Starting phenix.real_space_refine on Fri Aug 7 05:28:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rc2_19045/08_2026/8rc2_19045.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rc2_19045/08_2026/8rc2_19045.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8rc2_19045/08_2026/8rc2_19045.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rc2_19045/08_2026/8rc2_19045.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8rc2_19045/08_2026/8rc2_19045.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rc2_19045/08_2026/8rc2_19045.map" } resolution = 3.1 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.098 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 93 5.49 5 S 66 5.16 5 C 12143 2.51 5 N 3484 2.21 5 O 3968 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19755 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2639 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 14, 'TRANS': 326} Chain: "B" Number of atoms: 2639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2639 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 14, 'TRANS': 326} Chain: "C" Number of atoms: 2639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2639 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 14, 'TRANS': 326} Chain: "D" Number of atoms: 2587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2587 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 14, 'TRANS': 319} Chain breaks: 1 Chain: "E" Number of atoms: 1866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1866 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 14, 'TRANS': 232} Chain breaks: 2 Chain: "F" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1792 Classifications: {'peptide': 235} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 215} Chain: "G" Number of atoms: 2090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2090 Classifications: {'peptide': 263} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 246} Chain: "H" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 787 Classifications: {'RNA': 37} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 12, 'rna3p_pyr': 12} Link IDs: {'rna2p': 13, 'rna3p': 23} Chain: "I" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 792 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain: "J" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 372 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "L" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1551 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 11, 'TRANS': 190} Chain breaks: 3 Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14394 SG CYS G 30 44.527 42.695 165.563 1.00131.74 S ATOM 14412 SG CYS G 33 43.647 46.091 165.784 1.00146.67 S ATOM 14609 SG CYS G 58 41.811 43.588 168.122 1.00125.99 S ATOM 14633 SG CYS G 61 40.910 43.718 164.521 1.00124.64 S Time building chain proxies: 4.39, per 1000 atoms: 0.22 Number of scatterers: 19755 At special positions: 0 Unit cell: (110, 117.7, 188.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 66 16.00 P 93 15.00 O 3968 8.00 N 3484 7.00 C 12143 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.79 Conformation dependent library (CDL) restraints added in 723.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN G 301 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 33 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 30 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 61 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 58 " Number of angles added : 6 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4188 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 29 sheets defined 41.7% alpha, 20.7% beta 33 base pairs and 49 stacking pairs defined. Time for finding SS restraints: 2.58 Creating SS restraints... Processing helix chain 'A' and resid 44 through 65 removed outlier: 3.613A pdb=" N ILE A 48 " --> pdb=" O PRO A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 84 Processing helix chain 'A' and resid 103 through 110 Processing helix chain 'A' and resid 110 through 116 Processing helix chain 'A' and resid 148 through 153 removed outlier: 3.580A pdb=" N ASP A 153 " --> pdb=" O MET A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 159 Processing helix chain 'A' and resid 161 through 199 removed outlier: 3.993A pdb=" N LYS A 197 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N SER A 198 " --> pdb=" O LYS A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 225 removed outlier: 3.894A pdb=" N GLN A 208 " --> pdb=" O LYS A 204 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS A 225 " --> pdb=" O ARG A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 273 Processing helix chain 'A' and resid 281 through 285 Processing helix chain 'A' and resid 322 through 335 Processing helix chain 'B' and resid 44 through 65 removed outlier: 3.625A pdb=" N ILE B 48 " --> pdb=" O PRO B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 83 Processing helix chain 'B' and resid 103 through 110 Processing helix chain 'B' and resid 110 through 117 Processing helix chain 'B' and resid 148 through 153 Processing helix chain 'B' and resid 154 through 159 removed outlier: 3.548A pdb=" N GLU B 158 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 196 Processing helix chain 'B' and resid 200 through 225 removed outlier: 3.579A pdb=" N LYS B 225 " --> pdb=" O ARG B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 273 Processing helix chain 'B' and resid 281 through 285 Processing helix chain 'B' and resid 322 through 334 removed outlier: 3.584A pdb=" N PHE B 326 " --> pdb=" O GLY B 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 65 removed outlier: 3.699A pdb=" N ILE C 48 " --> pdb=" O PRO C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 85 Processing helix chain 'C' and resid 96 through 100 Processing helix chain 'C' and resid 102 through 110 Processing helix chain 'C' and resid 110 through 116 Processing helix chain 'C' and resid 148 through 153 Processing helix chain 'C' and resid 154 through 160 removed outlier: 3.821A pdb=" N GLU C 158 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 194 removed outlier: 3.609A pdb=" N ASP C 166 " --> pdb=" O THR C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 200 through 224 removed outlier: 4.174A pdb=" N ALA C 205 " --> pdb=" O LYS C 201 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU C 206 " --> pdb=" O ASP C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 273 Processing helix chain 'C' and resid 282 through 286 removed outlier: 4.083A pdb=" N CYS C 286 " --> pdb=" O ASN C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 334 removed outlier: 3.512A pdb=" N PHE C 326 " --> pdb=" O GLY C 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 65 removed outlier: 3.728A pdb=" N ILE D 48 " --> pdb=" O PRO D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 84 Processing helix chain 'D' and resid 102 through 110 Processing helix chain 'D' and resid 110 through 116 Processing helix chain 'D' and resid 148 through 153 Processing helix chain 'D' and resid 154 through 160 removed outlier: 3.740A pdb=" N GLU D 158 " --> pdb=" O SER D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 196 removed outlier: 3.614A pdb=" N MET D 196 " --> pdb=" O LEU D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 224 Processing helix chain 'D' and resid 258 through 273 Processing helix chain 'D' and resid 281 through 285 Processing helix chain 'D' and resid 322 through 335 Processing helix chain 'E' and resid 44 through 65 removed outlier: 3.805A pdb=" N ILE E 48 " --> pdb=" O PRO E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 85 Processing helix chain 'E' and resid 96 through 100 Processing helix chain 'E' and resid 101 through 110 removed outlier: 3.737A pdb=" N GLU E 105 " --> pdb=" O ASN E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 116 Processing helix chain 