Starting phenix.real_space_refine on Sun Aug 24 12:07:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rc2_19045/08_2025/8rc2_19045.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rc2_19045/08_2025/8rc2_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_2025/8rc2_19045.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rc2_19045/08_2025/8rc2_19045.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8rc2_19045/08_2025/8rc2_19045.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rc2_19045/08_2025/8rc2_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 5.36, per 1000 atoms: 0.27 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: 2.08 Conformation dependent library (CDL) restraints added in 736.7 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 2.85 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: 3.89 Time building geometry restraints manager: 2.56 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=" 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=" N LYS A 193 " pdb=" CA LYS A 193 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.56e+00 bond pdb=" N LYS A 204 " pdb=" CA LYS A 204 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.33e-02 5.65e+03 5.24e+00 bond pdb=" N ASP A 200 " pdb=" CA ASP A 200 " ideal model delta sigma weight residual 1.453 1.482 -0.029 1.31e-02 5.83e+03 4.89e+00 bond pdb=" N LYS G 235 " pdb=" CA LYS G 235 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.21e-02 6.83e+03 4.46e+00 ... (remaining 20342 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 27446 1.99 - 3.98: 454 3.98 - 5.96: 41 5.96 - 7.95: 5 7.95 - 9.94: 2 Bond angle restraints: 27948 Sorted by residual: angle pdb=" CA ASP A 200 " pdb=" CB ASP A 200 " pdb=" CG ASP A 200 " ideal model delta sigma weight residual 112.60 116.26 -3.66 1.00e+00 1.00e+00 1.34e+01 angle pdb=" CA GLN C 184 " pdb=" CB GLN C 184 " pdb=" CG GLN C 184 " ideal model delta sigma weight residual 114.10 121.35 -7.25 2.00e+00 2.50e-01 1.31e+01 angle pdb=" N HIS C 284 " pdb=" CA HIS C 284 " pdb=" C HIS C 284 " ideal model delta sigma weight residual 113.72 109.10 4.62 1.52e+00 4.33e-01 9.24e+00 angle pdb=" C4' DG I -7 " pdb=" O4' DG I -7 " pdb=" C1' DG I -7 " ideal model delta sigma weight residual 109.70 105.15 4.55 1.50e+00 4.44e-01 9.19e+00 angle pdb=" CA LEU F 89 " pdb=" CB LEU F 89 " pdb=" CG LEU F 89 " ideal model delta sigma weight residual 116.30 106.36 9.94 3.50e+00 8.16e-02 8.06e+00 ... (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: 2233 0.043 - 0.086: 694 0.086 - 0.129: 186 0.129 - 0.172: 22 0.172 - 0.215: 1 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 2.46 2.29 0.17 2.00e-01 2.50e+01 7.23e-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 7.12e-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: 3.070 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: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 24.730 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 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 : 0.006 0.074 20351 Z= 0.281 Angle : 0.621 10.692 27954 Z= 0.325 Chirality : 0.044 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 aren 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 covalent geometry : bond 0.00648 (20347) covalent geometry : angle 0.61556 (27948) hydrogen bonds : bond 0.16693 ( 972) hydrogen bonds : angle 7.10500 ( 2717) metal coordination : bond 0.01233 ( 4) metal coordination : angle 5.48519 ( 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 : 0.680 Fit side-chains revert: symmetry clash 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: 0.6813 (mmtt) REVERT: A 196 MET cc_start: 0.8111 (tpt) cc_final: 0.6511 (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: 0.7825 (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: 0.7939 (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: 0.8573 (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: F 105 ARG cc_start: 0.7443 (mtt180) cc_final: 0.6963 (mtt180) REVERT: G 100 ASP cc_start: 0.8980 (m-30) cc_final: 0.8627 (m-30) REVERT: G 132 GLN cc_start: 0.8640 (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: 0.8259 (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: 0.1952 time to fit residues: 81.0117 Evaluate side-chains 205 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 203 time to evaluate : 0.738 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 219 GLN A 224 GLN C 292 HIS 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.130583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.085209 restraints weight = 27724.973| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.18 r_work: 0.2824 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1360 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= 0.171 Angle : 0.598 8.758 27954 Z= 0.316 Chirality : 0.043 0.173 3136 Planarity : 0.005 0.073 3336 Dihedral : 19.349 175.139 3635 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.00 % Allowed : 8.06 % Favored : 89.94 % 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 aren not related in a simple way. whole: 1.24 (0.17), residues: 2276 helix: 1.90 (0.18), residues: 842 sheet: 