Starting phenix.real_space_refine (version: dev) on Wed Feb 22 14:00:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0i_15784/02_2023/8b0i_15784.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0i_15784/02_2023/8b0i_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_15784/02_2023/8b0i_15784.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0i_15784/02_2023/8b0i_15784.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0i_15784/02_2023/8b0i_15784.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0i_15784/02_2023/8b0i_15784.pdb" } resolution = 4.28 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 8.55, per 1000 atoms: 0.48 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: 14.07 Conformation dependent library (CDL) restraints added in 1.5 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: 6.46 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: 5.58 Time building geometry restraints manager: 14.54 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: 6836 35.99 - 71.99: 337 71.99 - 107.98: 87 107.98 - 143.98: 5 143.98 - 179.97: 37 Dihedral angle restraints: 7302 sinusoidal: 3792 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 7299 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 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. 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: 6.400 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: 0.290 Extract box with map and model: 23.170 Check model and map are aligned: 0.270 Process input model: 58.540 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.150 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6104 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 : 22.564 179.381 3864 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 % 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 *********************** 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 : 1.337 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 outliers start: 1 outliers final: 1 residues processed: 417 average time/residue: 0.5046 time to fit residues: 278.0859 Evaluate side-chains 294 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 293 time to evaluate : 1.283 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 1.0074 time to fit residues: 2.8200 ------------------------------------------------------------------------------- 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: 0.8980 chunk 88 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 30 optimal weight: 0.0970 chunk 59 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.7978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6106 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 10189 Z= 0.177 Angle : 0.700 7.299 14374 Z= 0.369 Chirality : 0.041 0.224 1788 Planarity : 0.005 0.080 1512 Dihedral : 24.893 176.885 2352 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer Outliers : 0.00 % 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: -0.88 (0.26), residues: 1055 helix: 0.12 (0.23), residues: 461 sheet: -1.37 (0.33), residues: 209 loop : -0.75 (0.34), residues: 385 *********************** 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 369 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 369 time to evaluate : 1.448 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 outliers start: 0 outliers final: 0 residues processed: 369 average time/residue: 0.5393 time to fit residues: 259.9185 Evaluate side-chains 291 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 291 time to evaluate : 1.328 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6320 ------------------------------------------------------------------------------- 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: 3.9990 chunk 32 optimal weight: 0.7980 chunk 88 optimal weight: 0.0670 chunk 72 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 114 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 85 optimal weight: 9.9990 overall best weight: 1.3122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6185 moved from start: 0.5131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 10189 Z= 0.168 Angle : 0.599 7.924 14374 Z= 0.319 Chirality : 0.039 0.202 1788 Planarity : 0.004 0.073 1512 Dihedral : 24.665 179.527 2352 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer Outliers : 0.00 % 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: -0.36 (0.26), residues: 1055 helix: 0.61 (0.24), residues: 469 sheet: -1.15 (0.33), residues: 209 loop : -0.55 (0.33), residues: 377 *********************** 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 342 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 342 time to evaluate : 1.291 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 outliers start: 0 outliers final: 0 residues processed: 342 average time/residue: 0.5056 time to fit residues: 228.2478 Evaluate side-chains 298 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 1.431 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5217 ------------------------------------------------------------------------------- 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: 3.9990 chunk 80 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 113 optimal weight: 8.9990 chunk 101 optimal weight: 3.9990 chunk 30 optimal weight: 0.1980 chunk 94 optimal weight: 0.0370 overall best weight: 1.8464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 GLN D 171 HIS C 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6288 moved from start: 0.5858 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= 0.191 Angle : 0.586 7.579 14374 Z= 0.312 Chirality : 0.038 0.202 1788 Planarity : 0.004 0.069 1512 Dihedral : 24.561 179.580 2352 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer Outliers : 0.00 % 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: -0.18 (0.26), residues: 1055 helix: 0.74 (0.24), residues: 468 sheet: -0.99 (0.34), residues: 205 loop : -0.51 (0.33), residues: 382 *********************** 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 327 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 327 time to evaluate : 1.414 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 outliers start: 0 outliers final: 0 residues processed: 327 average time/residue: 0.5107 time to fit residues: 220.7588 Evaluate side-chains 280 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 280 time to evaluate : 1.337 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5787 ------------------------------------------------------------------------------- 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: 3.9990 chunk 46 optimal weight: 10.0000 chunk 96 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 57 optimal weight: 8.9990 chunk 101 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 38 optimal weight: 0.2980 overall best weight: 2.6186 ------------------------------------------------------------------------------- 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 69 GLN A 73 ASN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6409 moved from start: 0.6574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 10189 Z= 0.245 Angle : 0.616 7.402 14374 Z= 0.331 Chirality : 0.039 0.201 1788 Planarity : 0.005 0.063 1512 Dihedral : 24.558 179.535 2352 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer Outliers : 0.00 % 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: -0.40 (0.26), residues: 1055 helix: 0.34 (0.23), residues: 464 sheet: -0.83 (0.36), residues: 194 loop : -0.49 (0.33), residues: 397 *********************** 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 317 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 317 time to evaluate : 1.322 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 outliers start: 0 outliers final: 0 residues processed: 317 average time/residue: 0.5024 time to fit residues: 211.4865 Evaluate side-chains 264 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 1.336 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5631 ------------------------------------------------------------------------------- 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: 4.9990 chunk 66 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 113 optimal weight: 8.9990 chunk 93 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 109 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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: 0.6588 moved from start: 0.7542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.059 10189 Z= 0.381 Angle : 0.765 7.219 14374 Z= 0.417 Chirality : 0.041 0.227 1788 Planarity : 0.006 0.079 1512 Dihedral : 25.033 179.847 2352 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 35.