Starting phenix.real_space_refine on Sun Mar 17 11:25:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0i_15784/03_2024/8b0i_15784.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0i_15784/03_2024/8b0i_15784.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0i_15784/03_2024/8b0i_15784.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0i_15784/03_2024/8b0i_15784.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0i_15784/03_2024/8b0i_15784.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0i_15784/03_2024/8b0i_15784.pdb" } resolution = 4.28 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 103 5.49 5 S 20 5.16 5 C 5767 2.51 5 N 1701 2.21 5 O 2214 1.98 5 H 7831 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 9": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 65": "OE1" <-> "OE2" Residue "B ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 119": "OE1" <-> "OE2" Residue "D ARG 58": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 119": "OE1" <-> "OE2" Residue "C ARG 58": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17636 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 3560 Classifications: {'peptide': 270} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 255} Chain breaks: 1 Unresolved non-hydrogen bonds: 285 Unresolved non-hydrogen angles: 354 Unresolved non-hydrogen dihedrals: 237 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 180 Chain: "B" Number of atoms: 3825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 3825 Classifications: {'peptide': 281} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 265} Chain breaks: 1 Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 346 Unresolved non-hydrogen dihedrals: 234 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 5, 'ASP:plan': 4, 'PHE:plan': 5, 'GLU:plan': 4, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 198 Chain: "D" Number of atoms: 3763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 3763 Classifications: {'peptide': 282} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 266} Unresolved non-hydrogen bonds: 275 Unresolved non-hydrogen angles: 342 Unresolved non-hydrogen dihedrals: 227 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 7, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 163 Chain: "C" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 3298 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 14, 'TRANS': 227} Chain breaks: 4 Unresolved non-hydrogen bonds: 211 Unresolved non-hydrogen angles: 254 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'HIS:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 117 Chain: "K" Number of atoms: 3190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 3190 Classifications: {'RNA': 103} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 27, 'rna3p_pur': 36, 'rna3p_pyr': 31} Link IDs: {'rna2p': 36, 'rna3p': 66} Chain breaks: 5 Time building chain proxies: 9.02, per 1000 atoms: 0.51 Number of scatterers: 17636 At special positions: 0 Unit cell: (93.888, 107.58, 142.788, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 20 16.00 P 103 15.00 O 2214 8.00 N 1701 7.00 C 5767 6.00 H 7831 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.94 Conformation dependent library (CDL) restraints added in 1.8 seconds 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2058 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 10 sheets defined 49.2% alpha, 8.5% beta 6 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 8.34 Creating SS restraints... Processing helix chain 'A' and resid 13 through 24 Processing helix chain 'A' and resid 36 through 48 Processing helix chain 'A' and resid 63 through 74 Processing helix chain 'A' and resid 88 through 96 removed outlier: 3.723A pdb=" N TYR A 96 " --> pdb=" O LEU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 129 removed outlier: 3.939A pdb=" N GLU A 119 " --> pdb=" O ALA A 115 " (cutoff:3.500A) Proline residue: A 125 - end of helix Processing helix chain 'A' and resid 140 through 153 Processing helix chain 'A' and resid 188 through 192 removed outlier: 3.762A pdb=" N TRP A 191 " --> pdb=" O ASN A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 212 Processing helix chain 'A' and resid 212 through 235 removed outlier: 3.728A pdb=" N HIS A 216 " --> pdb=" O HIS A 212 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR A 220 " --> pdb=" O HIS A 216 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TRP A 229 " --> pdb=" O TYR A 225 " (cutoff:3.500A) Proline residue: A 231 - end of helix removed outlier: 3.962A pdb=" N THR A 235 " --> pdb=" O PRO A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 268 removed outlier: 4.089A pdb=" N TYR A 256 " --> pdb=" O HIS A 252 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ILE A 257 " --> pdb=" O ARG A 253 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR A 264 " --> pdb=" O GLN A 260 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 281 removed outlier: 3.977A pdb=" N LYS A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 25 Processing helix chain 'B' and resid 36 through 41 removed outlier: 3.859A pdb=" N LEU B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 47 Processing helix chain 'B' and resid 64 through 73 Processing helix chain 'B' and resid 88 through 99 Processing helix chain 'B' and resid 111 through 123 removed outlier: 3.677A pdb=" N ASP B 121 " --> pdb=" O ASP B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 129 Processing helix chain 'B' and resid 140 through 155 removed outlier: 3.681A pdb=" N GLU B 146 " --> pdb=" O HIS B 142 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET B 147 " --> pdb=" O GLU B 143 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS B 155 " --> pdb=" O ARG B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 212 removed outlier: 4.102A pdb=" N HIS B 212 " --> pdb=" O PHE B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 235 removed outlier: 3.919A pdb=" N TRP B 229 " --> pdb=" O TYR B 225 " (cutoff:3.500A) Proline residue: B 231 - end of helix removed outlier: 4.053A pdb=" N THR B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 269 Processing helix chain 'D' and resid 13 through 25 removed outlier: 4.157A pdb=" N ALA D 17 " --> pdb=" O GLY D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 35 No H-bonds generated for 'chain 'D' and resid 33 through 35' Processing helix chain 'D' and resid 36 through 46 removed outlier: 4.142A pdb=" N ASP D 46 " --> pdb=" O ARG D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 72 Processing helix chain 'D' and resid 88 through 99 Processing helix chain 'D' and resid 111 through 130 removed outlier: 3.776A pdb=" N ALA D 115 " --> pdb=" O SER D 111 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE D 116 " --> pdb=" O LEU D 112 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ASP D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP D 121 " --> pdb=" O ASP D 117 " (cutoff:3.500A) Proline residue: D 125 - end of helix Processing helix chain 'D' and resid 140 through 148 removed outlier: 3.820A pdb=" N ALA D 145 " --> pdb=" O VAL D 141 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU D 146 " --> pdb=" O HIS D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 151 No H-bonds generated for 'chain 'D' and resid 149 through 151' Processing helix chain 'D' and resid 188 through 192 Processing helix chain 'D' and resid 205 through 212 Processing helix chain 'D' and resid 212 through 228 removed outlier: 3.668A pdb=" N LEU D 228 " --> pdb=" O SER D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 235 removed outlier: 3.737A pdb=" N THR D 235 " --> pdb=" O PRO D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 269 removed outlier: 5.922A pdb=" N TYR D 256 " --> pdb=" O HIS D 252 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ILE D 257 " --> pdb=" O ARG D 