1.04 (0.26), residues: 341 loop : -0.05 (0.19), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 52 TYR 0.019 0.001 TYR G 51 PHE 0.018 0.001 PHE L 6 TRP 0.012 0.001 TRP D 119 HIS 0.006 0.001 HIS E 57 Details of bonding type rmsd covalent geometry : bond 0.00380 (20347) covalent geometry : angle 0.59221 (27948) hydrogen bonds : bond 0.04503 ( 972) hydrogen bonds : angle 5.36747 ( 2717) metal coordination : bond 0.00824 ( 4) metal coordination : angle 5.77057 ( 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 283 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 245 time to evaluate : 0.789 Fit side-chains revert: symmetry clash REVERT: A 149 MET cc_start: 0.8675 (ptm) cc_final: 0.8468 (ptm) REVERT: A 189 GLN cc_start: 0.7602 (tt0) cc_final: 0.7337 (tt0) REVERT: A 208 GLN cc_start: 0.7885 (mp10) cc_final: 0.7641 (mp10) REVERT: A 213 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8106 (mm-30) REVERT: A 216 GLU cc_start: 0.8880 (mp0) cc_final: 0.8565 (mp0) REVERT: A 330 LYS cc_start: 0.8316 (ttpp) cc_final: 0.8055 (ttpp) REVERT: B 174 GLU cc_start: 0.8002 (tt0) cc_final: 0.7742 (tt0) REVERT: B 190 ASP cc_start: 0.7960 (p0) cc_final: 0.7753 (p0) REVERT: B 208 GLN cc_start: 0.7789 (pt0) cc_final: 0.7578 (pt0) REVERT: B 217 LYS cc_start: 0.8743 (mtmt) cc_final: 0.8379 (mtmt) REVERT: C 227 GLU cc_start: 0.7417 (mm-30) cc_final: 0.6974 (mt-10) REVERT: D 78 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7149 (mp0) REVERT: D 84 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8338 (mt0) REVERT: D 101 ASN cc_start: 0.8472 (t0) cc_final: 0.8242 (t0) REVERT: D 196 MET cc_start: 0.3344 (OUTLIER) cc_final: 0.2940 (ptm) REVERT: E 9 LYS cc_start: 0.9127 (mttm) cc_final: 0.8850 (mttm) REVERT: E 14 GLU cc_start: 0.8814 (mp0) cc_final: 0.8489 (mp0) REVERT: E 109 LYS cc_start: 0.8468 (mttt) cc_final: 0.8236 (pttp) REVERT: E 135 ASP cc_start: 0.7969 (t70) cc_final: 0.7723 (t70) REVERT: E 258 THR cc_start: 0.8314 (OUTLIER) cc_final: 0.8010 (p) REVERT: E 275 GLU cc_start: 0.8271 (tp30) cc_final: 0.8036 (tt0) REVERT: F 75 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8701 (mp0) REVERT: F 201 LYS cc_start: 0.8841 (mttp) cc_final: 0.8578 (mmtm) REVERT: G 16 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7726 (pp) REVERT: G 100 ASP cc_start: 0.9238 (m-30) cc_final: 0.9033 (m-30) REVERT: L 19 THR cc_start: 0.7682 (OUTLIER) cc_final: 0.7394 (p) REVERT: L 127 ILE cc_start: 0.8021 (mm) cc_final: 0.7762 (mm) REVERT: L 137 GLN cc_start: 0.8334 (mp10) cc_final: 0.7964 (mp10) REVERT: L 299 LYS cc_start: 0.8995 (tppp) cc_final: 0.8756 (tmmt) REVERT: L 334 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7635 (mp0) outliers start: 38 outliers final: 22 residues processed: 273 average time/residue: 0.1983 time to fit residues: 77.4129 Evaluate side-chains 221 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 193 time to evaluate : 0.734 ------------------------------------------------------------------------------- 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 148 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 105 GLU Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 84 GLN 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 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 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 140 THR Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain L residue 19 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 154 optimal weight: 2.9990 chunk 178 optimal weight: 0.6980 chunk 134 optimal weight: 0.9980 chunk 36 optimal weight: 0.4980 chunk 137 optimal weight: 0.0060 chunk 209 optimal weight: 3.9990 chunk 123 optimal weight: 8.9990 chunk 76 optimal weight: 0.9990 chunk 213 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN A 250 HIS C 226 GLN D 151 GLN ** D 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 292 HIS L 57 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- 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 = 50)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.086890 restraints weight = 27764.305| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.16 r_work: 0.2846 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20351 Z= 0.138 Angle : 0.547 7.953 27954 Z= 0.288 Chirality : 0.042 0.224 3136 Planarity : 0.004 0.064 3336 Dihedral : 19.274 171.827 3631 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.21 % Allowed : 8.64 % Favored : 89.15 % 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 aren not related in a simple way. whole: 1.37 (0.17), residues: 2276 helix: 2.04 (0.18), residues: 843 sheet: 0.86 (0.26), residues: 347 loop : 0.08 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 251 TYR 0.014 0.001 TYR G 51 PHE 0.018 0.001 PHE L 37 TRP 0.007 0.001 TRP D 119 HIS 0.006 0.001 HIS E 57 Details of bonding type rmsd covalent geometry : bond 0.00302 (20347) covalent geometry : angle 0.54138 (27948) hydrogen bonds : bond 0.03959 ( 972) hydrogen bonds : angle 5.01567 ( 2717) metal coordination : bond 0.00483 ( 4) metal coordination : angle 5.20107 ( 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 258 