'E' and resid 258 through 273 Processing helix chain 'E' and resid 322 through 335 removed outlier: 3.562A pdb=" N PHE E 326 " --> pdb=" O GLY E 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 38 Processing helix chain 'F' and resid 42 through 51 Processing helix chain 'F' and resid 140 through 151 Processing helix chain 'F' and resid 158 through 163 Processing helix chain 'F' and resid 194 through 196 No H-bonds generated for 'chain 'F' and resid 194 through 196' Processing helix chain 'F' and resid 229 through 233 Processing helix chain 'G' and resid 3 through 12 removed outlier: 3.656A pdb=" N SER G 7 " --> pdb=" O HIS G 3 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 40 Processing helix chain 'G' and resid 58 through 63 removed outlier: 3.576A pdb=" N THR G 63 " --> pdb=" O ARG G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 66 No H-bonds generated for 'chain 'G' and resid 64 through 66' Processing helix chain 'G' and resid 68 through 73 Processing helix chain 'G' and resid 85 through 89 removed outlier: 3.804A pdb=" N TRP G 89 " --> pdb=" O PHE G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 115 Processing helix chain 'G' and resid 116 through 123 removed outlier: 4.281A pdb=" N PHE G 120 " --> pdb=" O PRO G 116 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ASP G 121 " --> pdb=" O GLU G 117 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N HIS G 122 " --> pdb=" O HIS G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 131 No H-bonds generated for 'chain 'G' and resid 129 through 131' Processing helix chain 'G' and resid 132 through 140 Processing helix chain 'G' and resid 155 through 162 Processing helix chain 'G' and resid 191 through 203 removed outlier: 3.651A pdb=" N LYS G 203 " --> pdb=" O HIS G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 222 Processing helix chain 'G' and resid 226 through 238 Processing helix chain 'G' and resid 239 through 244 Processing helix chain 'G' and resid 249 through 263 removed outlier: 3.517A pdb=" N LYS G 262 " --> pdb=" O HIS G 258 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 64 removed outlier: 3.553A pdb=" N ILE L 48 " --> pdb=" O PRO L 44 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 110 Processing helix chain 'L' and resid 110 through 116 Processing helix chain 'L' and resid 258 through 273 removed outlier: 3.535A pdb=" N PHE L 265 " --> pdb=" O GLU L 261 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE L 266 " --> pdb=" O ALA L 262 " (cutoff:3.500A) Processing helix chain 'L' and resid 322 through 335 Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 132 removed outlier: 6.014A pdb=" N VAL A 125 " --> pdb=" O LYS A 255 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LYS A 255 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ILE A 127 " --> pdb=" O SER A 253 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N SER A 253 " --> pdb=" O ILE A 127 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ASN A 129 " --> pdb=" O ARG A 251 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ARG A 251 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN A 256 " --> pdb=" O ARG A 2 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ARG A 2 " --> pdb=" O ASN A 256 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N THR A 3 " --> pdb=" O TRP A 298 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N TRP A 298 " --> pdb=" O THR A 3 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 125 through 132 removed outlier: 6.014A pdb=" N VAL A 125 " --> pdb=" O LYS A 255 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LYS A 255 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ILE A 127 " --> pdb=" O SER A 253 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N SER A 253 " --> pdb=" O ILE A 127 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ASN A 129 " --> pdb=" O ARG A 251 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ARG A 251 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN A 256 " --> pdb=" O ARG A 2 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ARG A 2 " --> pdb=" O ASN A 256 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N THR A 3 " --> pdb=" O TRP A 298 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N TRP A 298 " --> pdb=" O THR A 3 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 138 through 142 Processing sheet with id=AA4, first strand: chain 'A' and resid 145 through 146 Processing sheet with id=AA5, first strand: chain 'B' and resid 125 through 127 Processing sheet with id=AA6, first strand: chain 'B' and resid 125 through 127 removed outlier: 6.710A pdb=" N GLU B 247 " --> pdb=" O THR B 12 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N THR B 12 " --> pdb=" O GLU B 247 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N SER B 249 " --> pdb=" O ILE B 10 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ILE B 10 " --> pdb=" O SER B 249 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ARG B 251 " --> pdb=" O GLY B 8 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N GLY B 8 " --> pdb=" O ARG B 251 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N SER B 253 " --> pdb=" O PHE B 6 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE B 6 " --> pdb=" O SER B 253 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N LYS B 255 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LEU B 4 " --> pdb=" O LYS B 255 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N THR B 297 " --> pdb=" O THR B 307 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N THR B 307 " --> pdb=" O THR B 297 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 138 through 141 Processing sheet with id=AA8, first strand: chain 'B' and resid 145 through 146 Processing sheet with id=AA9, first strand: chain 'C' and resid 125 through 132 removed outlier: 6.059A pdb=" N VAL C 125 " --> pdb=" O LYS C 255 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LYS C 255 " --> pdb=" O VAL C 125 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N ILE C 127 " --> pdb=" O SER C 253 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N SER C 253 " --> pdb=" O ILE C 127 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ASN C 129 " --> pdb=" O ARG C 251 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ARG C 251 " --> pdb=" O ASN C 129 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN C 256 " --> pdb=" O ARG C 2 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ARG C 2 " --> pdb=" O ASN C 256 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N THR C 297 " --> pdb=" O THR C 307 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N THR C 307 " --> pdb=" O THR C 297 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 138 through 141 Processing sheet with id=AB2, first strand: chain 'C' and resid 144 through 146 Processing sheet with id=AB3, first strand: chain 'D' and resid 125 through 127 Processing sheet with id=AB4, first strand: chain 'D' and resid 125 through 127 removed outlier: 6.676A pdb=" N GLU D 247 " --> pdb=" O THR D 12 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N THR D 12 " --> pdb=" O GLU D 247 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N SER D 249 " --> pdb=" O ILE D 10 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ILE D 10 " --> pdb=" O SER D 249 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ARG D 251 " --> pdb=" O GLY D 8 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N GLY D 8 " --> pdb=" O ARG D 251 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N SER D 253 " --> pdb=" O PHE D 6 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N PHE D 6 " --> pdb=" O SER D 253 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N LYS D 255 " --> pdb=" O LEU D 4 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU D 4 " --> pdb=" O LYS D 255 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N