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 25 removed outlier: 3.621A pdb=" N GLU C 22 " --> pdb=" O LEU C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 48 removed outlier: 4.172A pdb=" N ASP C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 74 Processing helix chain 'C' and resid 125 through 130 removed outlier: 3.663A pdb=" N ARG C 129 " --> pdb=" O PRO C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 145 Processing helix chain 'C' and resid 148 through 152 Processing helix chain 'C' and resid 188 through 192 Processing helix chain 'C' and resid 202 through 212 removed outlier: 3.544A pdb=" N PHE C 208 " --> pdb=" O PRO C 204 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG C 211 " --> pdb=" O ALA C 207 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N HIS C 212 " --> pdb=" O PHE C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 235 removed outlier: 3.708A pdb=" N HIS C 216 " --> pdb=" O HIS C 212 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TRP C 229 " --> pdb=" O TYR C 225 " (cutoff:3.500A) Proline residue: C 231 - end of helix Processing helix chain 'C' and resid 251 through 269 removed outlier: 4.497A pdb=" N TYR C 256 " --> pdb=" O HIS C 252 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ILE C 257 " --> pdb=" O ARG C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 281 removed outlier: 4.259A pdb=" N LYS C 281 " --> pdb=" O THR C 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 278 through 281' Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 removed outlier: 6.997A pdb=" N LEU A 3 " --> pdb=" O GLN A 81 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU A 83 " --> pdb=" O LEU A 3 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ILE A 5 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 132 " --> pdb=" O LEU A 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 164 through 168 removed outlier: 6.190A pdb=" N GLU A 165 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N CYS A 247 " --> pdb=" O GLU A 165 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N PHE A 167 " --> pdb=" O CYS A 247 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 180 through 181 removed outlier: 3.668A pdb=" N VAL A 180 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL B 180 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N TYR B 179 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLY B 246 " --> pdb=" O TYR B 179 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N PHE B 181 " --> pdb=" O GLY B 246 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N PHE B 167 " --> pdb=" O CYS B 247 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.633A pdb=" N ASP B 86 " --> pdb=" O VAL B 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 161 through 163 removed outlier: 5.583A pdb=" N THR B 161 " --> pdb=" O LEU B 241 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 5 through 6 removed outlier: 6.755A pdb=" N ILE D 5 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N LEU D 85 " --> pdb=" O ILE D 5 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 27 through 30 removed outlier: 5.493A pdb=" N TYR D 27 " --> pdb=" O ALA D 52 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N SER D 54 " --> pdb=" O TYR D 27 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL D 29 " --> pdb=" O SER D 54 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 272 through 274 removed outlier: 3.537A pdb=" N ILE D 245 " --> pdb=" O GLU D 165 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N TYR D 179 " --> pdb=" O ALA D 244 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N GLY D 246 " --> pdb=" O TYR D 179 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N PHE D 181 " --> pdb=" O GLY D 246 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL D 180 " --> pdb=" O VAL C 180 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 27 through 30 removed outlier: 6.678A pdb=" N TYR C 27 " --> pdb=" O ALA C 52 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N SER C 54 " --> pdb=" O TYR C 27 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N VAL C 29 " --> pdb=" O SER C 54 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 244 through 246 removed outlier: 7.874A pdb=" N ILE C 245 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLU C 165 " --> pdb=" O ILE C 245 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N MET C 162 " --> pdb=" O GLN C 273 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N ARG C 275 " --> pdb=" O MET C 162 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N PHE C 164 " --> pdb=" O ARG C 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 314 hydrogen bonds defined for protein. 912 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 13 hydrogen bonds 22 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 5.89 Time building geometry restraints manager: 15.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7379 1.03 - 1.23: 791 1.23 - 1.42: 4059 1.42 - 1.62: 5727 1.62 - 1.81: 64 Bond restraints: 18020 Sorted by residual: bond pdb=" N2 G K 115 " pdb=" H21 G K 115 " ideal model delta sigma weight residual 0.860 1.049 -0.189 2.00e-02 2.50e+03 8.91e+01 bond pdb=" N3 U K 32 " pdb=" H3 U K 32 " ideal model delta sigma weight residual 0.860 1.040 -0.180 2.00e-02 2.50e+03 8.12e+01 bond pdb=" N3 U K 70 " pdb=" H3 U K 70 " ideal model delta sigma weight residual 0.860 1.040 -0.180 2.00e-02 2.50e+03 8.12e+01 bond pdb=" N3 U K 69 " pdb=" H3 U K 69 " ideal model delta sigma weight residual 0.860 1.040 -0.180 2.00e-02 2.50e+03 8.10e+01 bond pdb=" N1 G K 135 " pdb=" H1 G K 135 " ideal model delta sigma weight residual 0.860 1.040 -0.180 2.00e-02 2.50e+03 8.08e+01 ... (remaining 18015 not shown) Histogram of bond angle deviations from ideal: 0.22 - 30.08: 5 30.08 - 59.95: 0 59.95 - 89.81: 2 89.81 - 119.68: 25871 119.68 - 149.54: 6415 Bond angle restraints: 32293 Sorted by residual: angle pdb=" H5' G K 73 " pdb=" C5' G K 73 " pdb="H5'' G K 73 " ideal model delta sigma weight residual 109.00 0.22 108.78 3.00e+00 1.11e-01 1.31e+03 angle pdb=" H5' U K 84 " pdb=" C5' U K 84 " pdb="H5'' U K 84 " ideal model delta sigma weight residual 109.00 0.53 108.47 3.00e+00 1.11e-01 1.31e+03 angle pdb=" H5' A K 45 " pdb=" C5' A K 45 " pdb="H5'' A K 45 " ideal model delta sigma weight residual 109.00 0.85 108.15 3.00e+00 1.11e-01 1.30e+03 angle pdb=" H5' A K 129 " pdb=" C5' A K 129 " pdb="H5'' A K 129 " ideal model delta sigma weight residual 109.00 0.96 108.04 3.00e+00 1.11e-01 1.30e+03 angle pdb=" O5' G K 123 " pdb=" C5' G K 123 " pdb="H5'' G K 123 " ideal model delta sigma weight residual 109.00 21.92 87.08 3.00e+00 1.11e-01 8.43e+02 ... (remaining 32288 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 8128 35.99 - 71.99: 566 71.99 - 107.98: 117 107.98 - 143.98: 5 143.98 - 179.97: 37 Dihedral angle restraints: 8853 sinusoidal: 5343 harmonic: 3510 Sorted by residual: dihedral pdb=" O4' U K 138 " pdb=" C1' U K 138 " pdb=" N1 U K 138 " pdb=" C2 U K 138 " ideal model delta sinusoidal sigma weight residual 200.00 43.52 156.48 1 1.50e+01 4.44e-03 8.18e+01 dihedral pdb=" O4' U K 84 " pdb=" C1' U K 84 " pdb=" N1 U K 84 " pdb=" C2 U K 84 " ideal model delta sinusoidal sigma weight residual 200.00 50.85 149.15 1 1.50e+01 4.44e-03 7.93e+01 dihedral pdb=" O4' C K 85 " pdb=" C1' C K 85 " pdb=" N1 C K 85 " pdb=" C2 C K 85 " ideal model delta sinusoidal sigma weight residual 200.00 51.23 148.77 1 1.50e+01 4.44e-03 7.92e+01 ... (remaining 8850 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 1374 0.129 - 0.257: 380 0.257 - 0.386: 29 0.386 - 0.514: 4 0.514 - 0.643: 1 Chirality restraints: 1788 Sorted by residual: chirality pdb=" C3' U K 36 " pdb=" C4' U K 36 " pdb=" O3' U K 36 " pdb=" C2' U K 36 " both_signs ideal model delta sigma weight residual False -2.74 -2.10 -0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" C3' G