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 216 time to evaluate : 0.753 Fit side-chains revert: symmetry clash REVERT: A 149 MET cc_start: 0.8668 (ptm) cc_final: 0.8318 (ptm) REVERT: A 208 GLN cc_start: 0.7943 (mp10) cc_final: 0.7743 (mp10) REVERT: C 151 GLN cc_start: 0.8542 (mt0) cc_final: 0.8314 (mt0) REVERT: C 227 GLU cc_start: 0.7163 (mm-30) cc_final: 0.6727 (mt-10) REVERT: D 78 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7067 (mp0) REVERT: D 101 ASN cc_start: 0.8448 (t0) cc_final: 0.8224 (t0) REVERT: D 196 MET cc_start: 0.3570 (OUTLIER) cc_final: 0.3051 (ptm) REVERT: E 9 LYS cc_start: 0.9096 (mttm) cc_final: 0.8761 (mttm) REVERT: E 14 GLU cc_start: 0.8818 (mp0) cc_final: 0.8413 (mp0) REVERT: E 109 LYS cc_start: 0.8465 (mttt) cc_final: 0.8216 (pttp) REVERT: E 258 THR cc_start: 0.8266 (OUTLIER) cc_final: 0.7982 (p) REVERT: E 275 GLU cc_start: 0.8157 (tp30) cc_final: 0.7886 (tt0) REVERT: E 334 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8364 (pp20) REVERT: F 42 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8495 (tp30) REVERT: F 75 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8705 (mp0) REVERT: F 105 ARG cc_start: 0.7854 (mtt180) cc_final: 0.7142 (mtt180) REVERT: G 16 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7598 (pp) REVERT: L 9 LYS cc_start: 0.6815 (mtpp) cc_final: 0.6430 (mmtt) REVERT: L 19 THR cc_start: 0.7259 (OUTLIER) cc_final: 0.6993 (p) REVERT: L 288 LEU cc_start: 0.8554 (tt) cc_final: 0.8272 (mm) REVERT: L 299 LYS cc_start: 0.9006 (tppp) cc_final: 0.8372 (tmmt) outliers start: 42 outliers final: 21 residues processed: 241 average time/residue: 0.1924 time to fit residues: 66.7594 Evaluate side-chains 217 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 190 time to evaluate : 0.698 ------------------------------------------------------------------------------- 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 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 12 THR Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 196 MET 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 140 THR Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain L residue 19 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 7 optimal weight: 3.9990 chunk 234 optimal weight: 10.0000 chunk 30 optimal weight: 0.8980 chunk 204 optimal weight: 3.9990 chunk 183 optimal weight: 0.2980 chunk 18 optimal weight: 7.9990 chunk 118 optimal weight: 9.9990 chunk 109 optimal weight: 0.9990 chunk 121 optimal weight: 20.0000 chunk 28 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN C 226 GLN ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN G 251 HIS 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 = 0.3587 r_free = 0.3587 target = 0.127624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.082097 restraints weight = 28065.845| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.16 r_work: 0.2771 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 20351 Z= 0.276 Angle : 0.625 9.669 27954 Z= 0.325 Chirality : 0.045 0.259 3136 Planarity : 0.005 0.060 3336 Dihedral : 19.440 173.521 3631 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.42 % Allowed : 8.85 % Favored : 88.72 % 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 aren not related in a simple way. whole: 1.13 (0.17), residues: 2276 helix: 1.84 (0.17), residues: 846 sheet: 0.65 (0.25), residues: 362 loop : -0.03 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 229 TYR 0.017 0.002 TYR G 51 PHE 0.020 0.002 PHE A 80 TRP 0.012 0.001 TRP E 119 HIS 0.006 0.001 HIS A 29 Details of bonding type rmsd covalent geometry : bond 0.00642 (20347) covalent geometry : angle 0.62085 (27948) hydrogen bonds : bond 0.04235 ( 972) hydrogen bonds : angle 5.08747 ( 2717) metal coordination : bond 0.01095 ( 4) metal coordination : angle 5.03101 ( 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 244 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 198 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 MET cc_start: 0.8906 (ptm) cc_final: 0.8525 (ptm) REVERT: A 208 GLN cc_start: 0.7920 (mp10) cc_final: 0.7691 (mp10) REVERT: A 210 LYS cc_start: 0.8664 (mtmm) cc_final: 0.8132 (mttp) REVERT: A 216 GLU cc_start: 0.8904 (mp0) cc_final: 0.8446 (mp0) REVERT: C 171 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7252 (tp) REVERT: C 227 GLU cc_start: 0.7465 (mm-30) cc_final: 0.7064 (mt-10) REVERT: D 78 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7033 (mp0) REVERT: D 101 ASN cc_start: 0.8539 (t0) cc_final: 0.8275 (t0) REVERT: D 196 MET cc_start: 0.3424 (OUTLIER) cc_final: 0.2839 (ptm) REVERT: E 14 GLU cc_start: 0.8920 (mp0) cc_final: 0.8457 (mp0) REVERT: E 109 LYS cc_start: 0.8472 (mttt) cc_final: 0.8245 (pttp) REVERT: E 258 THR cc_start: 0.8407 (OUTLIER) cc_final: 0.8117 (p) REVERT: E 275 GLU cc_start: 0.8407 (tp30) cc_final: 0.8199 (tt0) REVERT: E 334 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8364 (pp20) REVERT: F 2 LEU cc_start: 0.6779 (tt) cc_final: 0.6437 (tt) REVERT: F 3 ASN cc_start: 0.7316 (p0) cc_final: 0.7052 (t0) REVERT: F 98 MET cc_start: 0.9106 (mtt) cc_final: 0.8898 (mtt) REVERT: F 142 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.8067 (pm20) REVERT: F 201 LYS cc_start: 0.8946 (mttp) cc_final: 0.8652 (mmtm) REVERT: G 16 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7875 (pp) REVERT: G 228 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.8011 (tp30) REVERT: L 19 THR cc_start: 0.7133 (OUTLIER) cc_final: 0.6844 (p) REVERT: L 30 ARG cc_start: 0.6268 (tpp80) cc_final: 0.5938 (tpp80) REVERT: L 124 LYS cc_start: 0.8924 (mmtp) cc_final: 0.8711 (mttp) REVERT: L 137 GLN cc_start: 0.8576 (mm-40) cc_final: 0.8317 (mm-40) REVERT: L 249 SER cc_start: 0.8397 (t) cc_final: 0.8013 (m) REVERT: L 299 LYS cc_start: 0.8989 (tppp) cc_final: 0.8376 (tmmt) outliers start: 46 outliers final: 27 residues processed: 231 average time/residue: 0.1940 time to fit residues: 64.8502 Evaluate side-chains 226 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 190 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 148 ILE 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 C residue 19 THR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 171 LEU 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 253 SER Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain E residue 37 PHE 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 66 SER Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 142 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 140 THR 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 261 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 73 optimal weight: 0.7980 chunk 231 optimal weight: 7.9990 chunk 131 optimal weight: 0.5980 chunk 84 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 chunk 123 optimal weight: 10.0000 chunk 213 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 chunk 174 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 226 GLN C 335 ASN ** D 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 250 HIS L 281 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.130562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.085585 restraints weight = 27756.313| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.15 r_work: 0.2824 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20351 Z= 0.147 Angle : 0.546 7.703 27954 Z= 0.286 Chirality : 0.042 0.270 3136 Planarity : 0.004 0.052 3336 Dihedral : 19.316 171.376 3631 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.16 % Allowed : 9.80 % 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 aren not related in a simple way. whole: 1.26 (0.17), residues: 2276 helix: 2.02 (0.18), residues: 841 sheet: 0.52 (0.25), residues: 369 loop : 0.07 (0.19), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 105 TYR 0.012 0.001 TYR G 51 PHE 0.019 0.001 PHE L 37 TRP 0.007 0.001 TRP A 293 HIS 0.007 0.001 HIS E 57 Details of bonding type rmsd covalent geometry : bond 0.00329 (20347) covalent geometry : angle 0.54144 (27948) hydrogen bonds : bond 0.03772 ( 972) hydrogen bonds : angle 4.87999 ( 2717) metal coordination : bond 0.00389 ( 4) metal coordination : angle 4.73075 ( 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 249 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 208 time to evaluate : 0.743 Fit side-chains REVERT: A 149 MET cc_start: 0.8776 (ptm) cc_final: 0.8253 (ptm) REVERT: A 208 GLN cc_start: 0.7960 (mp10) cc_final: 0.7727 (mp10) REVERT: A 216 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8316 (mp0) REVERT: A 328 MET cc_start: 0.8995 (mtt) cc_final: 0.8780 (mtt) REVERT: C 227 GLU cc_start: 0.7294 (mm-30) cc_final: 0.6925 (mt-10) REVERT: D 78 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.6998 (mp0) REVERT: D 101 ASN cc_start: 0.8512 (t0) cc_final: 0.8270 (t0) REVERT: E 9 LYS cc_start: 0.8925 (mtpp) cc_final: 0.8642 (mttm) REVERT: E 14 GLU cc_start: 0.8908 (mp0) cc_final: 0.8397 (mp0) REVERT: E 109 LYS cc_start: 0.8465 (mttt) cc_final: 0.8215 (pttp) REVERT: E 258 THR cc_start: 0.8271 (OUTLIER) cc_final: 0.8001 (p) REVERT: E 275 GLU cc_start: 0.8355 (tp30) cc_final: 0.8130 (tt0) REVERT: E 330 LYS cc_start: 0.9136 (tppt) cc_final: 0.8871 (tptp) REVERT: E 334 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8462 (pp20) REVERT: F 75 GLU cc_start: 0.8899 (tp30) cc_final: 0.8688 (mp0) REVERT: F 84 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.8017 (tmt) REVERT: F 105 ARG cc_start: 0.7841 (mtt180) cc_final: 0.7176 (mtt180) REVERT: F 201 LYS cc_start: 0.8929 (mttp) cc_final: 0.8671 (mmtm) REVERT: G 16 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7726 (pp) REVERT: L 19 THR cc_start: 0.7100 (OUTLIER) cc_final: 0.6811 (p) REVERT: L 30 ARG cc_start: 0.6622 (tpp80) cc_final: 0.6419 (tpp80) REVERT: L 137 GLN cc_start: 0.8591 (mm-40) cc_final: 0.8371 (mm-40) REVERT: L 288 LEU cc_start: 0.8525 (tt) cc_final: 0.8235 (mm) REVERT: L 299 LYS cc_start: 0.8977 (tppp) cc_final: 0.8385 (tmmt) outliers start: 41 outliers final: 21 residues processed: 233 average time/residue: 0.1889 time to fit residues: 63.8680 Evaluate side-chains 206 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 179 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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 19 THR Chi-restraints excluded: chain C residue 105 GLU 