265 (mtpt) cc_final: 0.6962 (mttt) REVERT: R 58 HIS cc_start: 0.5254 (OUTLIER) cc_final: 0.4272 (m90) REVERT: R 86 GLN cc_start: 0.7397 (tt0) cc_final: 0.7155 (tt0) REVERT: R 210 TYR cc_start: 0.7141 (p90) cc_final: 0.6789 (p90) REVERT: S 213 ASN cc_start: 0.7174 (t0) cc_final: 0.6823 (t0) REVERT: T 169 LYS cc_start: 0.8358 (mtpp) cc_final: 0.7940 (mtmm) REVERT: T 185 ASP cc_start: 0.8053 (t70) cc_final: 0.7758 (t0) REVERT: U 217 THR cc_start: 0.8449 (p) cc_final: 0.8045 (t) REVERT: V 131 SER cc_start: 0.9028 (p) cc_final: 0.8822 (m) REVERT: W 80 THR cc_start: 0.9135 (m) cc_final: 0.8896 (m) REVERT: X 66 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7746 (mt-10) REVERT: X 105 PHE cc_start: 0.7850 (m-80) cc_final: 0.7536 (m-80) REVERT: X 200 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7871 (tt0) REVERT: a 69 ASP cc_start: 0.8743 (t0) cc_final: 0.8120 (t70) REVERT: b 64 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8614 (mt-10) outliers start: 113 outliers final: 60 residues processed: 970 average time/residue: 1.4991 time to fit residues: 1835.4731 Evaluate side-chains 922 residues out of total 5152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 854 time to evaluate : 5.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 58 HIS Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 194 HIS Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 217 ASP Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain H residue 186 LYS Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 72 GLN Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 136 TYR Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain M residue 167 ILE Chi-restraints excluded: chain N residue 78 ASN Chi-restraints excluded: chain O residue 33 VAL Chi-restraints excluded: chain O residue 88 MET Chi-restraints excluded: chain O residue 92 SER Chi-restraints excluded: chain O residue 167 VAL Chi-restraints excluded: chain O residue 169 GLU Chi-restraints excluded: chain O residue 185 THR Chi-restraints excluded: chain Q residue 214 LEU Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 58 HIS Chi-restraints excluded: chain R residue 71 MET Chi-restraints excluded: chain S residue 13 ASN Chi-restraints excluded: chain S residue 24 VAL Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 158 THR Chi-restraints excluded: chain S residue 194 HIS Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 233 THR Chi-restraints excluded: chain T residue 123 VAL Chi-restraints excluded: chain T residue 217 ASP Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 213 LEU Chi-restraints excluded: chain V residue 186 LYS Chi-restraints excluded: chain W residue 28 VAL Chi-restraints excluded: chain X residue 66 GLU Chi-restraints excluded: chain Y residue 139 VAL Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain Z residue 84 VAL Chi-restraints excluded: chain Z residue 136 TYR Chi-restraints excluded: chain Z residue 190 THR Chi-restraints excluded: chain a residue 97 GLU Chi-restraints excluded: chain a residue 167 ILE Chi-restraints excluded: chain b residue 78 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 356 optimal weight: 5.9990 chunk 573 optimal weight: 1.9990 chunk 350 optimal weight: 6.9990 chunk 272 optimal weight: 4.9990 chunk 398 optimal weight: 0.9990 chunk 601 optimal weight: 0.7980 chunk 553 optimal weight: 3.9990 chunk 479 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 370 optimal weight: 10.0000 chunk 293 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 GLN A 219 ASN C 30 GLN D 188 GLN E 150 ASN ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 GLN H 32 ASN ** H 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 54 ASN ** I 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 8 ASN ** J 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 GLN K 71 ASN ** L 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 149 GLN O 198 GLN O 219 ASN Q 30 GLN Q 215 GLN S 150 ASN ** U 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 91 GLN V 32 ASN V 83 ASN W 54 ASN X 8 