K 37 " pdb=" C4' G K 37 " pdb=" O3' G K 37 " pdb=" C2' G K 37 " both_signs ideal model delta sigma weight residual False -2.74 -2.24 -0.50 2.00e-01 2.50e+01 6.34e+00 chirality pdb=" C3' A K 53 " pdb=" C4' A K 53 " pdb=" O3' A K 53 " pdb=" C2' A K 53 " both_signs ideal model delta sigma weight residual False -2.74 -2.27 -0.47 2.00e-01 2.50e+01 5.56e+00 ... (remaining 1785 not shown) Planarity restraints: 2593 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 59 " -0.240 2.00e-02 2.50e+03 3.52e-01 1.86e+03 pdb=" CG ASN A 59 " 0.018 2.00e-02 2.50e+03 pdb=" OD1 ASN A 59 " 0.228 2.00e-02 2.50e+03 pdb=" ND2 ASN A 59 " 0.006 2.00e-02 2.50e+03 pdb="HD21 ASN A 59 " -0.569 2.00e-02 2.50e+03 pdb="HD22 ASN A 59 " 0.557 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 271 " -0.238 2.00e-02 2.50e+03 3.07e-01 1.41e+03 pdb=" CG ASN B 271 " 0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN B 271 " 0.228 2.00e-02 2.50e+03 pdb=" ND2 ASN B 271 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN B 271 " -0.485 2.00e-02 2.50e+03 pdb="HD22 ASN B 271 " 0.470 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 69 " -0.191 2.00e-02 2.50e+03 2.22e-01 7.36e+02 pdb=" CD GLN C 69 " 0.013 2.00e-02 2.50e+03 pdb=" OE1 GLN C 69 " 0.186 2.00e-02 2.50e+03 pdb=" NE2 GLN C 69 " -0.004 2.00e-02 2.50e+03 pdb="HE21 GLN C 69 " 0.333 2.00e-02 2.50e+03 pdb="HE22 GLN C 69 " -0.336 2.00e-02 2.50e+03 ... (remaining 2590 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 1155 2.23 - 2.82: 34628 2.82 - 3.42: 44190 3.42 - 4.01: 55099 4.01 - 4.60: 81309 Nonbonded interactions: 216381 Sorted by model distance: nonbonded pdb=" O SER D 114 " pdb=" HG SER D 114 " model vdw 1.640 1.850 nonbonded pdb=" H3 MET A 1 " pdb=" O ALA A 77 " model vdw 1.647 1.850 nonbonded pdb=" O TYR B 96 " pdb=" HG1 THR B 99 " model vdw 1.665 1.850 nonbonded pdb=" O GLN A 221 " pdb=" HG SER A 224 " model vdw 1.696 1.850 nonbonded pdb=" H8 A K 23 " pdb=" H2 A K 54 " model vdw 1.706 2.100 ... (remaining 216376 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 or (resid 3 through 4 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 5 through 6 or resid 13 or \ (resid 14 and (name N or name CA or name C or name O or name CB or name H or nam \ e HA )) or resid 15 through 18 or (resid 19 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 20 through 21 or (resid 22 an \ d (name N or name CA or name C or name O or name CB or name H or name HA )) or r \ esid 23 or (resid 24 and (name N or name CA or name C or name O or name CB or na \ me H or name HA )) or resid 25 or (resid 26 through 29 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 30 or (resid 31 th \ rough 32 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 33 or (resid 34 and (name N or name CA or name C or name O or na \ me CB or name H or name HA )) or resid 35 or (resid 36 through 37 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 38 thro \ ugh 41 or (resid 42 and (name N or name CA or name C or name O or name CB or nam \ e H or name HA )) or resid 43 or (resid 44 and (name N or name CA or name C or n \ ame O or name CB or name H or name HA )) or resid 45 or (resid 46 through 49 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or re \ sid 50 through 55 or (resid 56 and (name N or name CA or name C or name O or nam \ e CB or name H or name HA )) or resid 57 through 58 or (resid 59 through 60 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or res \ id 61 or resid 63 through 65 or (resid 66 through 69 and (name N or name CA or n \ ame C or name O or name CB or name H or name HA )) or resid 70 through 73 or (re \ sid 74 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 75 through 77 or (resid 78 and (name N or name CA or name C or nam \ e O or name CB or name H or name HA )) or resid 79 through 80 or (resid 81 throu \ gh 84 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 86 through 87 or (resid 88 through 91 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 92 or resid 124 throug \ h 128 or (resid 129 and (name N or name CA or name C or name O or name CB or nam \ e H or name HA )) or resid 130 through 132 or (resid 133 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 134 through 141 \ or (resid 142 through 144 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 145 or resid 147 through 150 or (resid 151 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or res \ id 152 through 156 or (resid 157 through 158 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 159 or (resid 160 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 161 \ through 162 or (resid 163 through 165 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 166 or (resid 167 and (name N or n \ ame CA or name C or name O or name CB or name H or name HA )) or resid 168 throu \ gh 169 or (resid 170 and (name N or name CA or name C or name O or name CB or na \ me CG or name CD or name CE or name H or name HA or name HB2 or name HB3 or name \ HG2 or name HG3 or name HD2 or name HD3)) or resid 171 through 172 or (resid 17 \ 3 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 174 through 177 or (resid 178 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 179 through 181 or (resid 182 thro \ ugh 186 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 187 through 194 or (resid 195 through 196 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 197 through 200 \ or (resid 201 through 203 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 204 through 214 or (resid 215 and (name N or na \ me CA or name C or name O or name CB or name H or name HA )) or resid 216 throug \ h 217 or (resid 218 and (name N or name CA or name C or name O or name CB or nam \ e H or name HA )) or resid 219 through 221 or (resid 222 through 223 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 224 \ through 227 or (resid 228 through 230 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 231 through 234 or (resid 235 throu \ gh 238 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 239 through 240 or (resid 241 through 242 and (name N or name CA o \ r name C or name O or name CB or name H or name HA )) or resid 243 through 252 o \ r (resid 253 through 257 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 258 through 260 or (resid 261 and (name N or nam \ e CA or name C or name O or name CB or name H or name HA )) or resid 262 through \ 263 or (resid 264 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 265 or (resid 266 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 267 through 269 or (resid 270 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 271 through 275 or (resid 276 through 280 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 281 through 282)) selection = (chain 'B' and (resid 2 or (resid 3 through 4 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 5 through 6 or resid 13 or \ (resid 14 and (name N or name CA or name C or name O or name CB or name H or nam \ e HA )) or resid 15 through 17 or (resid 18 through 19 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 20 or (resid 21 th \ rough 22 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 23 through 25 or (resid 26 through 29 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 30 through 48 or (r \ esid 49 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 50 through 64 or (resid 65 through 69 and (name N or name CA or n \ ame C or name O or name CB or name H or name HA )) or resid 70 through 73 or (re \ sid 74 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 75 through 84 or (resid 86 and (name N or name CA or name C or nam \ e O or name CB or name H or name HA )) or resid 87 through 88 or (resid 89 throu \ gh 91 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 92 or (resid 124 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 125 or (resid 126 through 127 