THR D 297 " --> pdb=" O THR D 307 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N THR D 307 " --> pdb=" O THR D 297 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 138 through 141 Processing sheet with id=AB6, first strand: chain 'D' and resid 145 through 146 Processing sheet with id=AB7, first strand: chain 'E' and resid 125 through 127 Processing sheet with id=AB8, first strand: chain 'E' and resid 125 through 127 removed outlier: 3.537A pdb=" N ASN E 256 " --> pdb=" O ARG E 2 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ARG E 2 " --> pdb=" O ASN E 256 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N THR E 297 " --> pdb=" O THR E 307 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N THR E 307 " --> pdb=" O THR E 297 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 138 through 141 Processing sheet with id=AC1, first strand: chain 'F' and resid 167 through 174 removed outlier: 5.545A pdb=" N ASN F 169 " --> pdb=" O SER F 12 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N SER F 12 " --> pdb=" O ASN F 169 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS F 5 " --> pdb=" O GLY F 139 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N PHE F 70 " --> pdb=" O GLN F 227 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 56 through 57 Processing sheet with id=AC3, first strand: chain 'F' and resid 79 through 85 Processing sheet with id=AC4, first strand: chain 'F' and resid 103 through 104 Processing sheet with id=AC5, first strand: chain 'F' and resid 182 through 183 Processing sheet with id=AC6, first strand: chain 'F' and resid 191 through 192 Processing sheet with id=AC7, first strand: chain 'G' and resid 24 through 25 Processing sheet with id=AC8, first strand: chain 'G' and resid 124 through 127 removed outlier: 6.840A pdb=" N SER G 103 " --> pdb=" O GLU G 124 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ILE G 126 " --> pdb=" O SER G 103 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU G 105 " --> pdb=" O ILE G 126 " (cutoff:3.500A) removed outlier: 8.819A pdb=" N LEU G 146 " --> pdb=" O TYR G 173 " (cutoff:3.500A) removed outlier: 8.913A pdb=" N CYS G 175 " --> pdb=" O LEU G 146 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N TYR G 148 " --> pdb=" O CYS G 175 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 125 through 127 Processing sheet with id=AD1, first strand: chain 'L' and resid 125 through 127 removed outlier: 3.666A pdb=" N ASN L 256 " --> pdb=" O ARG L 2 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ARG L 2 " --> pdb=" O ASN L 256 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR L 297 " --> pdb=" O THR L 307 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N THR L 307 " --> pdb=" O THR L 297 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 138 through 141 907 hydrogen bonds defined for protein. 2535 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 91 hydrogen bonds 182 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 49 stacking parallelities Total time for adding SS restraints: 3.91 Time building geometry restraints manager: 2.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5210 1.33 - 1.45: 4006 1.45 - 1.57: 10828 1.57 - 1.69: 184 1.69 - 1.81: 119 Bond restraints: 20347 Sorted by residual: bond pdb=" C1' DC I -27 " pdb=" N1 DC I -27 " ideal model delta sigma weight residual 1.468 1.529 -0.061 1.40e-02 5.10e+03 1.89e+01 bond pdb=" C ILE F 38 " pdb=" N PRO F 39 " ideal model delta sigma weight residual 1.334 1.259 0.074 2.34e-02 1.83e+03 1.01e+01 bond pdb=" C3' DC I -25 " pdb=" C2' DC I -25 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.92e+00 bond pdb=" C3' DC J 5 " pdb=" C2' DC J 5 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.72e+00 bond pdb=" C3' DG I -7 " pdb=" C2' DG I -7 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.71e+00 ... (remaining 20342 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 27319 1.99 - 3.98: 579 3.98 - 5.96: 43 5.96 - 7.95: 5 7.95 - 9.94: 2 Bond angle restraints: 27948 Sorted by residual: angle pdb=" O4' DG I -19 " pdb=" C4' DG I -19 " pdb=" C3' DG I -19 " ideal model delta sigma weight residual 106.00 102.73 3.27 6.00e-01 2.78e+00 2.97e+01 angle pdb=" O4' DC I 8 " pdb=" C4' DC I 8 " pdb=" C3' DC I 8 " ideal model delta sigma weight residual 106.00 103.00 3.00 6.00e-01 2.78e+00 2.50e+01 angle pdb=" C4' DG I -7 " pdb=" O4' DG I -7 " pdb=" C1' DG I -7 " ideal model delta sigma weight residual 110.10 105.15 4.95 1.00e+00 1.00e+00 2.45e+01 angle pdb=" O4' DC I -4 " pdb=" C4' DC I -4 " pdb=" C3' DC I -4 " ideal model delta sigma weight residual 106.00 103.04 2.96 6.00e-01 2.78e+00 2.44e+01 angle pdb=" O4' DG I -7 " pdb=" C1' DG I -7 " pdb=" N9 DG I -7 " ideal model delta sigma weight residual 108.00 111.43 -3.43 7.00e-01 2.04e+00 2.40e+01 ... (remaining 27943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.96: 11592 34.96 - 69.92: 436 69.92 - 104.89: 40 104.89 - 139.85: 6 139.85 - 174.81: 4 Dihedral angle restraints: 12078 sinusoidal: 5570 harmonic: 6508 Sorted by residual: dihedral pdb=" O4' U H 30 " pdb=" C1' U H 30 " pdb=" N1 U H 30 " pdb=" C2 U H 30 " ideal model delta sinusoidal sigma weight residual 200.00 45.21 154.79 1 1.50e+01 4.44e-03 8.13e+01 dihedral pdb=" O4' C H 19 " pdb=" C1' C H 19 " pdb=" N1 C H 19 " pdb=" C2 C H 19 " ideal model delta sinusoidal sigma weight residual -160.00 -100.59 -59.41 1 1.50e+01 4.44e-03 2.10e+01 dihedral pdb=" C4' DC I -9 " pdb=" C3' DC I -9 " pdb=" O3' DC I -9 " pdb=" P DC I -8 " ideal model delta sinusoidal sigma weight residual -140.00 34.81 -174.81 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 12075 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2152 0.043 - 0.086: 707 0.086 - 0.129: 240 0.129 - 0.172: 34 0.172 - 0.215: 3 Chirality restraints: 3136 Sorted by residual: chirality pdb=" CB VAL L 18 " pdb=" CA VAL L 18 " pdb=" CG1 VAL L 18 " pdb=" CG2 VAL L 18 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" C1' G H 25 " pdb=" O4' G H 25 " pdb=" C2' G H 25 " pdb=" N9 G H 25 " both_signs ideal model delta sigma weight residual False 2.47 2.29 0.18 2.00e-01 2.50e+01 8.41e-01 chirality pdb=" C1' C H 1 " pdb=" O4' C H 1 " pdb=" C2' C H 1 " pdb=" N1 C H 1 " both_signs ideal model delta sigma weight residual False 2.47 2.30 0.17 2.00e-01 2.50e+01 7.55e-01 ... (remaining 3133 not shown) Planarity restraints: 3336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY F 116 " 0.048 5.00e-02 4.00e+02 7.32e-02 8.58e+00 pdb=" N PRO F 117 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO F 117 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO F 117 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 234 " -0.045 5.00e-02 4.00e+02 6.84e-02 7.48e+00 pdb=" N PRO A 235 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 235 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 235 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 234 " -0.043 5.00e-02 4.00e+02 6.56e-02 6.89e+00 pdb=" N PRO D 235 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO D 235 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 235 " -0.036 5.00e-02 4.00e+02 ... (remaining 3333 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 222 2.62 - 3.19: 17423 3.19 - 3.76: 31757 3.76 - 4.33: 45178 4.33 - 4.90: 74099 Nonbonded interactions: 168679 Sorted by model distance: nonbonded pdb=" OG1 THR D 46 " pdb=" OP1 C H 19 " model vdw 2.046 3.040 nonbonded pdb=" NH1 ARG B 49 " pdb=" OP1 A H 5 " model vdw 2.166 3.120 nonbonded pdb=" OG1 THR E 46 " pdb=" OP1 G H 25 " model vdw 2.186 3.040 nonbonded pdb=" NH2 ARG A 107 " pdb=" O SER A 122 " model vdw 2.192 3.120 nonbonded pdb=" NH1 ARG C 49 " pdb=" OP1 A H 11 " model vdw 2.200 3.120 ... (remaining 168674 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 197 or resid 205 through 341)) selection = (chain 'B' and (resid 1 through 197 or resid 205 through 341)) selection = (chain 