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 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 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 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: 0.9990 chunk 100 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 167 optimal weight: 3.9990 chunk 200 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 172 optimal weight: 2.9990 chunk 157 optimal weight: 0.0170 chunk 232 optimal weight: 0.7980 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 226 GLN L 250 HIS L 256 ASN L 281 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.131242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.086397 restraints weight = 27842.690| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.16 r_work: 0.2842 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20351 Z= 0.136 Angle : 0.538 9.736 27954 Z= 0.280 Chirality : 0.042 0.280 3136 Planarity : 0.004 0.047 3336 Dihedral : 19.248 177.043 3631 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.00 % Allowed : 10.27 % Favored : 87.72 % 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 aren not related in a simple way. whole: 1.41 (0.17), residues: 2276 helix: 2.17 (0.18), residues: 839 sheet: 0.61 (0.25), residues: 366 loop : 0.13 (0.19), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 229 TYR 0.008 0.001 TYR G 136 PHE 0.011 0.001 PHE L 6 TRP 0.010 0.001 TRP E 119 HIS 0.007 0.001 HIS E 57 Details of bonding type rmsd covalent geometry : bond 0.00304 (20347) covalent geometry : angle 0.53368 (27948) hydrogen bonds : bond 0.03586 ( 972) hydrogen bonds : angle 4.72203 ( 2717) metal coordination : bond 0.00545 ( 4) metal coordination : angle 4.64052 ( 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 245 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 207 time to evaluate : 0.773 Fit side-chains REVERT: A 106 LEU cc_start: 0.8849 (tp) cc_final: 0.8621 (tp) REVERT: A 149 MET cc_start: 0.8757 (ptm) cc_final: 0.8289 (ptm) REVERT: A 208 GLN cc_start: 0.7986 (mp10) cc_final: 0.7751 (mp10) REVERT: A 210 LYS cc_start: 0.8583 (mtmm) cc_final: 0.8374 (mtmm) REVERT: A 216 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8233 (mp0) REVERT: A 328 MET cc_start: 0.8935 (mtt) cc_final: 0.8693 (mtt) REVERT: B 213 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8582 (pp20) REVERT: C 227 GLU cc_start: 0.7345 (mm-30) cc_final: 0.7013 (mt-10) REVERT: D 78 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.6966 (mp0) REVERT: E 9 LYS cc_start: 0.8884 (mtpp) cc_final: 0.8592 (mttm) REVERT: E 14 GLU cc_start: 0.8904 (mp0) cc_final: 0.8649 (mm-30) REVERT: E 106 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8488 (tp) REVERT: E 109 LYS cc_start: 0.8465 (mttt) cc_final: 0.8212 (pttp) REVERT: E 135 ASP cc_start: 0.8017 (t70) cc_final: 0.7718 (t70) REVERT: E 258 THR cc_start: 0.8243 (OUTLIER) cc_final: 0.7989 (p) REVERT: E 290 GLU cc_start: 0.8565 (tm-30) cc_final: 0.8316 (pt0) REVERT: F 75 GLU cc_start: 0.8873 (tp30) cc_final: 0.8645 (mp0) REVERT: F 84 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.8021 (tmt) REVERT: F 105 ARG cc_start: 0.7813 (mtt180) cc_final: 0.7270 (mtt180) REVERT: F 201 LYS cc_start: 0.8961 (mttp) cc_final: 0.8687 (mmtm) REVERT: G 16 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7611 (pp) REVERT: L 19 THR cc_start: 0.7064 (OUTLIER) cc_final: 0.6785 (p) REVERT: L 124 LYS cc_start: 0.8841 (mttp) cc_final: 0.8522 (mttt) REVERT: L 137 GLN cc_start: 0.8682 (mm-40) cc_final: 0.8412 (mm-40) REVERT: L 288 LEU cc_start: 0.8504 (tt) cc_final: 0.8209 (mm) REVERT: L 299 LYS cc_start: 0.8974 (tppp) cc_final: 0.8457 (tmmt) outliers start: 38 outliers final: 20 residues processed: 235 average time/residue: 0.1863 time to fit residues: 63.7153 Evaluate side-chains 212 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 185 time to evaluate : 0.749 ------------------------------------------------------------------------------- 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 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 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 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: 3.9990 chunk 197 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 120 optimal weight: 9.9990 chunk 104 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 169 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN C 226 GLN ** E 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 132 GLN L 281 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.129064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.083745 restraints weight = 28055.102| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 2.17 r_work: 0.2802 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 20351 Z= 0.204 Angle : 0.577 9.187 27954 Z= 0.299 Chirality : 0.043 0.307 3136 Planarity : 0.004 0.048 3336 Dihedral : 19.257 177.085 3631 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.00 % Allowed : 10.80 % Favored : 87.20 % 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 aren not related in a simple way. whole: 1.37 (0.17), residues: 2276 helix: 2.15 (0.18), residues: 837 sheet: 0.53 (0.24), residues: 