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 128 th \ rough 132 or (resid 133 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 134 through 135 or (resid 136 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 137 or (resi \ d 138 through 139 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 140 through 141 or (resid 142 through 144 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 145 or \ resid 147 through 148 or (resid 149 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 150 or (resid 151 and (name N or nam \ e CA or name C or name O or name CB or name H or name HA )) or resid 152 or (res \ id 153 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or (resid 154 and (name N or name CA or name C or name O or name H )) or (r \ esid 155 through 158 and (name N or name CA or name C or name O or name CB or na \ me H or name HA )) or resid 159 or (resid 160 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 161 through 169 or (resid 1 \ 70 and (name N or name CA or name C or name O or name CB or name CG or name CD o \ r name CE or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 o \ r name HD2 or name HD3)) or resid 171 through 172 or (resid 173 and (name N or n \ ame CA or name C or name O or name CB or name H or name HA )) or resid 174 throu \ gh 181 or (resid 182 through 186 and (name N or name CA or name C or name O or n \ ame CB or name H or name HA )) or resid 187 or (resid 188 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 189 or (resid 1 \ 90 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 191 or (resid 192 and (name N or name CA or name C or name O or name C \ B or name H or name HA )) or resid 193 or (resid 194 through 196 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 197 or ( \ resid 198 through 199 and (name N or name CA or name C or name O or name CB or n \ ame H or name HA )) or resid 200 or (resid 201 through 203 and (name N or name C \ A or name C or name O or name CB or name H or name HA )) or resid 204 through 20 \ 7 or (resid 208 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 209 through 210 or (resid 211 and (name N or name CA or n \ ame C or name O or name CB or name H or name HA )) or resid 212 through 213 or ( \ resid 214 through 215 and (name N or name CA or name C or name O or name CB or n \ ame H or name HA )) or resid 216 through 217 or (resid 218 and (name N or name C \ A or name C or name O or name CB or name H or name HA )) or resid 219 through 22 \ 7 or (resid 228 through 230 and (name N or name CA or name C or name O or name C \ B or name H or name HA )) or resid 231 through 234 or (resid 235 through 238 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or re \ sid 239 through 240 or (resid 241 through 242 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 243 through 253 or (resid 2 \ 54 through 257 and (name N or name CA or name C or name O or name CB or name H o \ r name HA )) or resid 258 through 259 or (resid 260 through 261 and (name N or n \ ame CA or name C or name O or name CB or name H or name HA )) or resid 262 throu \ gh 269 or (resid 270 and (name N or name CA or name C or name O or name CB or na \ me H or name HA )) or resid 271 through 274 or (resid 275 through 280 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 281 \ through 282)) selection = (chain 'C' and (resid 2 or (resid 3 through 4 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 5 through 17 or (resid 18 t \ hrough 19 and (name N or name CA or name C or name O or name CB or name H or nam \ e HA )) or resid 20 or (resid 21 through 22 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 23 through 25 or (resid 26 th \ rough 29 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 30 or (resid 31 through 32 and (name N or name CA or name C or n \ ame O or name CB or name H or name HA )) or resid 33 or (resid 34 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 35 thro \ ugh 36 or (resid 37 and (name N or name CA or name C or name O or name CB or nam \ e H or name HA )) or resid 38 through 39 or (resid 40 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 41 or (resid 42 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or re \ sid 43 through 45 or (resid 46 through 49 and (name N or name CA or name C or na \ me O or name CB or name H or name HA )) or resid 50 through 55 or (resid 56 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or res \ id 57 or (resid 58 through 60 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 61 or resid 63 through 65 or (resid 66 thro \ ugh 69 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 70 through 73 or (resid 74 and (name N or name CA or name C or nam \ e O or name CB or name H or name HA )) or resid 75 through 77 or (resid 78 and ( \ name N or name CA or name C or name O or name CB or name H or name HA )) or resi \ d 79 through 80 or (resid 81 through 86 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 87 or (resid 88 through 91 and (n \ ame N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 92 or (resid 124 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 125 or (resid 126 through 127 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 128 or (resid 129 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 130 through 135 or (resid 136 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 137 through 142 or (resid 143 throug \ h 144 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 145 through 152 or (resid 153 and (name N or name CA or name C or n \ ame O or name CB or name H or name HA )) or resid 154 through 162 or (resid 163 \ through 165 and (name N or name CA or name C or name O or name CB or name H or n \ ame HA )) or resid 166 or (resid 167 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 168 through 177 or (resid 178 and (n \ ame N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 179 through 181 or (resid 182 through 186 and (name N or name CA or name C or n \ ame O or name CB or name H or name HA )) or resid 187 or (resid 188 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 189 o \ r (resid 190 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 191 or (resid 192 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 193 or (resid 194 through 196 and ( \ name N or name CA or name C or name O or name CB or name H or name HA )) or resi \ d 197 through 198 or (resid 199 and (name N or name CA or name C or name O or na \ me CB or name H or name HA )) or resid 200 or (resid 201 through 203 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 204 \ through 207 or (resid 208 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 209 through 210 or (resid 211 and (name N or na \ me CA or name C or name O or name CB or name H or name HA )) or resid 212 throug \ h 213 or (resid 214 through 215 and (name N or name CA or name C or name O or na \ me CB or name H or name HA )) or resid 216 through 217 or (resid 218 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 219 \ through 220 or (resid 221 through 223 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 224 through 227 or (resid 228 throu \ gh 230 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 231 or (resid 232 and (name N or name CA or name C or name O or na \ me CB or name H or name HA )) or resid 233 through 234 or (resid 235 through 238 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 239 through 254 or (resid 255 through 257 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 258 through 259 or (res \ id 260 through 261 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 262 through 263 or (resid 264 and (name N or name CA o \ r name C or name O or name CB or name H or name HA )) or resid 265 through 272 o \ r (resid 273 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 274 or (resid 275 through 280 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 281 through 282)) selection = (chain 'D' and (resid 2 through 3 or (resid 4 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 5 through 6 or resid 13 or \ (resid 14 and (name N or name CA or name C or name O or name CB or name H or nam \ e HA )) or resid 15 through 17 or (resid 18 through 19 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 20 or (resid 21 th \ rough 22 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 23 or (resid 24 and (name N or name CA or name C or name O or na \ me CB or name H or name HA )) or resid 25 through 30 or (resid 31 through 32 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or re \ sid 33 or (resid 34 and (name N or name CA or name C or name O or name CB or nam \ e H or name HA )) or resid 35 or (resid 36 through 37 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 38 through 41 or (r \ esid 42 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 43 through 45 or (resid 46 through 49 and (name N or name CA or n \ ame C or name O or name CB or name H or name HA )) or resid 50 through 55 or (re \ sid 56 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 57 or (resid 58 through 60 and (name N or name CA or name C or nam \ e O or name CB or name H or name HA )) or resid 61 or resid 63 through 66 or (re \ sid 67 through 69 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 70 through 77 or (resid 78 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 79 through 81 or (res \ id 82 through 84 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or (resid 86 and (name N or name CA or name C or name O or name C \ B or name H or name HA )) or resid 87 or (resid 88 through 91 and (name N or nam \ e CA or name C or name O or name CB or name H or name HA )) or resid 92 or (resi \ d 124 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 125 through 126 or (resid 127 and (name N or name CA or name C or n \ ame O or name CB or name H or name HA )) or resid 128 through 132 or (resid 133 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 134 through 135 or (resid 136 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 137 or (resid 138 through 139 and (n \ ame N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 140 through 141 or (resid 142 through 144 and (name N or name CA or name C or n \ ame O or name CB or name H or name HA )) or resid 145 or (resid 147 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 148 o \ r (resid 149 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 150 or (resid 151 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 152 through 157 or (resid 158 and ( \ name N or name CA or name C or name O or name CB or name H or name HA )) or resi \ d 159 or (resid 160 and (name N or name CA or name C or name O or name CB or nam \ e H or name HA )) or resid 161 or (resid 162 through 165 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 166 or (resid 16 \ 7 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 168 through 169 or (resid 170 and (name N or name CA or name C or name \ O or name CB or name CG or name CD or name CE or name H or name HA or name HB2 o \ r name HB3 or name HG2 or name HG3 or name HD2 or name HD3)) or resid 171 throug \ h 172 or (resid 173 and (name N or name CA or name C or name O or name CB or nam \ e H or name HA )) or resid 174 through 177 or (resid 178 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 179 through 183 \ or (resid 184 through 186 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 187 or (resid 188 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 189 or (resid 190 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or res \ id 191 or (resid 192 and (name N or name CA or name C or name O or name CB or na \ me H or name HA )) or resid 193 or (resid 194 through 196 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 197 or (resid 1 \ 98 through 199 and (name N or name CA or name C or name O or name CB or name H o \ r name HA )) or resid 200 through 220 or (resid 221 through 223 and (name N or n \ ame CA or name C or name O or name CB or name H or name HA )) or resid 224 throu \ gh 228 or (resid 229 through 230 and (name N or name CA or name C or name O or n \ ame CB or name H or name HA )) or resid 231 through 235 or (resid 236 through 23 \ 8 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 239 through 240 or (resid 241 through 242 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 243 through 246 or (re \ sid 247 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 248 through 251 or (resid 252 through 257 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 258 through 259 \ or (resid 260 through 261 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 262 through 263 or (resid 264 and (name N or na \ me CA or name C or name O or name CB or name H or name HA )) or resid 265 throug \ h 267 or (resid 268 and (name N or name CA or name C or name O or name CB or nam \ e H or name HA )) or resid 269 or (resid 270 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 271 through 272 or (resid 27 \ 3 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 274 through 275 or (resid 276 through 280 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 281 through 282)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.280 Extract box with map and model: 21.400 Check model and map are aligned: 0.350 Set scattering table: 0.190 Process input model: 66.700 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6548 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.087 10189 Z= 0.803 Angle : 1.979 13.684 14374 Z= 1.480 Chirality : 0.108 0.643 1788 Planarity : 0.011 0.076 1512 Dihedral : 24.774 179.381 4228 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.14 % Allowed : 6.17 % Favored : 93.69 % Cbeta Deviations : 0.10 % 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: -1.62 (0.25), residues: 1055 helix: -0.52 (0.24), residues: 431 sheet: -1.70 (0.37), residues: 175 loop : -1.20 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRP B 229 HIS 0.013 0.003 HIS D 276 PHE 0.034 0.003 PHE B 218 TYR 0.042 0.004 TYR A 256 ARG 0.014 0.001 ARG D 89 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue ILE 93 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LEU 279 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue SER 254 is missing expected H atoms. Skipping. Residue ILE 257 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Evaluate side-chains 418 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 417 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLN cc_start: 0.9685 (tt0) cc_final: 0.9295 (tp-100) REVERT: A 73 ASN cc_start: 0.8993 (m-40) cc_final: 0.8282 (m-40) REVERT: A 112 LEU cc_start: 0.9174 (mp) cc_final: 0.8862 (tp) REVERT: A 210 ASP cc_start: 0.9403 (p0) cc_final: 0.9149 (p0) REVERT: A 212 HIS cc_start: 0.8830 (m-70) cc_final: 0.8205 (m-70) REVERT: A 266 ARG cc_start: 0.9490 (tpp-160) cc_final: 0.9228 (ttm-80) REVERT: A 276 HIS cc_start: 0.8602 (p-80) cc_final: 0.8372 (p-80) REVERT: B 91 THR cc_start: 0.9541 (m) cc_final: 0.9058 (t) REVERT: B 98 ASP cc_start: 0.9350 (m-30) cc_final: 0.9037 (m-30) REVERT: B 112 LEU cc_start: 0.9524 (tp) cc_final: 0.9262 (tp) REVERT: B 148 LEU cc_start: 0.9560 (mt) cc_final: 0.9239 (mt) REVERT: B 171 HIS cc_start: 0.8851 (m-70) cc_final: 0.8377 (t-90) REVERT: B 186 LEU cc_start: 0.8875 (mt) cc_final: 0.8640 (mt) REVERT: B 236 ASN cc_start: 0.8934 (m-40) cc_final: 0.8624 (t0) REVERT: D 107 SER cc_start: 0.9733 (t) cc_final: 0.9447 (p) REVERT: D 149 ARG cc_start: 0.9478 (tpp-160) cc_final: 0.8990 (tpt90) REVERT: D 263 ASP cc_start: 0.9008 (m-30) cc_final: 0.8763 (m-30) REVERT: C 212 HIS cc_start: 0.8669 (m-70) cc_final: 0.8413 (m90) outliers start: 1 outliers final: 1 residues processed: 417 average time/residue: 0.5096 time to fit residues: 281.1901 Evaluate side-chains 306 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 305 