'C' and (resid 1 through 197 or resid 205 through 341)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.640 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: 0.030 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 22.720 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 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 : 0.007 0.074 20351 Z= 0.366 Angle : 0.660 10.692 27954 Z= 0.441 Chirality : 0.047 0.215 3136 Planarity : 0.005 0.073 3336 Dihedral : 17.109 174.812 7890 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.42 % Allowed : 7.69 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.17), residues: 2276 helix: 1.51 (0.17), residues: 832 sheet: 0.92 (0.26), residues: 350 loop : -0.25 (0.18), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 234 TYR 0.029 0.002 TYR G 51 PHE 0.027 0.002 PHE A 80 TRP 0.018 0.002 TRP D 119 HIS 0.006 0.001 HIS A 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00665 / 0.37 (20347) covalent geometry : angle 0.65472 / 0.44 (27948) hydrogen bonds : bond 0.16693 / 11.36 ( 972) hydrogen bonds : angle 7.10500 / 5.10 ( 2717) metal coordination : bond 0.01233 / 0.62 ( 4) metal coordination : angle 5.48519 / 2.73 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 285 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 ASN cc_start: 0.9090 (m110) cc_final: 0.8859 (m-40) REVERT: A 184 GLN cc_start: 0.7178 (mt0) cc_final: 0.6925 (mm110) REVERT: A 189 GLN cc_start: 0.7491 (tt0) cc_final: 0.7185 (tt0) REVERT: A 193 LYS cc_start: 0.7092 (OUTLIER) cc_final: 0.6814 (mmtt) REVERT: A 196 MET cc_start: 0.8111 (tpt) cc_final: 0.6512 (tpt) REVERT: A 213 GLU cc_start: 0.8427 (mt-10) cc_final: 0.7982 (mm-30) REVERT: A 216 GLU cc_start: 0.8853 (mp0) cc_final: 0.8562 (mp0) REVERT: B 78 GLU cc_start: 0.7251 (mm-30) cc_final: 0.6861 (mt-10) REVERT: B 190 ASP cc_start: 0.8042 (p0) cc_final: 0.7824 (p0) REVERT: B 216 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7717 (mp0) REVERT: B 336 GLN cc_start: 0.8914 (mt0) cc_final: 0.8618 (mm110) REVERT: C 7 ASN cc_start: 0.8776 (t0) cc_final: 0.8519 (t0) REVERT: D 58 LYS cc_start: 0.8186 (mttt) cc_final: 0.7940 (mppt) REVERT: D 87 ASP cc_start: 0.8232 (p0) cc_final: 0.7850 (p0) REVERT: D 101 ASN cc_start: 0.8485 (t0) cc_final: 0.8177 (t0) REVERT: D 158 GLU cc_start: 0.7569 (mp0) cc_final: 0.6866 (tm-30) REVERT: E 9 LYS cc_start: 0.8972 (mttm) cc_final: 0.8574 (mtpp) REVERT: E 109 LYS cc_start: 0.8214 (mttt) cc_final: 0.7982 (pttp) REVERT: E 135 ASP cc_start: 0.7838 (t70) cc_final: 0.7512 (t70) REVERT: E 275 GLU cc_start: 0.8224 (tp30) cc_final: 0.7958 (tt0) REVERT: F 59 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8360 (mp0) REVERT: G 100 ASP cc_start: 0.8980 (m-30) cc_final: 0.8627 (m-30) REVERT: G 132 GLN cc_start: 0.8641 (mt0) cc_final: 0.8140 (mt0) REVERT: G 164 ARG cc_start: 0.8409 (ttm-80) cc_final: 0.7640 (mtp180) REVERT: G 189 MET cc_start: 0.8174 (ttm) cc_final: 0.7932 (tmm) REVERT: L 18 VAL cc_start: 0.8606 (p) cc_final: 0.8301 (p) REVERT: L 19 THR cc_start: 0.7645 (m) cc_final: 0.7230 (p) REVERT: L 124 LYS cc_start: 0.8529 (mmtp) cc_final: 0.8257 (mmtp) REVERT: L 260 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7377 (tp30) REVERT: L 277 ARG cc_start: 0.6732 (mtp180) cc_final: 0.6478 (mtp180) REVERT: L 299 LYS cc_start: 0.9018 (tppp) cc_final: 0.8611 (tmmt) REVERT: L 302 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8310 (mt-10) REVERT: L 328 MET cc_start: 0.9322 (mtp) cc_final: 0.8898 (mtp) REVERT: L 334 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7782 (mp0) outliers start: 8 outliers final: 1 residues processed: 292 average time/residue: 0.1781 time to fit residues: 75.4844 Evaluate side-chains 207 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 205 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain G residue 89 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 0.5980 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.2980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 GLN A 224 GLN C 335 ASN D 84 GLN ** D 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.129342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.083911 restraints weight = 27545.940| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 2.16 r_work: 0.2792 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20351 Z= 0.179 Angle : 0.614 9.502 27954 Z= 0.337 Chirality : 0.047 0.270 3136 Planarity : 0.005 0.077 3336 Dihedral : 19.230 169.756 3635 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.21 % Allowed : 7.96 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.17), residues: 2276 helix: 1.78 (0.17), residues: 840 sheet: 1.06 (0.26), residues: 350 loop : -0.03 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 49 TYR 0.018 0.001 TYR G 51 PHE 0.020 0.001 PHE L 6 TRP 0.009 0.001 TRP D 119 HIS 0.006 0.001 HIS E 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.18 (20347) covalent geometry : angle 0.60848 / 0.34 (27948) hydrogen bonds : bond 0.05040 / 3.42 ( 972) hydrogen bonds : angle 5.63151 / 3.99 ( 2717) metal coordination : bond 0.00765 / 0.38 ( 4) metal coordination : angle 5.83011 / 2.76 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 236 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 GLN cc_start: 0.7759 (tt0) cc_final: 0.7505 (tt0) REVERT: A 193 LYS cc_start: 0.7180 (OUTLIER) cc_final: 0.6961 (mttt) REVERT: A 210 LYS cc_start: 0.8605 (mtmm) cc_final: 0.8284 (mttp) REVERT: A 213 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8026 (mm-30) REVERT: A 216 GLU cc_start: 0.8909 (mp0) cc_final: 0.8645 (mp0) REVERT: B 190 ASP cc_start: 0.7996 (p0) cc_final: 0.7776 (p0) REVERT: B 217 LYS cc_start: 0.8747 (mtmt) cc_final: 0.8443 (mtmt) REVERT: C 81 MET cc_start: 0.8918 (tpp) cc_final: 0.8457 (tpp) REVERT: C 227 GLU cc_start: 0.7563 (mm-30) cc_final: 0.6976 (mt-10) REVERT: D 78 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7071 (mp0) REVERT: D 101 ASN cc_start: 0.8454 (t0) cc_final: 0.8238 (t0) REVERT: D 196 MET cc_start: 0.3340 (OUTLIER) cc_final: 0.2944 (ptm) REVERT: E 9 LYS cc_start: 0.9122 (mttm) cc_final: 0.8842 (mtpp) REVERT: E 14 GLU cc_start: 0.8786 (mp0) cc_final: 0.8491 (mp0) REVERT: E 109 LYS cc_start: 0.8499 (mttt) cc_final: 0.8274 (pttp) REVERT: E 135 ASP cc_start: 0.7833 (t70) cc_final: 0.7592 (t70) REVERT: E 258 THR cc_start: 0.8262 (OUTLIER) cc_final: 0.7937 (p) REVERT: E 275 GLU cc_start: 0.8119 (tp30) cc_final: 0.7890 (tt0) REVERT: F 75 GLU cc_start: 0.8925 (mm-30) cc_final: 0.8691 (mp0) REVERT: G 16 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7803 (pp) REVERT: G 100 ASP cc_start: 0.9236 (m-30) cc_final: 0.9008 (m-30) REVERT: G 164 ARG cc_start: 0.8511 (ttm-80) cc_final: 0.8251 (mtp180) REVERT: L 49 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7401 (ttm170) REVERT: L 299 LYS cc_start: 0.9047 (tppp) cc_final: 0.8799 (tmmt) REVERT: L 334 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7567 (mp0) outliers start: 42 outliers final: 22 residues processed: 266 average time/residue: 0.1819 time to fit residues: 70.2230 Evaluate side-chains 230 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 202 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 253 SER Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 89 TRP Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 49 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 154 optimal weight: 5.9990 chunk 178 optimal weight: 0.5980 chunk 134 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 137 optimal weight: 0.0770 chunk 209 optimal weight: 7.9990 chunk 123 optimal weight: 9.9990 chunk 76 optimal weight: 0.9980 chunk 213 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 GLN C 226 GLN C 292 HIS D 84 GLN ** D 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.131014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.086739 restraints weight = 