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer Outliers : 0.00 % 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: -1.53 (0.25), residues: 1055 helix: -0.89 (0.22), residues: 449 sheet: -1.07 (0.37), residues: 194 loop : -0.88 (0.32), residues: 412 *********************** 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 289 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 289 time to evaluate : 1.422 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 outliers start: 0 outliers final: 0 residues processed: 289 average time/residue: 0.5113 time to fit residues: 195.8008 Evaluate side-chains 249 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 249 time to evaluate : 1.320 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5824 ------------------------------------------------------------------------------- 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: 1.9990 chunk 82 optimal weight: 7.9990 chunk 95 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 112 optimal weight: 8.9990 chunk 70 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS B 171 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6393 moved from start: 0.7552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 10189 Z= 0.145 Angle : 0.553 6.962 14374 Z= 0.291 Chirality : 0.038 0.189 1788 Planarity : 0.005 0.066 1512 Dihedral : 24.328 179.985 2352 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer Outliers : 0.00 % 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: -0.39 (0.26), residues: 1055 helix: 0.32 (0.24), residues: 465 sheet: -0.75 (0.38), residues: 182 loop : -0.50 (0.32), residues: 408 *********************** 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 320 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 320 time to evaluate : 1.411 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 outliers start: 0 outliers final: 0 residues processed: 320 average time/residue: 0.5003 time to fit residues: 212.2382 Evaluate side-chains 270 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 1.285 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4347 ------------------------------------------------------------------------------- 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: 4.9990 chunk 33 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 88 optimal weight: 9.9990 chunk 102 optimal weight: 3.9990 chunk 108 optimal weight: 9.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6484 moved from start: 0.7901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 10189 Z= 0.231 Angle : 0.603 6.878 14374 Z= 0.322 Chirality : 0.038 0.197 1788 Planarity : 0.005 0.070 1512 Dihedral : 24.430 179.540 2352 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 20.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer Outliers : 0.00 % 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: -0.50 (0.26), residues: 1055 helix: 0.15 (0.24), residues: 465 sheet: -0.77 (0.38), residues: 184 loop : -0.46 (0.33), residues: 406 *********************** 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 299 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 1.268 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 outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.4729 time to fit residues: 188.9251 Evaluate side-chains 252 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 1.348 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5791 ------------------------------------------------------------------------------- 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: 3.9990 chunk 105 optimal weight: 3.9990 chunk 108 optimal weight: 9.9990 chunk 63 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6474 moved from start: 0.8134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 10189 Z= 0.213 Angle : 0.585 6.667 14374 Z= 0.313 Chirality : 0.038 0.196 1788 Planarity : 0.005 0.064 1512 Dihedral : 24.299 178.774 2352 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 18.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer Outliers : 0.00 % 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: -0.44 (0.26), residues: 1055 helix: 0.27 (0.24), residues: 463 sheet: -0.86 (0.40), residues: 173 loop : -0.49 (0.32), residues: 419 *********************** 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 296 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 296 time to evaluate : 1.287 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 outliers start: 0 outliers final: 0 residues processed: 296 average time/residue: 0.4508 time to fit residues: 180.7531 Evaluate side-chains 258 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 258 time to evaluate : 1.308 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6422 ------------------------------------------------------------------------------- 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: 0.1980 chunk 52 optimal weight: 4.9990 chunk 77 optimal weight: 0.0970 chunk 116 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6417 moved from start: 0.8305 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= 0.155 Angle : 0.544 6.642 14374 Z= 0.286 Chirality : 0.037 0.178 1788 Planarity : 0.005 0.060 1512 Dihedral : 23.999 177.559 2352 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer Outliers : 0.00 % 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: 0.04 (0.27), residues: 1055 helix: 0.68 (0.25), residues: 466 sheet: -0.62 (0.40), residues: 173 loop : -0.24 (0.33), residues: 416 ********************** 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 306 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 306 time to evaluate : 1.303 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 outliers start: 0 outliers final: 0 residues processed: 306 average time/residue: 0.4600 time to fit residues: 190.8940 Evaluate side-chains 267 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 267 time to evaluate : 1.302 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5559 ------------------------------------------------------------------------------- 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: 0.6980 chunk 28 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.082325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.061095 restraints weight = 133316.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.063750 restraints weight = 75411.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.065742 restraints weight = 50887.102| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3627 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3627 r_free = 0.3627 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3626 r_free = 0.3626 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3626 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.8387 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= 0.141 Angle : 0.529 6.779 14374 Z= 0.277 Chirality : 0.037 0.172 1788 Planarity : 0.004 0.060 1512 Dihedral : 23.815 177.404 2352 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer Outliers : 0.00 % 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: 0.38 (0.27), residues: 1055 helix: 1.04 (0.25), residues: 468 sheet: -0.66 (0.39), residues: 180 loop : -0.06 (0.34), residues: 407 =============================================================================== Job complete usr+sys time: 5325.34 seconds wall clock time: 94 minutes 21.22 seconds (5661.22 seconds total)