ASN ** X 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 61 GLN Y 71 ASN ** Z 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 77 HIS b 146 GLN ** b 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 48686 Z= 0.294 Angle : 0.596 15.133 65884 Z= 0.314 Chirality : 0.046 0.269 7434 Planarity : 0.004 0.063 8518 Dihedral : 7.143 129.291 6868 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.71 % Allowed : 21.78 % Favored : 76.51 % 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: 0.55 (0.11), residues: 6082 helix: 1.32 (0.10), residues: 2266 sheet: -0.51 (0.13), residues: 1536 loop : 0.22 (0.14), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 158 HIS 0.006 0.001 HIS b 77 PHE 0.020 0.002 PHE X 70 TYR 0.026 0.002 TYR S 232 ARG 0.014 0.001 ARG F 189 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 958 residues out of total 5152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 870 time to evaluate : 5.552 Fit side-chains REVERT: A 49 GLN cc_start: 0.7777 (pm20) cc_final: 0.7555 (pm20) REVERT: A 88 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7109 (tmt) REVERT: A 169 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.7073 (tt0) REVERT: A 178 LYS cc_start: 0.6942 (mttt) cc_final: 0.6697 (mmmt) REVERT: B 107 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7726 (mm-30) REVERT: B 213 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7392 (pp20) REVERT: C 107 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7628 (tm-30) REVERT: C 236 MET cc_start: 0.7411 (mmm) cc_final: 0.6401 (tmm) REVERT: D 58 HIS cc_start: 0.5196 (OUTLIER) cc_final: 0.4217 (m90) REVERT: D 86 GLN cc_start: 0.7451 (tt0) cc_final: 0.7226 (tt0) REVERT: E 78 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8214 (mtp) REVERT: E 84 ASP cc_start: 0.8838 (m-30) cc_final: 0.8530 (m-30) REVERT: E 213 ASN cc_start: 0.7225 (t0) cc_final: 0.6862 (t0) REVERT: F 122 LYS cc_start: 0.7101 (mmtm) cc_final: 0.6782 (mmmt) REVERT: F 169 LYS cc_start: 0.8402 (mtpp) cc_final: 0.7993 (mtmm) REVERT: G 217 THR cc_start: 0.8472 (p) cc_final: 0.8066 (t) REVERT: I 80 THR cc_start: 0.9153 (m) cc_final: 0.8903 (m) REVERT: J 66 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.7803 (mt-10) REVERT: J 105 PHE cc_start: 0.7901 (m-80) cc_final: 0.7594 (m-80) REVERT: J 119 GLU cc_start: 0.7596 (tp30) cc_final: 0.7155 (mm-30) REVERT: M 69 ASP cc_start: 0.8874 (t0) cc_final: 0.8248 (t70) REVERT: N 64 GLU cc_start: 0.8920 (mt-10) cc_final: 0.8634 (mt-10) REVERT: O 49 GLN cc_start: 0.7786 (pm20) cc_final: 0.7557 (pm20) REVERT: O 169 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.7071 (tt0) REVERT: O 178 LYS cc_start: 0.6941 (mttt) cc_final: 0.6696 (mmmt) REVERT: P 213 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7390 (pp20) REVERT: Q 107 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7642 (tm-30) REVERT: Q 236 MET cc_start: 0.7201 (mmm) cc_final: 0.6361 (tmm) REVERT: R 58 HIS cc_start: 0.5256 (OUTLIER) cc_final: 0.4305 (m90) REVERT: R 86 GLN cc_start: 0.7450 (tt0) cc_final: 0.7227 (tt0) REVERT: R 210 TYR cc_start: 0.7238 (p90) cc_final: 0.6859 (p90) REVERT: S 213 ASN cc_start: 0.7205 (t0) cc_final: 0.6854 (t0) REVERT: T 122 LYS cc_start: 0.7097 (mmtm) cc_final: 0.6780 (mmmt) REVERT: T 169 LYS cc_start: 0.8388 (mtpp) cc_final: 0.7987 (mtmm) REVERT: U 217 THR cc_start: 0.8470 (p) cc_final: 0.8067 (t) REVERT: W 80 THR cc_start: 0.9154 (m) cc_final: 0.8900 (m) REVERT: X 66 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.7783 (mt-10) REVERT: X 105 PHE cc_start: 0.7925 (m-80) cc_final: 0.7618 (m-80) REVERT: X 119 GLU cc_start: 0.7588 (tp30) cc_final: 0.7144 (mm-30) REVERT: X 200 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7894 (tt0) REVERT: a 69 ASP cc_start: 0.8862 (t0) cc_final: 0.8153 (t70) REVERT: b 64 GLU cc_start: 0.8923 (mt-10) cc_final: 0.8630 (mt-10) outliers start: 88 outliers final: 57 residues processed: 923 average time/residue: 1.5149 time to fit residues: 1759.0943 Evaluate side-chains 900 residues out of total 5152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 835 time to evaluate : 4.