27743.513| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.36 r_work: 0.2826 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20351 Z= 0.151 Angle : 0.567 9.180 27954 Z= 0.310 Chirality : 0.045 0.287 3136 Planarity : 0.004 0.056 3336 Dihedral : 19.299 172.788 3635 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.00 % Allowed : 8.69 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.17), residues: 2276 helix: 1.83 (0.18), residues: 848 sheet: 0.95 (0.26), residues: 347 loop : -0.03 (0.19), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 251 TYR 0.015 0.001 TYR G 51 PHE 0.015 0.001 PHE L 37 TRP 0.010 0.001 TRP D 119 HIS 0.006 0.001 HIS E 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 (20347) covalent geometry : angle 0.56158 / 0.31 (27948) hydrogen bonds : bond 0.04459 / 3.05 ( 972) hydrogen bonds : angle 5.24131 / 3.69 ( 2717) metal coordination : bond 0.00641 / 0.32 ( 4) metal coordination : angle 5.33867 / 2.61 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 213 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 MET cc_start: 0.7845 (tpt) cc_final: 0.7560 (tpt) REVERT: A 213 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8273 (mm-30) REVERT: A 328 MET cc_start: 0.8982 (mtt) cc_final: 0.8775 (mtt) REVERT: A 330 LYS cc_start: 0.8345 (ttpp) cc_final: 0.8082 (ttpp) REVERT: B 186 LYS cc_start: 0.7573 (mttt) cc_final: 0.7343 (mttt) REVERT: B 190 ASP cc_start: 0.7976 (p0) cc_final: 0.7768 (p0) REVERT: B 216 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8027 (mt-10) REVERT: B 217 LYS cc_start: 0.8774 (mtmt) cc_final: 0.8476 (mtmt) REVERT: C 227 GLU cc_start: 0.7375 (mm-30) cc_final: 0.6992 (mt-10) REVERT: D 78 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7143 (mp0) REVERT: D 84 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8416 (mt0) REVERT: D 101 ASN cc_start: 0.8466 (t0) cc_final: 0.8252 (t0) REVERT: D 196 MET cc_start: 0.3409 (OUTLIER) cc_final: 0.3001 (ptm) REVERT: E 9 LYS cc_start: 0.9121 (mttm) cc_final: 0.8781 (mtpp) REVERT: E 14 GLU cc_start: 0.8801 (mp0) cc_final: 0.8573 (mm-30) REVERT: E 81 MET cc_start: 0.7756 (tpp) cc_final: 0.7491 (tpp) REVERT: E 109 LYS cc_start: 0.8492 (mttt) cc_final: 0.8257 (pttp) REVERT: E 135 ASP cc_start: 0.7926 (t70) cc_final: 0.7632 (t70) REVERT: E 258 THR cc_start: 0.8265 (OUTLIER) cc_final: 0.7962 (p) REVERT: E 275 GLU cc_start: 0.8104 (tp30) cc_final: 0.7873 (tt0) REVERT: E 330 LYS cc_start: 0.9101 (tppt) cc_final: 0.8676 (tptp) REVERT: F 42 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8484 (tp30) REVERT: F 75 GLU cc_start: 0.8945 (mm-30) cc_final: 0.8704 (mp0) REVERT: G 16 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7657 (pp) REVERT: G 100 ASP cc_start: 0.9239 (m-30) cc_final: 0.9030 (m-30) REVERT: L 9 LYS cc_start: 0.7118 (mtpp) cc_final: 0.6748 (mttm) REVERT: L 19 THR cc_start: 0.7606 (m) cc_final: 0.7333 (p) REVERT: L 137 GLN cc_start: 0.8389 (mp10) cc_final: 0.8026 (mm-40) REVERT: L 288 LEU cc_start: 0.8534 (tt) cc_final: 0.8233 (mm) REVERT: L 299 LYS cc_start: 0.8974 (tppp) cc_final: 0.8760 (tmmt) REVERT: L 334 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7648 (mp0) outliers start: 38 outliers final: 24 residues processed: 240 average time/residue: 0.1716 time to fit residues: 59.3936 Evaluate side-chains 217 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 188 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 253 SER Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 89 TRP Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 49 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 7 optimal weight: 2.9990 chunk 234 optimal weight: 20.0000 chunk 30 optimal weight: 0.8980 chunk 204 optimal weight: 3.9990 chunk 183 optimal weight: 0.9980 chunk 18 optimal weight: 7.9990 chunk 118 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 121 optimal weight: 20.0000 chunk 28 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 7 ASN C 226 GLN ** D 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.128195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.082501 restraints weight = 27946.194| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.17 r_work: 0.2777 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 20351 Z= 0.260 Angle : 0.614 10.950 27954 Z= 0.329 Chirality : 0.048 0.288 3136 Planarity : 0.005 0.055 3336 Dihedral : 19.284 174.105 3631 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.21 % Allowed : 8.75 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.17), residues: 2276 helix: 1.79 (0.18), residues: 848 sheet: 0.81 (0.25), residues: 348 loop : -0.09 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 229 TYR 0.021 0.002 TYR G 173 PHE 0.018 0.002 PHE A 80 TRP 0.009 0.001 TRP D 119 HIS 0.007 0.001 HIS E 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00593 / 0.26 (20347) covalent geometry : angle 0.61001 / 0.33 (27948) hydrogen bonds : bond 0.04437 / 3.03 ( 972) hydrogen bonds : angle 5.14467 / 3.63 ( 2717) metal coordination : bond 0.01206 / 0.60 ( 4) metal coordination : angle 4.98270 / 2.47 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 205 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 LYS cc_start: 0.8667 (mtmm) cc_final: 0.8267 (mttp) REVERT: A 213 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8124 (mm-30) REVERT: A 216 GLU cc_start: 0.8903 (mp0) cc_final: 0.8426 (mp0) REVERT: A 328 MET cc_start: 0.9068 (mtt) cc_final: 0.8845 (mtt) REVERT: B 186 LYS cc_start: 0.7583 (mttt) cc_final: 0.7342 (mttt) REVERT: B 208 GLN cc_start: 0.7807 (pt0) cc_final: 0.7580 (pt0) REVERT: B 217 LYS cc_start: 0.8743 (mtmt) cc_final: 0.8531 (mtmt) REVERT: C 227 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7094 (mt-10) REVERT: D 78 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7032 (mp0) REVERT: D 101 ASN cc_start: 0.8542 (t0) cc_final: 0.8288 (t0) REVERT: D 196 MET cc_start: 0.3363 (OUTLIER) cc_final: 0.2953 (ptm) REVERT: E 9 LYS cc_start: 0.9118 (mttm) cc_final: 0.8790 (mtpp) REVERT: E 14 GLU cc_start: 0.8852 (mp0) cc_final: 0.8619 (mm-30) REVERT: E 109 LYS cc_start: 0.8503 (mttt) cc_final: 0.8249 (pttp) REVERT: E 258 THR cc_start: 0.8374 (OUTLIER) cc_final: 0.8084 (p) REVERT: E 275 GLU cc_start: 0.8368 (tp30) cc_final: 0.8149 (tt0) REVERT: F 105 ARG cc_start: 0.7882 (mtt180) cc_final: 0.7428 (mtt180) REVERT: F 201 LYS cc_start: 0.8932 (mttp) cc_final: 0.8614 (mmtm) REVERT: G 16 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7889 (pp) REVERT: L 19 THR cc_start: 0.7320 (OUTLIER) cc_final: 0.7033 (p) REVERT: L 137 GLN cc_start: 0.8414 (mp10) cc_final: 0.8056 (mm-40) REVERT: L 299 LYS cc_start: 0.8999 (tppp) cc_final: 0.8371 (tmmt) REVERT: L 334 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7546 (mp0) outliers start: 42 outliers final: 26 residues processed: 233 average time/residue: 0.1756 time to fit residues: 59.8285 Evaluate side-chains 220 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 189 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 253 SER Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 89 TRP Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 20 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 73 optimal weight: 1.9990 chunk 231 optimal weight: 5.9990 chunk 131 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 chunk 123 optimal weight: 9.9990 chunk 213 optimal weight: 9.9990 chunk 99 optimal weight: 0.0770 chunk 98 optimal weight: 0.0370 chunk 174 optimal weight: 0.7980 chunk 124 optimal weight: 4.9990 overall best weight: 0.7618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 84 GLN C 7 ASN C 226 GLN ** D 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 292 HIS L 250 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.130591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.085362 restraints weight = 27677.965| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.16 r_work: 0.2829 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20351 