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.9990 chunk 88 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 91 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 212 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6562 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10189 Z= 0.174 Angle : 0.703 7.388 14374 Z= 0.367 Chirality : 0.041 0.217 1788 Planarity : 0.005 0.078 1512 Dihedral : 27.503 178.293 2716 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % 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: -0.82 (0.26), residues: 1055 helix: 0.15 (0.23), residues: 463 sheet: -1.38 (0.33), residues: 210 loop : -0.66 (0.34), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 229 HIS 0.006 0.001 HIS A 216 PHE 0.009 0.002 PHE C 167 TYR 0.012 0.001 TYR B 220 ARG 0.006 0.001 ARG B 149 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue ILE 93 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LEU 279 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue SER 254 is missing expected H atoms. Skipping. Residue ILE 257 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Evaluate side-chains 371 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 371 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 PHE cc_start: 0.9444 (m-80) cc_final: 0.9206 (m-80) REVERT: A 55 ILE cc_start: 0.8992 (mm) cc_final: 0.8460 (mm) REVERT: A 69 GLN cc_start: 0.9783 (tt0) cc_final: 0.9502 (tp-100) REVERT: A 112 LEU cc_start: 0.9074 (mp) cc_final: 0.8657 (tp) REVERT: A 146 GLU cc_start: 0.9416 (tp30) cc_final: 0.8953 (tp30) REVERT: A 178 ASP cc_start: 0.9093 (m-30) cc_final: 0.8708 (p0) REVERT: A 191 TRP cc_start: 0.9145 (m-10) cc_final: 0.8680 (m-10) REVERT: A 265 PHE cc_start: 0.9493 (m-80) cc_final: 0.9102 (m-80) REVERT: A 272 VAL cc_start: 0.7297 (p) cc_final: 0.6907 (p) REVERT: A 276 HIS cc_start: 0.8493 (p-80) cc_final: 0.8139 (p-80) REVERT: B 26 PHE cc_start: 0.9383 (m-80) cc_final: 0.8930 (m-10) REVERT: B 91 THR cc_start: 0.9351 (m) cc_final: 0.8929 (t) REVERT: B 98 ASP cc_start: 0.9084 (m-30) cc_final: 0.8819 (m-30) REVERT: B 171 HIS cc_start: 0.8860 (m-70) cc_final: 0.8251 (t-90) REVERT: B 220 TYR cc_start: 0.9006 (m-80) cc_final: 0.8668 (m-80) REVERT: B 271 ASN cc_start: 0.9537 (t0) cc_final: 0.9013 (t0) REVERT: D 113 GLU cc_start: 0.9013 (tp30) cc_final: 0.8807 (tp30) REVERT: D 149 ARG cc_start: 0.9480 (tpp-160) cc_final: 0.8962 (tpt90) REVERT: C 230 LEU cc_start: 0.9625 (tp) cc_final: 0.9319 (tp) outliers start: 0 outliers final: 0 residues processed: 371 average time/residue: 0.5341 time to fit residues: 259.4245 Evaluate side-chains 297 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 297 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 chunk 114 optimal weight: 9.9990 chunk 94 optimal weight: 6.9990 chunk 105 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 260 GLN D 217 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6713 moved from start: 0.5190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10189 Z= 0.209 Angle : 0.619 7.050 14374 Z= 0.336 Chirality : 0.039 0.203 1788 Planarity : 0.004 0.070 1512 Dihedral : 27.285 179.177 2716 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % 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: -0.46 (0.26), residues: 1055 helix: 0.46 (0.23), residues: 468 sheet: -1.16 (0.34), residues: 204 loop : -0.56 (0.33), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 229 HIS 0.006 0.001 HIS B 216 PHE 0.017 0.001 PHE C 218 TYR 0.011 0.001 TYR A 225 ARG 0.005 0.001 ARG A 151 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue ILE 93 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LEU 279 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue SER 254 is missing expected H atoms. Skipping. Residue ILE 257 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Evaluate side-chains 334 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 334 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLN cc_start: 0.9783 (tt0) cc_final: 0.9512 (tp-100) REVERT: A 85 LEU cc_start: 0.9578 (mp) cc_final: 0.9048 (tt) REVERT: A 112 LEU cc_start: 0.9053 (mp) cc_final: 0.8643 (tp) REVERT: A 146 GLU cc_start: 0.9436 (tp30) cc_final: 0.9021 (tp30) REVERT: A 178 ASP cc_start: 0.9260 (m-30) cc_final: 0.8885 (p0) REVERT: A 264 TYR cc_start: 0.9460 (t80) cc_final: 0.9240 (t80) REVERT: A 265 PHE cc_start: 0.9568 (m-80) cc_final: 0.9174 (m-80) REVERT: A 276 HIS cc_start: 0.8503 (p-80) cc_final: 0.8123 (p-80) REVERT: B 22 GLU cc_start: 0.9578 (pt0) cc_final: 0.9346 (pt0) REVERT: B 91 THR cc_start: 0.9433 (m) cc_final: 0.9008 (t) REVERT: B 98 ASP cc_start: 0.9193 (m-30) cc_final: 0.8941 (m-30) REVERT: B 171 HIS cc_start: 0.8952 (m-70) cc_final: 0.8365 (t-90) REVERT: B 186 LEU cc_start: 0.8976 (mt) cc_final: 0.8749 (mt) REVERT: B 220 TYR cc_start: 0.9017 (m-80) cc_final: 0.8684 (m-80) REVERT: B 263 ASP cc_start: 0.9575 (t0) cc_final: 0.9358 (t0) REVERT: D 31 ASN cc_start: 0.7896 (t0) cc_final: 0.6840 (t0) REVERT: D 149 ARG cc_start: 0.9497 (tpp-160) cc_final: 0.8925 (tpt90) outliers start: 0 outliers final: 0 residues processed: 334 average time/residue: 0.5419 time to fit residues: 238.2468 Evaluate side-chains 286 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 286 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 55 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 chunk 113 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 94 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6701 moved from start: 0.5784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10189 Z= 0.153 Angle : 0.559 6.885 14374 Z= 0.295 Chirality : 0.038 0.195 1788 Planarity : 0.004 0.067 1512 Dihedral : 27.015 179.120 2716 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % 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: -0.05 (0.26), residues: 1055 helix: 0.84 (0.24), residues: 470 sheet: -0.94 (0.34), residues: 202 loop : -0.44 (0.34), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 229 HIS 0.007 0.001 HIS B 216 PHE 0.010 0.001 PHE D 84 TYR 0.008 0.001 TYR D 179 ARG 0.005 0.000 ARG D 94 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue ILE 93 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LEU 279 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue SER 254 is missing expected H atoms. Skipping. Residue ILE 257 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Evaluate side-chains 332 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 332 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.9605 (mm-30) cc_final: 0.9246 (mm-30) REVERT: A 28 CYS cc_start: 0.8674 (p) cc_final: 0.7886 (m) REVERT: A 69 GLN cc_start: 0.9797 (tt0) cc_final: 0.9534 (tp-100) REVERT: A 85 LEU cc_start: 0.9543 (mp) cc_final: 0.8987 (tt) REVERT: A 112 LEU cc_start: 0.8976 (mp) cc_final: 0.8543 (tp) REVERT: A 146 GLU cc_start: 0.9452 (tp30) cc_final: 0.9065 (tp30) REVERT: A 178 ASP cc_start: 0.9163 (m-30) cc_final: 0.8889 (p0) REVERT: A 264 TYR cc_start: 0.9463 (t80) cc_final: 0.9119 (t80) REVERT: A 265 PHE cc_start: 0.9608 (m-80) cc_final: 0.9225 (m-80) REVERT: A 276 HIS cc_start: 0.8470 (p-80) cc_final: 0.8103 (p-80) REVERT: B 18 LEU cc_start: 0.9542 (tp) cc_final: 0.9274 (tp) REVERT: B 22 GLU cc_start: 0.9551 (pt0) cc_final: 0.9295 (pt0) REVERT: B 26 PHE cc_start: 0.9393 (m-80) cc_final: 0.8950 (m-80) REVERT: B 92 LEU cc_start: 0.9563 (mt) cc_final: 0.9350 (mt) REVERT: B 98 ASP cc_start: 0.9183 (m-30) cc_final: 0.8933 (m-30) REVERT: B 146 GLU cc_start: 0.8774 (mp0) cc_final: 0.8540 (mp0) REVERT: B 151 ARG cc_start: 0.8863 (mmt-90) cc_final: 0.8629 (tpp-160) REVERT: B 171 HIS cc_start: 0.9039 (m-70) cc_final: 0.8416 (t-90) REVERT: B 230 LEU cc_start: 0.9725 (tp) cc_final: 0.9383 (tp) REVERT: D 116 ILE cc_start: 0.9607 (pt) cc_final: 0.9315 (tp) REVERT: D 149 ARG cc_start: 0.9475 (tpp-160) cc_final: 0.9132 (mmm160) outliers start: 0 outliers final: 0 residues processed: 332 average time/residue: 0.5076 time to fit residues: 222.6689 Evaluate side-chains 299 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 96 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 HIS ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 HIS D 171 HIS C 69 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.6612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10189 Z= 0.325 Angle : 0.712 7.883 14374 Z= 0.385 Chirality : 0.040 0.219 1788 Planarity : 0.005 0.060 1512 Dihedral : 27.270 178.112 2716 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 28.