368 loop : 0.12 (0.19), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 229 TYR 0.014 0.001 TYR G 9 PHE 0.017 0.001 PHE L 37 TRP 0.013 0.001 TRP E 119 HIS 0.007 0.001 HIS E 57 Details of bonding type rmsd covalent geometry : bond 0.00470 (20347) covalent geometry : angle 0.57299 (27948) hydrogen bonds : bond 0.03761 ( 972) hydrogen bonds : angle 4.83316 ( 2717) metal coordination : bond 0.00781 ( 4) metal coordination : angle 4.80911 ( 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 233 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 195 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 MET cc_start: 0.8850 (ptm) cc_final: 0.8251 (ptm) REVERT: A 216 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8221 (mp0) REVERT: A 328 MET cc_start: 0.9039 (mtt) cc_final: 0.8822 (mtt) REVERT: B 213 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8706 (pt0) REVERT: C 99 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7139 (mt-10) REVERT: C 227 GLU cc_start: 0.7230 (mm-30) cc_final: 0.6921 (mt-10) REVERT: D 78 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7066 (mp0) REVERT: D 101 ASN cc_start: 0.8543 (t0) cc_final: 0.8286 (t0) REVERT: E 9 LYS cc_start: 0.8958 (mtpp) cc_final: 0.8604 (mttm) REVERT: E 14 GLU cc_start: 0.8914 (mp0) cc_final: 0.8399 (mp0) REVERT: E 106 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8543 (tp) REVERT: E 109 LYS cc_start: 0.8462 (mttt) cc_final: 0.8222 (pttp) REVERT: E 135 ASP cc_start: 0.8022 (t70) cc_final: 0.7690 (t70) REVERT: E 258 THR cc_start: 0.8419 (OUTLIER) cc_final: 0.8132 (p) REVERT: E 290 GLU cc_start: 0.8582 (tm-30) cc_final: 0.8355 (pt0) REVERT: F 84 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.8029 (tmt) REVERT: F 105 ARG cc_start: 0.7734 (mtt180) cc_final: 0.7277 (mtt180) REVERT: F 201 LYS cc_start: 0.8950 (mttp) cc_final: 0.8676 (mmtm) REVERT: G 16 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7795 (pp) REVERT: G 191 ASP cc_start: 0.9135 (t0) cc_final: 0.8893 (t0) REVERT: L 19 THR cc_start: 0.6856 (OUTLIER) cc_final: 0.6590 (p) REVERT: L 124 LYS cc_start: 0.8840 (mttp) cc_final: 0.8628 (mttt) REVERT: L 137 GLN cc_start: 0.8740 (mm-40) cc_final: 0.8488 (mm-40) REVERT: L 288 LEU cc_start: 0.8554 (tt) cc_final: 0.8239 (mm) REVERT: L 299 LYS cc_start: 0.8971 (tppp) cc_final: 0.8740 (tppt) outliers start: 38 outliers final: 25 residues processed: 223 average time/residue: 0.1849 time to fit residues: 60.2697 Evaluate side-chains 212 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 180 time to evaluate : 0.756 ------------------------------------------------------------------------------- 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 213 GLU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 105 GLU 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 90 optimal weight: 0.0970 chunk 86 optimal weight: 0.9980 chunk 194 optimal weight: 1.9990 chunk 223 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 145 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 98 optimal weight: 0.5980 chunk 201 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN B 7 ASN ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 GLN L 281 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.130856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.085995 restraints weight = 27802.181| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 2.15 r_work: 0.2840 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20351 Z= 0.141 Angle : 0.556 13.969 27954 Z= 0.288 Chirality : 0.042 0.293 3136 Planarity : 0.004 0.048 3336 Dihedral : 19.188 170.539 3631 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.05 % Allowed : 11.06 % 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 aren not related in a simple way. whole: 1.46 (0.18), residues: 2276 helix: 2.22 (0.18), residues: 834 sheet: 0.52 (0.24), residues: 373 loop : 0.21 (0.19), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 229 TYR 0.006 0.001 TYR G 51 PHE 0.026 0.001 PHE L 6 TRP 0.020 0.001 TRP E 119 HIS 0.009 0.001 HIS E 57 Details of bonding type rmsd covalent geometry : bond 0.00316 (20347) covalent geometry : angle 0.55211 (27948) hydrogen bonds : bond 0.03594 ( 972) hydrogen bonds : angle 4.74086 ( 2717) metal coordination : bond 0.00504 ( 4) metal coordination : angle 4.65997 ( 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 236 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 197 time to evaluate : 0.759 Fit side-chains revert: symmetry clash REVERT: A 106 LEU cc_start: 0.8864 (tp) cc_final: 0.8618 (tp) REVERT: A 149 MET cc_start: 0.8746 (ptm) cc_final: 0.8345 (ptm) REVERT: A 210 LYS cc_start: 0.8742 (mtmm) cc_final: 0.8541 (mttp) REVERT: A 216 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8166 (mp0) REVERT: A 328 MET cc_start: 0.8937 (mtt) cc_final: 0.8689 (mtt) REVERT: C 99 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7064 (mt-10) REVERT: C 184 GLN cc_start: 0.8104 (tp40) cc_final: 0.7765 (tp-100) REVERT: D 78 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7059 (mp0) REVERT: E 9 LYS cc_start: 0.8876 (mtpp) cc_final: 0.8586 (mttm) REVERT: E 14 GLU cc_start: 0.8897 (mp0) cc_final: 0.8380 (mp0) REVERT: E 106 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8532 (tp) REVERT: E 109 LYS cc_start: 0.8457 (mttt) cc_final: 0.8209 (pttp) REVERT: E 258 THR cc_start: 0.8339 (OUTLIER) cc_final: 0.8045 (p) REVERT: E 290 GLU cc_start: 0.8553 (tm-30) cc_final: 0.8319 (pt0) REVERT: E 334 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8243 (pp20) REVERT: F 3 ASN cc_start: 0.7032 (p0) cc_final: 0.6690 (t0) REVERT: F 105 ARG cc_start: 0.7665 (mtt180) cc_final: 0.7108 (mtt180) REVERT: F 201 LYS cc_start: 0.8948 (mttp) cc_final: 0.8681 (mmtm) REVERT: G 16 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7656 (pp) REVERT: L 53 ARG cc_start: 0.8041 (mmm-85) cc_final: 0.7770 (mmm-85) REVERT: L 124 LYS cc_start: 0.8805 (mttp) cc_final: 0.8574 (mttt) REVERT: L 137 GLN cc_start: 0.8751 (mm-40) cc_final: 0.8551 (mm-40) REVERT: L 288 LEU cc_start: 0.8545 (tt) cc_final: 0.8249 (mm) outliers start: 39 outliers final: 19 residues processed: 228 average time/residue: 0.1773 time to fit residues: 59.1360 Evaluate side-chains 206 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 182 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain C residue 109 LYS Chi-restraints excluded: chain C residue 171 LEU 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 9 VAL 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 254 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 169 optimal weight: 0.5980 chunk 70 optimal weight: 0.9990 chunk 194 optimal weight: 0.9980 chunk 177 optimal weight: 2.9990 chunk 193 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 87 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 3 optimal weight: 0.1980 chunk 156 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 GLN E 284 HIS L 281 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.131246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.086532 restraints weight = 27774.897| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.15 r_work: 0.2840 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2561 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= 0.140 Angle : 0.563 15.184 27954 Z= 0.290 Chirality : 0.043 0.356 3136 Planarity : 0.004 0.055 3336 Dihedral : 19.144 170.713 3631 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.58 % Allowed : 11.59 % Favored : 86.83 % 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 aren not related in a simple way. whole: 1.46 (0.17), residues: 2276 helix: 2.22 (0.18), residues: 836 sheet: 0.51 (0.24), residues: 368 loop : 0.21 (0.19), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 229 TYR 0.015 0.001 TYR G 9 PHE 0.025 0.001 PHE L 6 TRP 0.023 0.001 TRP E 119 HIS 0.009 0.001 HIS E 57 Details of bonding type rmsd covalent geometry : bond 0.00316 (20347) covalent geometry : angle 0.55874 (27948) hydrogen bonds : bond 0.03558 ( 972) hydrogen bonds : angle 4.73333 ( 2717) metal coordination : bond 0.00449 ( 4) metal coordination : angle 4.50329 ( 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 222 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 192 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 LEU cc_start: 0.8855 (tp) cc_final: 0.8606 (tp) REVERT: A 149 MET cc_start: 0.8746 (ptm) cc_final: 0.8306 (ptm) REVERT: A 210 LYS cc_start: 0.8674 (mtmm) cc_final: 0.8456 (mttp) REVERT: A 213 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8344 (mm-30) REVERT: A 216 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8091 (mp0) REVERT: A 328 MET cc_start: 0.8932 (mtt) cc_final: 0.8691 (mtt) REVERT: C 99 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7062 (mt-10) REVERT: C 184 GLN cc_start: 0.8084 (tp40) cc_final: 0.7750 (tp-100) REVERT: D 78 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7064 (mp0) REVERT: E 9 LYS cc_start: 0.8862 (mtpp) cc_final: 0.8578 (mttm) REVERT: E 14 GLU cc_start: 0.8895 (mp0) cc_final: 0.8378 (mp0) REVERT: E 106 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8513 (tp) REVERT: E 109 LYS cc_start: 0.8453 (mttt) cc_final: 0.8204 (pttp) REVERT: E 135 ASP cc_start: 0.8053 (t70) cc_final: 0.7836 (t70) REVERT: E 258 THR cc_start: 0.8326 (OUTLIER) cc_final: 0.8021 (p) REVERT: E 290 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8329 (pt0) REVERT: F 3 ASN cc_start: 0.7121 (p0) cc_final: 0.6759 (t0) REVERT: F 201 LYS cc_start: 0.8930 (mttp) cc_final: 0.8655 (mmtm) REVERT: G 16 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7644 (pp) REVERT: L 124 LYS cc_start: 0.8761 (mttp) cc_final: 0.8352 (mttt) REVERT: L 137 GLN cc_start: 0.8756 (mm-40) cc_final: 0.8525 (mm-40) REVERT: L 261 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8294 (pt0) REVERT: L 288 LEU cc_start: 0.8561 (tt) cc_final: 0.8258 (mm) outliers start: 30 outliers final: 22 residues processed: 214 average time/residue: 0.1847 time to fit residues: 57.8126 Evaluate side-chains 220 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 192 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 109 LYS Chi-restraints excluded: chain C residue 171 LEU 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 290 GLU Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain F residue 