Z= 0.144 Angle : 0.545 8.979 27954 Z= 0.298 Chirality : 0.045 0.301 3136 Planarity : 0.004 0.049 3336 Dihedral : 19.281 173.747 3631 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.21 % Allowed : 9.75 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.17), residues: 2276 helix: 1.92 (0.18), residues: 847 sheet: 0.55 (0.24), residues: 363 loop : 0.02 (0.19), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 30 TYR 0.012 0.001 TYR G 51 PHE 0.024 0.001 PHE L 37 TRP 0.008 0.001 TRP D 119 HIS 0.007 0.001 HIS E 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (20347) covalent geometry : angle 0.54049 / 0.30 (27948) hydrogen bonds : bond 0.04055 / 2.78 ( 972) hydrogen bonds : angle 4.97849 / 3.51 ( 2717) metal coordination : bond 0.00589 / 0.29 ( 4) metal coordination : angle 4.88716 / 2.41 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 203 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8142 (mm-30) REVERT: A 216 GLU cc_start: 0.8877 (mp0) cc_final: 0.8368 (mp0) REVERT: A 328 MET cc_start: 0.9005 (mtt) cc_final: 0.8797 (mtt) REVERT: B 208 GLN cc_start: 0.7831 (pt0) cc_final: 0.7618 (pt0) REVERT: B 213 GLU cc_start: 0.9086 (OUTLIER) cc_final: 0.8708 (pp20) REVERT: B 216 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8181 (mt-10) REVERT: B 217 LYS cc_start: 0.8719 (mtmt) cc_final: 0.8300 (mtmt) REVERT: C 227 GLU cc_start: 0.7432 (mm-30) cc_final: 0.7019 (mt-10) REVERT: D 78 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7090 (mp0) REVERT: D 101 ASN cc_start: 0.8531 (t0) cc_final: 0.8297 (t0) REVERT: D 196 MET cc_start: 0.3431 (OUTLIER) cc_final: 0.2903 (ptm) REVERT: E 14 GLU cc_start: 0.8863 (mp0) cc_final: 0.8495 (mp0) REVERT: E 109 LYS cc_start: 0.8488 (mttt) cc_final: 0.8239 (pttp) REVERT: E 119 TRP cc_start: 0.9050 (t-100) cc_final: 0.8786 (t-100) REVERT: E 258 THR cc_start: 0.8315 (OUTLIER) cc_final: 0.8036 (p) REVERT: E 275 GLU cc_start: 0.8304 (tp30) cc_final: 0.8075 (tt0) REVERT: G 16 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7688 (pp) REVERT: L 9 LYS cc_start: 0.6844 (mtpp) cc_final: 0.6332 (mmtt) REVERT: L 19 THR cc_start: 0.7269 (OUTLIER) cc_final: 0.6987 (p) REVERT: L 137 GLN cc_start: 0.8528 (mp10) cc_final: 0.8001 (mm-40) REVERT: L 261 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8162 (pm20) REVERT: L 288 LEU cc_start: 0.8494 (tt) cc_final: 0.8218 (mm) REVERT: L 299 LYS cc_start: 0.8984 (tppp) cc_final: 0.8344 (tmmt) outliers start: 42 outliers final: 24 residues processed: 232 average time/residue: 0.1544 time to fit residues: 52.2435 Evaluate side-chains 222 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 191 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 109 LYS Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 253 SER Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 89 TRP Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 261 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 228 optimal weight: 10.0000 chunk 106 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 1 optimal weight: 0.1980 chunk 167 optimal weight: 0.7980 chunk 200 optimal weight: 0.0670 chunk 93 optimal weight: 0.8980 chunk 172 optimal weight: 2.9990 chunk 157 optimal weight: 4.9990 chunk 232 optimal weight: 10.0000 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 250 HIS C 7 ASN C 226 GLN ** D 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 250 HIS L 281 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.131771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.086664 restraints weight = 27730.354| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.16 r_work: 0.2843 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20351 Z= 0.126 Angle : 0.528 8.118 27954 Z= 0.288 Chirality : 0.044 0.302 3136 Planarity : 0.004 0.066 3336 Dihedral : 19.262 174.912 3631 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.05 % Allowed : 10.01 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.17), residues: 2276 helix: 2.03 (0.18), residues: 843 sheet: 0.45 (0.24), residues: 368 loop : 0.05 (0.19), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 33 TYR 0.014 0.001 TYR G 9 PHE 0.027 0.001 PHE L 6 TRP 0.008 0.001 TRP A 293 HIS 0.007 0.001 HIS E 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.13 (20347) covalent geometry : angle 0.52333 / 0.29 (27948) hydrogen bonds : bond 0.03841 / 2.64 ( 972) hydrogen bonds : angle 4.85938 / 3.44 ( 2717) metal coordination : bond 0.00419 / 0.21 ( 4) metal coordination : angle 4.72398 / 2.29 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 213 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 184 GLN cc_start: 0.7976 (tp40) cc_final: 0.7688 (mm110) REVERT: A 213 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8054 (mm-30) REVERT: A 216 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8271 (mp0) REVERT: A 328 MET cc_start: 0.8926 (mtt) cc_final: 0.8689 (mtt) REVERT: B 216 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8116 (mt-10) REVERT: C 227 GLU cc_start: 0.7335 (mm-30) cc_final: 0.6887 (mt-10) REVERT: D 78 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.6992 (mp0) REVERT: D 196 MET cc_start: 0.3456 (OUTLIER) cc_final: 0.2937 (ptm) REVERT: E 9 LYS cc_start: 0.8898 (mttm) cc_final: 0.8509 (mttm) REVERT: E 14 GLU cc_start: 0.8888 (mp0) cc_final: 0.8419 (mp0) REVERT: E 109 LYS cc_start: 0.8471 (mttt) cc_final: 0.8209 (pttp) REVERT: E 119 TRP cc_start: 0.9046 (t-100) cc_final: 0.8831 (t-100) REVERT: E 258 THR cc_start: 0.8281 (OUTLIER) cc_final: 0.7998 (p) REVERT: E 275 GLU cc_start: 0.8193 (tp30) cc_final: 0.7917 (tt0) REVERT: E 334 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8338 (pp20) REVERT: F 42 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8508 (tp30) REVERT: F 84 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.7960 (tmt) REVERT: G 16 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7592 (pp) REVERT: L 9 LYS cc_start: 0.6794 (mtpp) cc_final: 0.6246 (mmtt) REVERT: L 19 THR cc_start: 0.7242 (OUTLIER) cc_final: 0.6974 (p) REVERT: L 137 GLN cc_start: 0.8606 (mp10) cc_final: 0.8103 (mm-40) REVERT: L 249 SER cc_start: 0.8353 (t) cc_final: 0.7750 (m) REVERT: L 288 LEU cc_start: 0.8476 (tt) cc_final: 0.8221 (mm) REVERT: L 299 LYS cc_start: 0.8966 (tppp) cc_final: 0.8353 (tmmt) outliers start: 39 outliers final: 22 residues processed: 237 average time/residue: 0.1520 time to fit residues: 52.7484 Evaluate side-chains 217 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 188 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 109 LYS Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 253 SER Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 89 TRP Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 254 ILE Chi-restraints excluded: chain L residue 306 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 164 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 146 optimal weight: 0.6980 chunk 197 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 98 optimal weight: 0.6980 chunk 120 optimal weight: 10.0000 chunk 104 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 169 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 GLN C 7 ASN C 226 GLN C 335 ASN ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 250 HIS L 281 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.130258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.084856 restraints weight = 27869.974| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.16 r_work: 0.2819 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20351 Z= 0.185 Angle : 0.557 10.151 27954 Z= 0.301 Chirality : 0.045 0.302 3136 Planarity : 0.004 0.046 3336 Dihedral : 19.277 175.842 3631 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.11 % Allowed : 10.75 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.17), residues: 2276 helix: 2.01 (0.18), residues: 848 sheet: 0.48 (0.24), residues: 