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % 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: -0.93 (0.25), residues: 1055 helix: -0.23 (0.23), residues: 465 sheet: -0.85 (0.36), residues: 191 loop : -0.73 (0.33), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 229 HIS 0.011 0.002 HIS B 142 PHE 0.022 0.002 PHE D 67 TYR 0.020 0.002 TYR D 179 ARG 0.005 0.001 ARG D 277 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue ILE 93 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LEU 279 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue SER 254 is missing expected H atoms. Skipping. Residue ILE 257 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Evaluate side-chains 293 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 293 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.9555 (mm-30) cc_final: 0.9237 (mm-30) REVERT: A 69 GLN cc_start: 0.9801 (tt0) cc_final: 0.9575 (tp-100) REVERT: A 146 GLU cc_start: 0.9460 (tp30) cc_final: 0.9041 (tp30) REVERT: B 18 LEU cc_start: 0.9601 (tp) cc_final: 0.9332 (tp) REVERT: B 22 GLU cc_start: 0.9587 (pt0) cc_final: 0.9351 (pt0) REVERT: B 26 PHE cc_start: 0.9398 (m-80) cc_final: 0.8898 (m-80) REVERT: B 151 ARG cc_start: 0.8919 (mmt-90) cc_final: 0.8530 (tpp-160) REVERT: B 171 HIS cc_start: 0.9183 (m-70) cc_final: 0.8516 (t70) REVERT: B 186 LEU cc_start: 0.9205 (mt) cc_final: 0.8939 (mt) REVERT: B 220 TYR cc_start: 0.9018 (m-80) cc_final: 0.8668 (m-80) REVERT: B 259 GLU cc_start: 0.9345 (tm-30) cc_final: 0.9145 (tm-30) REVERT: D 149 ARG cc_start: 0.9467 (tpp-160) cc_final: 0.9149 (mmm160) REVERT: D 162 MET cc_start: 0.9200 (pmm) cc_final: 0.8993 (pmm) REVERT: D 220 TYR cc_start: 0.9102 (t80) cc_final: 0.8725 (t80) REVERT: C 71 MET cc_start: 0.9082 (mmp) cc_final: 0.8882 (mmm) REVERT: C 259 GLU cc_start: 0.9072 (mm-30) cc_final: 0.8595 (mm-30) outliers start: 0 outliers final: 0 residues processed: 293 average time/residue: 0.5006 time to fit residues: 193.1463 Evaluate side-chains 252 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 113 optimal weight: 8.9990 chunk 93 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 109 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.7551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 10189 Z= 0.397 Angle : 0.770 7.208 14374 Z= 0.422 Chirality : 0.041 0.222 1788 Planarity : 0.006 0.058 1512 Dihedral : 27.524 178.930 2716 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 35.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % 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: -1.92 (0.25), residues: 1055 helix: -1.21 (0.22), residues: 457 sheet: -1.19 (0.37), residues: 188 loop : -1.13 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 229 HIS 0.013 0.003 HIS B 142 PHE 0.023 0.003 PHE C 218 TYR 0.030 0.003 TYR D 179 ARG 0.006 0.001 ARG A 47 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue ILE 93 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LEU 279 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue SER 254 is missing expected H atoms. Skipping. Residue ILE 257 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Evaluate side-chains 284 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 284 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.9571 (mm-30) cc_final: 0.9073 (mm-30) REVERT: A 28 CYS cc_start: 0.8308 (p) cc_final: 0.7577 (p) REVERT: A 69 GLN cc_start: 0.9801 (tt0) cc_final: 0.9575 (tp-100) REVERT: A 146 GLU cc_start: 0.9391 (tp30) cc_final: 0.9069 (tp30) REVERT: A 186 LEU cc_start: 0.9470 (mt) cc_final: 0.9269 (mt) REVERT: A 264 TYR cc_start: 0.9490 (t80) cc_final: 0.9008 (t80) REVERT: B 18 LEU cc_start: 0.9653 (tp) cc_final: 0.9361 (tp) REVERT: B 22 GLU cc_start: 0.9593 (pt0) cc_final: 0.9375 (pt0) REVERT: B 26 PHE cc_start: 0.9308 (m-80) cc_final: 0.8820 (m-80) REVERT: B 28 CYS cc_start: 0.9429 (p) cc_final: 0.9205 (p) REVERT: B 171 HIS cc_start: 0.9246 (m-70) cc_final: 0.9019 (m-70) REVERT: B 259 GLU cc_start: 0.9391 (tm-30) cc_final: 0.9174 (tm-30) REVERT: D 149 ARG cc_start: 0.9469 (tpp-160) cc_final: 0.9163 (mmm160) REVERT: D 178 ASP cc_start: 0.7887 (m-30) cc_final: 0.7495 (m-30) REVERT: D 220 TYR cc_start: 0.9094 (t80) cc_final: 0.8768 (t80) REVERT: D 242 THR cc_start: 0.8001 (p) cc_final: 0.7249 (p) REVERT: C 265 PHE cc_start: 0.9761 (m-80) cc_final: 0.9464 (m-80) outliers start: 0 outliers final: 0 residues processed: 284 average time/residue: 0.5003 time to fit residues: 188.0318 Evaluate side-chains 251 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 10.0000 chunk 64 optimal weight: 0.6980 chunk 82 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 112 optimal weight: 9.9990 chunk 70 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.7610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10189 Z= 0.163 Angle : 0.568 6.802 14374 Z= 0.301 Chirality : 0.039 0.196 1788 Planarity : 0.004 0.060 1512 Dihedral : 26.949 179.984 2716 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.27), residues: 1055 helix: -0.02 (0.24), residues: 456 sheet: -0.97 (0.38), residues: 187 loop : -0.46 (0.34), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 229 HIS 0.007 0.001 HIS B 216 PHE 0.011 0.001 PHE C 265 TYR 0.013 0.002 TYR D 179 ARG 0.003 0.000 ARG D 89 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue ILE 93 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LEU 279 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue SER 254 is missing expected H atoms. Skipping. Residue ILE 257 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Evaluate side-chains 301 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 301 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.9577 (mm-30) cc_final: 0.9000 (mm-30) REVERT: A 28 CYS cc_start: 0.8320 (p) cc_final: 0.7279 (p) REVERT: A 69 GLN cc_start: 0.9807 (tt0) cc_final: 0.9586 (tp-100) REVERT: A 146 GLU cc_start: 0.9393 (tp30) cc_final: 0.9069 (tp30) REVERT: B 18 LEU cc_start: 0.9632 (tp) cc_final: 0.9334 (tp) REVERT: B 22 GLU cc_start: 0.9573 (pt0) cc_final: 0.9309 (pt0) REVERT: B 26 PHE cc_start: 0.9325 (m-80) cc_final: 0.8795 (m-80) REVERT: B 146 GLU cc_start: 0.8877 (mp0) cc_final: 0.8626 (mp0) REVERT: B 171 HIS cc_start: 0.9260 (m-70) cc_final: 0.8993 (m-70) REVERT: B 259 GLU cc_start: 0.9307 (tm-30) cc_final: 0.9089 (tm-30) REVERT: D 149 ARG cc_start: 0.9467 (tpp-160) cc_final: 0.9151 (mmm160) REVERT: D 162 MET cc_start: 0.9272 (pmm) cc_final: 0.8973 (pmm) REVERT: D 178 ASP cc_start: 0.7786 (m-30) cc_final: 0.7489 (m-30) REVERT: D 242 THR cc_start: 0.7798 (p) cc_final: 0.7069 (p) REVERT: C 265 PHE cc_start: 0.9655 (m-80) cc_final: 0.9368 (m-80) outliers start: 0 outliers final: 0 residues processed: 301 average time/residue: 0.5078 time to fit residues: 200.4460 Evaluate side-chains 268 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 chunk 10 optimal weight: 0.0970 chunk 88 optimal weight: 0.5980 chunk 102 optimal weight: 0.7980 chunk 108 optimal weight: 10.0000 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.7829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10189 Z= 0.132 Angle : 0.542 8.246 14374 Z= 0.280 Chirality : 0.037 0.165 1788 Planarity : 0.004 0.070 1512 Dihedral : 26.580 179.804 2716 