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 220 TYR Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 58 HIS Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 194 HIS Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain F residue 217 ASP Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain H residue 186 LYS Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 136 TYR Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain M residue 167 ILE Chi-restraints excluded: chain N residue 78 ASN Chi-restraints excluded: chain O residue 33 VAL Chi-restraints excluded: chain O residue 92 SER Chi-restraints excluded: chain O residue 167 VAL Chi-restraints excluded: chain O residue 169 GLU Chi-restraints excluded: chain O residue 185 THR Chi-restraints excluded: chain O residue 195 SER Chi-restraints excluded: chain Q residue 214 LEU Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 58 HIS Chi-restraints excluded: chain R residue 71 MET Chi-restraints excluded: chain S residue 24 VAL Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 158 THR Chi-restraints excluded: chain S residue 194 HIS Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 233 THR Chi-restraints excluded: chain T residue 217 ASP Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 213 LEU Chi-restraints excluded: chain V residue 186 LYS Chi-restraints excluded: chain W residue 28 VAL Chi-restraints excluded: chain X residue 66 GLU Chi-restraints excluded: chain Y residue 21 VAL Chi-restraints excluded: chain Y residue 139 VAL Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain Z residue 84 VAL Chi-restraints excluded: chain Z residue 136 TYR Chi-restraints excluded: chain Z residue 190 THR Chi-restraints excluded: chain a residue 97 GLU Chi-restraints excluded: chain a residue 167 ILE Chi-restraints excluded: chain b residue 78 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 380 optimal weight: 0.4980 chunk 510 optimal weight: 2.9990 chunk 146 optimal weight: 0.5980 chunk 441 optimal weight: 0.0970 chunk 70 optimal weight: 8.9990 chunk 133 optimal weight: 5.9990 chunk 479 optimal weight: 6.9990 chunk 200 optimal weight: 6.9990 chunk 492 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 GLN A 219 ASN C 29 ASN C 30 GLN E 150 ASN ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 GLN H 32 ASN ** H 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 54 ASN ** I 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 8 ASN J 47 ASN ** J 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 GLN K 71 ASN ** L 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 HIS ** N 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 198 GLN O 219 ASN Q 30 GLN Q 215 GLN R 55 GLN S 150 ASN ** U 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 91 GLN V 32 ASN W 54 ASN ** W 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 8 ASN X 47 ASN ** X 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 61 GLN Y 71 ASN ** Z 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 77 HIS ** b 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.137131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.119947 restraints weight = 59733.990| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.19 r_work: 0.3171 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 48686 Z= 0.246 Angle : 0.575 15.454 65884 Z= 0.305 Chirality : 0.045 0.244 7434 Planarity : 0.004 0.056 8518 Dihedral : 7.096 128.108 6868 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.75 % Allowed : 21.76 % Favored : 76.49 % 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: 0.58 (0.11), residues: 6082 helix: 1.33 (0.10), residues: 2284 sheet: -0.47 (0.13), residues: 1516 loop : 0.24 (0.14), residues: 2282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP Q 158 HIS 0.007 0.001 HIS N 77 PHE 0.022 0.002 PHE J 70 TYR 0.024 0.002 TYR E 232 ARG 0.013 0.001 ARG R 10 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26832.21 seconds wall clock time: 468 minutes 4.09 seconds (28084.09 seconds total)