368 loop : 0.05 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 229 TYR 0.011 0.001 TYR G 51 PHE 0.023 0.001 PHE L 6 TRP 0.007 0.001 TRP A 293 HIS 0.007 0.001 HIS E 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (20347) covalent geometry : angle 0.55259 / 0.30 (27948) hydrogen bonds : bond 0.03943 / 2.72 ( 972) hydrogen bonds : angle 4.85336 / 3.44 ( 2717) metal coordination : bond 0.00697 / 0.35 ( 4) metal coordination : angle 4.68607 / 2.33 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 200 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 GLU cc_start: 0.7964 (pt0) cc_final: 0.7697 (pt0) REVERT: A 213 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8048 (mm-30) REVERT: A 216 GLU cc_start: 0.8931 (mt-10) cc_final: 0.8251 (mp0) REVERT: A 328 MET cc_start: 0.8980 (mtt) cc_final: 0.8731 (mtt) REVERT: B 216 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8045 (mt-10) REVERT: C 227 GLU cc_start: 0.7393 (mm-30) cc_final: 0.7038 (mt-10) REVERT: D 78 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.6966 (mp0) REVERT: E 9 LYS cc_start: 0.8916 (mttm) cc_final: 0.8452 (mttm) REVERT: E 14 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8422 (mp0) REVERT: E 109 LYS cc_start: 0.8478 (mttt) cc_final: 0.8227 (pttp) REVERT: E 119 TRP cc_start: 0.9057 (t-100) cc_final: 0.8833 (t-100) REVERT: E 135 ASP cc_start: 0.8080 (t70) cc_final: 0.7822 (t70) REVERT: E 258 THR cc_start: 0.8282 (OUTLIER) cc_final: 0.8004 (p) REVERT: E 290 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8319 (pt0) REVERT: F 84 MET cc_start: 0.8286 (OUTLIER) cc_final: 0.7965 (tmt) REVERT: F 87 ASP cc_start: 0.8882 (m-30) cc_final: 0.8663 (m-30) REVERT: F 105 ARG cc_start: 0.7849 (mtt180) cc_final: 0.7330 (mtt180) REVERT: G 16 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7720 (pp) REVERT: L 9 LYS cc_start: 0.6896 (mtpp) cc_final: 0.6431 (mmtt) REVERT: L 19 THR cc_start: 0.7079 (OUTLIER) cc_final: 0.6807 (p) REVERT: L 124 LYS cc_start: 0.8804 (mttp) cc_final: 0.8506 (mttt) REVERT: L 137 GLN cc_start: 0.8539 (mp10) cc_final: 0.8033 (mm-40) REVERT: L 288 LEU cc_start: 0.8497 (tt) cc_final: 0.8233 (mm) REVERT: L 299 LYS cc_start: 0.8958 (tppp) cc_final: 0.8377 (tmmt) outliers start: 40 outliers final: 28 residues processed: 225 average time/residue: 0.1667 time to fit residues: 55.1728 Evaluate side-chains 226 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 192 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 109 LYS Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 253 SER Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 89 TRP Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 254 ILE Chi-restraints excluded: chain L residue 306 VAL Chi-restraints excluded: chain L residue 313 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 90 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 194 optimal weight: 4.9990 chunk 223 optimal weight: 9.9990 chunk 73 optimal weight: 2.9990 chunk 145 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 201 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 HIS ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 ASN C 226 GLN C 335 ASN ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 250 HIS L 281 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.129657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.084317 restraints weight = 27662.757| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.15 r_work: 0.2813 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20351 Z= 0.186 Angle : 0.556 7.333 27954 Z= 0.301 Chirality : 0.045 0.308 3136 Planarity : 0.004 0.047 3336 Dihedral : 19.312 178.828 3631 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.37 % Allowed : 10.64 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.17), residues: 2276 helix: 2.01 (0.18), residues: 847 sheet: 0.49 (0.24), residues: 363 loop : 0.04 (0.19), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 229 TYR 0.012 0.001 TYR G 51 PHE 0.023 0.001 PHE L 6 TRP 0.007 0.001 TRP A 293 HIS 0.008 0.001 HIS E 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.19 (20347) covalent geometry : angle 0.55217 / 0.30 (27948) hydrogen bonds : bond 0.03927 / 2.71 ( 972) hydrogen bonds : angle 4.85775 / 3.44 ( 2717) metal coordination : bond 0.00715 / 0.36 ( 4) metal coordination : angle 4.67140 / 2.32 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 198 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 184 GLN cc_start: 0.7878 (tm-30) cc_final: 0.7529 (mm-40) REVERT: A 186 LYS cc_start: 0.8082 (mmmt) cc_final: 0.7817 (mttt) REVERT: A 213 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8021 (mm-30) REVERT: A 216 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8218 (mp0) REVERT: A 328 MET cc_start: 0.9020 (mtt) cc_final: 0.8807 (mtt) REVERT: B 216 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8075 (mt-10) REVERT: C 227 GLU cc_start: 0.7368 (mm-30) cc_final: 0.7015 (mt-10) REVERT: D 78 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7027 (mp0) REVERT: E 9 LYS cc_start: 0.8919 (mttm) cc_final: 0.8443 (mttm) REVERT: E 14 GLU cc_start: 0.8902 (mp0) cc_final: 0.8428 (mp0) REVERT: E 106 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8566 (tp) REVERT: E 109 LYS cc_start: 0.8476 (mttt) cc_final: 0.8233 (pttp) REVERT: E 135 ASP cc_start: 0.8037 (t70) cc_final: 0.7735 (t70) REVERT: E 258 THR cc_start: 0.8292 (OUTLIER) cc_final: 0.8023 (p) REVERT: E 290 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8353 (pt0) REVERT: E 330 LYS cc_start: 0.9137 (tppt) cc_final: 0.8883 (tptp) REVERT: E 334 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8394 (pp20) REVERT: F 84 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.7965 (tmt) REVERT: F 87 ASP cc_start: 0.8895 (m-30) cc_final: 0.8685 (m-30) REVERT: F 201 LYS cc_start: 0.8938 (mttp) cc_final: 0.8641 (mmtm) REVERT: G 16 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7736 (pp) REVERT: G 191 ASP cc_start: 0.9168 (t0) cc_final: 0.8935 (t0) REVERT: L 9 LYS cc_start: 0.6904 (mtpp) cc_final: 0.6495 (mmtt) REVERT: L 19 THR cc_start: 0.7111 (OUTLIER) cc_final: 0.6817 (p) REVERT: L 30 ARG cc_start: 0.6404 (tpp80) cc_final: 0.6188 (tpp80) REVERT: L 49 ARG cc_start: 0.8010 (ttt90) cc_final: 0.7708 (ttt90) REVERT: L 124 LYS cc_start: 0.8853 (mttp) cc_final: 0.8509 (mttt) REVERT: L 288 LEU cc_start: 0.8548 (tt) cc_final: 0.8274 (mm) REVERT: L 299 LYS cc_start: 0.8972 (tppp) cc_final: 0.8393 (tmmt) outliers start: 45 outliers final: 30 residues processed: 230 average time/residue: 0.1500 time to fit residues: 50.4347 Evaluate side-chains 224 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 187 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 109 LYS Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 253 SER Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 89 TRP Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 254 ILE Chi-restraints excluded: chain L residue 306 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 169 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 194 optimal weight: 4.9990 chunk 177 optimal weight: 3.9990 chunk 193 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 ASN C 226 GLN C 335 ASN D 84 GLN ** E 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 251 HIS L 250 HIS L 281 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.128993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.083599 restraints weight = 27754.087| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.15 r_work: 0.2795 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 20351 Z= 0.214 Angle : 0.583 7.526 27954 Z= 0.313 Chirality : 0.046 0.328 3136 Planarity : 0.004 0.047 3336 Dihedral : 19.299 176.977 3631 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.32 % Allowed : 10.80 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.17), residues: 2276 helix: 1.96 (0.18), residues: 841 