9 VAL 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 254 ILE Chi-restraints excluded: chain L residue 261 GLU 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: 3.9990 chunk 94 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 210 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 190 optimal weight: 0.6980 chunk 215 optimal weight: 8.9990 chunk 114 optimal weight: 2.9990 chunk 143 optimal weight: 6.9990 chunk 113 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 ASN C 226 GLN ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 281 HIS 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 = 0.127915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.084149 restraints weight = 28064.978| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.37 r_work: 0.2786 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 20351 Z= 0.254 Angle : 0.627 15.239 27954 Z= 0.322 Chirality : 0.046 0.387 3136 Planarity : 0.004 0.048 3336 Dihedral : 19.189 172.565 3631 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.63 % Allowed : 11.64 % Favored : 86.72 % 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 aren not related in a simple way. whole: 1.28 (0.17), residues: 2276 helix: 2.03 (0.18), residues: 841 sheet: 0.45 (0.24), residues: 367 loop : 0.11 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 229 TYR 0.011 0.002 TYR L 239 PHE 0.025 0.002 PHE L 6 TRP 0.028 0.001 TRP E 119 HIS 0.009 0.001 HIS E 57 Details of bonding type rmsd covalent geometry : bond 0.00593 (20347) covalent geometry : angle 0.62374 (27948) hydrogen bonds : bond 0.03871 ( 972) hydrogen bonds : angle 4.90858 ( 2717) metal coordination : bond 0.00960 ( 4) metal coordination : angle 4.68090 ( 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 222 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 191 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 MET cc_start: 0.8893 (ptm) cc_final: 0.8220 (ptm) REVERT: A 210 LYS cc_start: 0.8720 (mtmm) cc_final: 0.8486 (mttp) REVERT: A 216 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8140 (mp0) REVERT: A 328 MET cc_start: 0.9046 (mtt) cc_final: 0.8819 (mtt) REVERT: C 184 GLN cc_start: 0.8141 (tp40) cc_final: 0.7792 (tp-100) REVERT: E 14 GLU cc_start: 0.8905 (mp0) cc_final: 0.8413 (mp0) REVERT: E 106 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8595 (tp) REVERT: E 109 LYS cc_start: 0.8482 (mttt) cc_final: 0.8249 (pttp) REVERT: E 135 ASP cc_start: 0.8079 (t70) cc_final: 0.7846 (t70) REVERT: E 258 THR cc_start: 0.8399 (OUTLIER) cc_final: 0.8107 (p) REVERT: E 290 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8311 (pt0) REVERT: F 3 ASN cc_start: 0.7262 (p0) cc_final: 0.6903 (t0) REVERT: F 201 LYS cc_start: 0.8941 (mttp) cc_final: 0.8671 (mmtm) REVERT: G 16 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7899 (pp) REVERT: L 124 LYS cc_start: 0.8893 (mttp) cc_final: 0.8514 (mttt) REVERT: L 137 GLN cc_start: 0.8763 (mm-40) cc_final: 0.8512 (mm-40) outliers start: 31 outliers final: 21 residues processed: 216 average time/residue: 0.1849 time to fit residues: 58.2836 Evaluate side-chains 207 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 182 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 D residue 58 LYS 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 290 GLU Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 81 THR 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 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: 0.5980 chunk 100 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 120 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 220 optimal weight: 9.9990 chunk 80 optimal weight: 0.5980 chunk 218 optimal weight: 1.9990 chunk 217 optimal weight: 0.0870 chunk 4 optimal weight: 0.3980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 GLN ** E 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 HIS L 281 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.132193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.088118 restraints weight = 27842.561| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.39 r_work: 0.2841 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20351 Z= 0.126 Angle : 0.566 15.617 27954 Z= 0.290 Chirality : 0.042 0.338 3136 Planarity : 0.004 0.048 3336 Dihedral : 19.114 169.784 3631 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.26 % Allowed : 12.07 % Favored : 86.67 % 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 aren not related in a simple way. whole: 1.41 (0.18), residues: 2276 helix: 2.23 (0.18), residues: 836 sheet: 0.35 (0.24), residues: 382 loop : 0.19 (0.19), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 229 TYR 0.007 0.001 TYR G 188 PHE 0.025 0.001 PHE L 6 TRP 0.022 0.001 TRP E 119 HIS 0.011 0.001 HIS E 57 Details of bonding type rmsd covalent geometry : bond 0.00281 (20347) covalent geometry : angle 0.55837 (27948) hydrogen bonds : bond 0.03542 ( 972) hydrogen bonds : angle 4.74612 ( 2717) metal coordination : bond 0.00909 ( 4) metal coordination : angle 6.40782 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6033.14 seconds wall clock time: 104 minutes 5.64 seconds (6245.64 seconds total)