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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 (0.27), residues: 1055 helix: 0.69 (0.25), residues: 467 sheet: -0.80 (0.37), residues: 189 loop : -0.18 (0.35), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 229 HIS 0.004 0.001 HIS B 142 PHE 0.025 0.001 PHE D 67 TYR 0.013 0.001 TYR A 220 ARG 0.007 0.000 ARG C 58 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue ILE 93 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LEU 279 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue SER 254 is missing expected H atoms. Skipping. Residue ILE 257 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Evaluate side-chains 309 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 309 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.9574 (mm-30) cc_final: 0.9031 (mm-30) REVERT: A 28 CYS cc_start: 0.8433 (p) cc_final: 0.7416 (p) REVERT: A 69 GLN cc_start: 0.9802 (tt0) cc_final: 0.9576 (tp-100) REVERT: A 112 LEU cc_start: 0.8938 (mp) cc_final: 0.8592 (tp) REVERT: A 146 GLU cc_start: 0.9343 (tp30) cc_final: 0.9016 (tp30) REVERT: B 18 LEU cc_start: 0.9620 (tp) cc_final: 0.9288 (tp) REVERT: B 22 GLU cc_start: 0.9548 (pt0) cc_final: 0.9293 (pt0) REVERT: B 26 PHE cc_start: 0.9300 (m-80) cc_final: 0.8830 (m-80) REVERT: B 146 GLU cc_start: 0.8883 (mp0) cc_final: 0.8574 (mp0) REVERT: B 148 LEU cc_start: 0.9579 (mt) cc_final: 0.9337 (mt) REVERT: B 171 HIS cc_start: 0.9244 (m-70) cc_final: 0.8980 (m-70) REVERT: B 259 GLU cc_start: 0.9275 (tm-30) cc_final: 0.9046 (tm-30) REVERT: D 162 MET cc_start: 0.9311 (pmm) cc_final: 0.9030 (pmm) REVERT: C 165 GLU cc_start: 0.8743 (mp0) cc_final: 0.8366 (mp0) outliers start: 0 outliers final: 0 residues processed: 309 average time/residue: 0.5112 time to fit residues: 208.2472 Evaluate side-chains 274 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 274 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.3980 chunk 105 optimal weight: 3.9990 chunk 108 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 94 optimal weight: 0.0370 chunk 99 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.4864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.8115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10189 Z= 0.157 Angle : 0.537 6.759 14374 Z= 0.282 Chirality : 0.037 0.173 1788 Planarity : 0.004 0.059 1512 Dihedral : 26.515 178.430 2716 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: 0.16 (0.27), residues: 1055 helix: 0.80 (0.24), residues: 472 sheet: -0.62 (0.37), residues: 190 loop : -0.17 (0.35), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 229 HIS 0.005 0.001 HIS A 142 PHE 0.012 0.001 PHE A 218 TYR 0.008 0.001 TYR C 225 ARG 0.006 0.001 ARG D 149 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue ILE 93 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LEU 279 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue SER 254 is missing expected H atoms. Skipping. Residue ILE 257 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Evaluate side-chains 299 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.9609 (mm-30) cc_final: 0.8993 (mm-30) REVERT: A 28 CYS cc_start: 0.8467 (p) cc_final: 0.7225 (p) REVERT: A 69 GLN cc_start: 0.9803 (tt0) cc_final: 0.9577 (tp-100) REVERT: A 112 LEU cc_start: 0.8916 (mp) cc_final: 0.8590 (tp) REVERT: A 146 GLU cc_start: 0.9378 (tp30) cc_final: 0.9068 (tp30) REVERT: B 18 LEU cc_start: 0.9626 (tp) cc_final: 0.9290 (tp) REVERT: B 22 GLU cc_start: 0.9550 (pt0) cc_final: 0.9300 (pt0) REVERT: B 26 PHE cc_start: 0.9304 (m-80) cc_final: 0.8857 (m-80) REVERT: B 146 GLU cc_start: 0.8838 (mp0) cc_final: 0.8519 (mp0) REVERT: B 171 HIS cc_start: 0.9243 (m-70) cc_final: 0.8977 (m-70) REVERT: B 259 GLU cc_start: 0.9292 (tm-30) cc_final: 0.9033 (tm-30) REVERT: D 94 ARG cc_start: 0.9405 (ttp80) cc_final: 0.9141 (mtp85) REVERT: D 162 MET cc_start: 0.9316 (pmm) cc_final: 0.9059 (pmm) REVERT: D 220 TYR cc_start: 0.9008 (t80) cc_final: 0.8610 (t80) REVERT: C 71 MET cc_start: 0.9091 (mmp) cc_final: 0.8889 (mmm) outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.4785 time to fit residues: 190.0800 Evaluate side-chains 267 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 267 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 8.9990 chunk 67 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 116 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 73 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.8375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10189 Z= 0.221 Angle : 0.584 7.033 14374 Z= 0.311 Chirality : 0.037 0.196 1788 Planarity : 0.004 0.058 1512 Dihedral : 26.613 177.041 2716 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 19.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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: -0.25 (0.27), residues: 1055 helix: 0.45 (0.24), residues: 468 sheet: -0.66 (0.38), residues: 182 loop : -0.48 (0.34), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 229 HIS 0.006 0.001 HIS C 212 PHE 0.020 0.001 PHE C 218 TYR 0.014 0.002 TYR B 225 ARG 0.005 0.001 ARG D 149 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue ILE 93 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LEU 279 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue ILE 173 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue SER 254 is missing expected H atoms. Skipping. Residue ILE 257 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Evaluate side-chains 291 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 291 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLN cc_start: 0.9806 (tt0) cc_final: 0.9582 (tp-100) REVERT: A 83 LEU cc_start: 0.9250 (mt) cc_final: 0.9038 (mt) REVERT: A 112 LEU cc_start: 0.8924 (mp) cc_final: 0.8611 (tp) REVERT: A 146 GLU cc_start: 0.9409 (tp30) cc_final: 0.9071 (tp30) REVERT: A 186 LEU cc_start: 0.9479 (mt) cc_final: 0.9274 (mt) REVERT: B 18 LEU cc_start: 0.9626 (tp) cc_final: 0.9307 (tp) REVERT: B 22 GLU cc_start: 0.9566 (pt0) cc_final: 0.9317 (pt0) REVERT: B 26 PHE cc_start: 0.9291 (m-80) cc_final: 0.8249 (m-80) REVERT: B 146 GLU cc_start: 0.8841 (mp0) cc_final: 0.8571 (mp0) REVERT: B 171 HIS cc_start: 0.9246 (m-70) cc_final: 0.8971 (m-70) REVERT: B 259 GLU cc_start: 0.9312 (tm-30) cc_final: 0.9064 (tm-30) REVERT: D 162 MET cc_start: 0.9303 (pmm) cc_final: 0.9101 (pmm) REVERT: C 265 PHE cc_start: 0.9678 (m-80) cc_final: 0.9310 (m-80) outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.4875 time to fit residues: 189.0708 Evaluate side-chains 255 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 255 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 85 optimal weight: 8.9990 chunk 13 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 92 optimal weight: 9.9990 chunk 38 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.082068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.060111 restraints weight = 135507.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.062782 restraints weight = 75397.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.064748 restraints weight = 50493.823| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3228 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3226 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.8577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10189 Z= 0.133 Angle : 0.530 6.705 14374 Z= 0.273 Chirality : 0.037 0.162 1788 Planarity : 0.004 0.067 1512 Dihedral : 26.299 179.745 2716 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.27 (0.27), residues: 1055 helix: 0.94 (0.25), residues: 472 sheet: -0.68 (0.38), residues: 183 loop : -0.12 (0.35), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 229 HIS 0.004 0.001 HIS D 252 PHE 0.012 0.001 PHE A 218 TYR 0.010 0.001 TYR A 220 ARG 0.008 0.001 ARG B 151 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5452.92 seconds wall clock time: 96 minutes 31.69 seconds (5791.69 seconds total)