sheet: 0.45 (0.24), residues: 361 loop : 0.02 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 229 TYR 0.012 0.001 TYR G 51 PHE 0.023 0.001 PHE L 6 TRP 0.016 0.001 TRP E 119 HIS 0.010 0.001 HIS E 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.21 (20347) covalent geometry : angle 0.57932 / 0.31 (27948) hydrogen bonds : bond 0.04007 / 2.76 ( 972) hydrogen bonds : angle 4.89561 / 3.47 ( 2717) metal coordination : bond 0.00864 / 0.43 ( 4) metal coordination : angle 4.77851 / 2.38 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 193 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 LYS cc_start: 0.8077 (mmmt) cc_final: 0.7867 (mttt) REVERT: A 213 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8015 (mm-30) REVERT: A 216 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8180 (mp0) REVERT: A 328 MET cc_start: 0.9041 (mtt) cc_final: 0.8818 (mtt) REVERT: B 216 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8077 (mt-10) REVERT: C 227 GLU cc_start: 0.7361 (mm-30) cc_final: 0.7053 (mt-10) REVERT: D 78 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7054 (mp0) REVERT: E 9 LYS cc_start: 0.8921 (mttm) cc_final: 0.8439 (mttm) REVERT: E 14 GLU cc_start: 0.8910 (mp0) cc_final: 0.8422 (mp0) REVERT: E 106 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8580 (tp) REVERT: E 109 LYS cc_start: 0.8478 (mttt) cc_final: 0.8234 (pttp) REVERT: E 135 ASP cc_start: 0.8040 (t70) cc_final: 0.7733 (t70) REVERT: E 258 THR cc_start: 0.8421 (OUTLIER) cc_final: 0.8144 (p) REVERT: E 330 LYS cc_start: 0.9145 (tppt) cc_final: 0.8884 (tptp) REVERT: E 334 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8405 (pp20) REVERT: F 84 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.7980 (tmt) REVERT: F 87 ASP cc_start: 0.8914 (m-30) cc_final: 0.8707 (m-30) REVERT: F 201 LYS cc_start: 0.8938 (mttp) cc_final: 0.8651 (mmtm) REVERT: G 16 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7796 (pp) REVERT: G 191 ASP cc_start: 0.9179 (t0) cc_final: 0.8945 (t0) REVERT: G 228 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7987 (tp30) REVERT: L 19 THR cc_start: 0.7124 (OUTLIER) cc_final: 0.6834 (p) REVERT: L 288 LEU cc_start: 0.8582 (tt) cc_final: 0.8280 (mm) outliers start: 44 outliers final: 30 residues processed: 226 average time/residue: 0.1642 time to fit residues: 54.1530 Evaluate side-chains 221 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 183 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 109 LYS Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 253 SER Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 89 TRP Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 254 ILE Chi-restraints excluded: chain L residue 306 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 93 optimal weight: 0.8980 chunk 94 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 210 optimal weight: 7.9990 chunk 136 optimal weight: 3.9990 chunk 190 optimal weight: 0.6980 chunk 215 optimal weight: 8.9990 chunk 114 optimal weight: 0.4980 chunk 143 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 ASN C 226 GLN C 335 ASN ** E 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 250 HIS L 281 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.130913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.085617 restraints weight = 27838.085| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.16 r_work: 0.2835 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20351 Z= 0.141 Angle : 0.545 8.068 27954 Z= 0.296 Chirality : 0.045 0.325 3136 Planarity : 0.004 0.047 3336 Dihedral : 19.257 176.812 3631 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.90 % Allowed : 11.22 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.17), residues: 2276 helix: 2.07 (0.18), residues: 836 sheet: 0.41 (0.24), residues: 366 loop : 0.11 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 229 TYR 0.007 0.001 TYR G 51 PHE 0.023 0.001 PHE L 6 TRP 0.012 0.001 TRP E 119 HIS 0.010 0.001 HIS E 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (20347) covalent geometry : angle 0.54036 / 0.30 (27948) hydrogen bonds : bond 0.03817 / 2.64 ( 972) hydrogen bonds : angle 4.82471 / 3.42 ( 2717) metal coordination : bond 0.00472 / 0.23 ( 4) metal coordination : angle 4.80901 / 2.36 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 198 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 GLN cc_start: 0.7871 (tm-30) cc_final: 0.7549 (mm-40) REVERT: A 213 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8009 (mm-30) REVERT: A 216 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8147 (mp0) REVERT: A 328 MET cc_start: 0.8944 (mtt) cc_final: 0.8732 (mtt) REVERT: B 216 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8040 (mt-10) REVERT: C 227 GLU cc_start: 0.7228 (mm-30) cc_final: 0.6903 (mt-10) REVERT: D 78 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7072 (mp0) REVERT: E 9 LYS cc_start: 0.8905 (mttm) cc_final: 0.8463 (mttm) REVERT: E 14 GLU cc_start: 0.8898 (mp0) cc_final: 0.8412 (mp0) REVERT: E 106 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8536 (tp) REVERT: E 109 LYS cc_start: 0.8466 (mttt) cc_final: 0.8218 (pttp) REVERT: E 258 THR cc_start: 0.8344 (OUTLIER) cc_final: 0.8034 (p) REVERT: F 84 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.8005 (tmt) REVERT: F 87 ASP cc_start: 0.8867 (m-30) cc_final: 0.8660 (m-30) REVERT: F 166 GLU cc_start: 0.9099 (tp30) cc_final: 0.8840 (tt0) REVERT: F 201 LYS cc_start: 0.8916 (mttp) cc_final: 0.8654 (mmtm) REVERT: G 16 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7695 (pp) REVERT: L 19 THR cc_start: 0.7084 (OUTLIER) cc_final: 0.6806 (p) REVERT: L 288 LEU cc_start: 0.8571 (tt) cc_final: 0.8287 (mm) outliers start: 36 outliers final: 24 residues processed: 226 average time/residue: 0.1747 time to fit residues: 57.6737 Evaluate side-chains 219 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 189 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 109 LYS Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 253 SER Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 89 TRP Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 254 ILE Chi-restraints excluded: chain L residue 306 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 60 optimal weight: 1.9990 chunk 100 optimal weight: 0.2980 chunk 99 optimal weight: 0.7980 chunk 120 optimal weight: 10.0000 chunk 85 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 220 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 chunk 218 optimal weight: 0.9990 chunk 217 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 ASN C 226 GLN C 335 ASN ** E 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 250 HIS L 281 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.130608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.085224 restraints weight = 27780.932| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.15 r_work: 0.2828 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 20351 Z= 0.160 Angle : 0.558 9.807 27954 Z= 0.300 Chirality : 0.045 0.328 3136 Planarity : 0.004 0.047 3336 Dihedral : 19.214 177.517 3631 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.84 % Allowed : 11.38 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.17), residues: 2276 helix: 2.09 (0.18), residues: 836 sheet: 0.43 (0.24), residues: 368 loop : 0.11 (0.19), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 229 TYR 0.016 0.001 TYR G 9 PHE 0.022 0.001 PHE L 6 TRP 0.025 0.001 TRP E 119 HIS 0.010 0.001 HIS E 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (20347) covalent geometry : angle 0.55383 / 0.30 (27948) hydrogen bonds : bond 0.03811 / 2.63 ( 972) hydrogen bonds : angle 4.81248 / 3.41 ( 2717) metal coordination : bond 0.00571 / 0.28 ( 4) metal coordination : angle 4.76082 / 2.35 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5243.96 seconds wall clock time: 90 minutes 26.17 seconds (5426.17 seconds total)