Starting phenix.real_space_refine on Thu Jan 23 05:21:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rc2_19045/01_2025/8rc2_19045.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rc2_19045/01_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8rc2_19045/01_2025/8rc2_19045.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rc2_19045/01_2025/8rc2_19045.map" model { file = "/net/cci-nas-00/data/ceres_data/8rc2_19045/01_2025/8rc2_19045.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rc2_19045/01_2025/8rc2_19045.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.098 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 12.57, per 1000 atoms: 0.64 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: 4.80 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 7.29 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: 7.19 Time building geometry restraints manager: 5.48 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: 2.840 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: 0.730 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 53.810 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.100 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.460 ------------------------------------------------------------------------------- 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 20347 Z= 0.416 Angle : 0.616 9.939 27948 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 : 7.49 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (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 TRP 0.018 0.002 TRP D 119 HIS 0.006 0.001 HIS A 29 PHE 0.027 0.002 PHE A 80 TYR 0.029 0.002 TYR G 51 ARG 0.010 0.001 ARG F 234 *********************** 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 : 2.214 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: 0.4036 time to fit residues: 168.5546 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 : 1.947 ------------------------------------------------------------------------------- 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 198 optimal weight: 2.9990 chunk 178 optimal weight: 0.6980 chunk 98 optimal weight: 0.5980 chunk 60 optimal weight: 0.5980 chunk 120 optimal weight: 9.9990 chunk 95 optimal weight: 0.7980 chunk 184 optimal weight: 0.0030 chunk 71 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 137 optimal weight: 6.9990 chunk 213 optimal weight: 1.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- 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** L 57 HIS L 336 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.131993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.086825 restraints weight = 27662.270| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.18 r_work: 0.2850 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20347 Z= 0.192 Angle : 0.575 8.553 27948 Z= 0.308 Chirality : 0.042 0.166 3136 Planarity : 0.005 0.067 3336 Dihedral : 19.338 175.028 3635 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.84 % Allowed : 8.17 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.17), residues: 2276 helix: 1.99 (0.18), residues: 836 sheet: 1.01 (0.26), residues: 355 loop : -0.01 (0.19), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 119 HIS 0.005 0.001 HIS E 57 PHE 0.017 0.001 PHE L 6 TYR 0.017 0.001 TYR G 51 ARG 0.006 0.001 ARG G 52 *********************** 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 287 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 252 time to evaluate : 2.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 GLN cc_start: 0.7585 (tt0) cc_final: 0.7320 (tt0) REVERT: A 208 GLN cc_start: 0.7952 (mp10) cc_final: 0.7697 (mp10) REVERT: A 213 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8104 (mm-30) REVERT: A 216 GLU cc_start: 0.8899 (mp0) cc_final: 0.8567 (mp0) REVERT: A 330 LYS cc_start: 0.8247 (ttpp) cc_final: 0.7964 (ttpp) REVERT: B 174 GLU cc_start: 0.7999 (tt0) cc_final: 0.7738 (tt0) REVERT: B 190 ASP cc_start: 0.7956 (p0) cc_final: 0.7749 (p0) REVERT: B 217 LYS cc_start: 0.8746 (mtmt) cc_final: 0.8366 (mtmt) REVERT: C 151 GLN cc_start: 0.8395 (mt0) cc_final: 0.8195 (mt0) REVERT: C 157 MET cc_start: 0.9006 (mmm) cc_final: 0.8801 (mmm) REVERT: C 227 GLU cc_start: 0.7392 (mm-30) cc_final: 0.6938 (mt-10) REVERT: D 78 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7109 (mp0) REVERT: D 196 MET cc_start: 0.3436 (OUTLIER) cc_final: 0.3032 (ptm) REVERT: E 9 LYS cc_start: 0.9116 (mttm) cc_final: 0.8859 (mttm) REVERT: E 14 GLU cc_start: 0.8803 (mp0) cc_final: 0.8536 (mp0) REVERT: E 109 LYS cc_start: 0.8460 (mttt) cc_final: 0.8227 (pttp) REVERT: E 135 ASP cc_start: 0.7994 (t70) cc_final: 0.7764 (t70) REVERT: E 258 THR cc_start: 0.8269 (OUTLIER) cc_final: 0.7962 (p) REVERT: E 275 GLU cc_start: 0.8234 (tp30) cc_final: 0.7996 (tt0) REVERT: F 3 ASN cc_start: 0.7157 (p0) cc_final: 0.6955 (p0) REVERT: F 42 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8475 (tp30) REVERT: F 75 GLU cc_start: 0.8956 (mm-30) cc_final: 0.8709 (mp0) REVERT: F 201 LYS cc_start: 0.8823 (mttp) cc_final: 0.8560 (mmtm) REVERT: G 16 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7618 (pp) REVERT: L 19 THR cc_start: 0.7675 (OUTLIER) cc_final: 0.7396 (p) REVERT: L 127 ILE cc_start: 0.8013 (mm) cc_final: 0.7759 (mm) REVERT: L 137 GLN cc_start: 0.8350 (mp10) cc_final: 0.7991 (mp10) REVERT: L 288 LEU cc_start: 0.8578 (tt) cc_final: 0.8256 (mm) REVERT: L 299 LYS cc_start: 0.8994 (tppp) cc_final: 0.8761 (tmmt) REVERT: L 334 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7648 (mp0) outliers start: 35 outliers final: 19 residues processed: 276 average time/residue: 0.4075 time to fit residues: 161.1921 Evaluate side-chains 219 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 195 time to evaluate : 2.083 ------------------------------------------------------------------------------- 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 D residue 78 GLU Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 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 42 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 201 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 216 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 213 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 HIS A 151 GLN A 219 GLN C 226 GLN ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 ASN ** D 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 292 HIS ** G 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.129162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.083775 restraints weight = 27509.776| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.16 r_work: 0.2801 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 20347 Z= 0.319 Angle : 0.583 7.734 27948 Z= 0.308 Chirality : 0.044 0.239 3136 Planarity : 0.005 0.068 3336 Dihedral : 19.322 173.143 3631 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.53 % Allowed : 8.38 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.17), residues: 2276 helix: 1.91 (0.18), residues: 848 sheet: 0.81 (0.26), residues: 357 loop : -0.01 (0.19), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 119 HIS 0.005 0.001 HIS A 29 PHE 0.017 0.002 PHE A 80 TYR 0.017 0.002 TYR G 51 ARG 0.006 0.001 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 203 time to evaluate : 2.075 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 ARG cc_start: 0.9090 (mmt90) cc_final: 0.8739 (mmt-90) REVERT: A 208 GLN cc_start: 0.7943 (mp10) cc_final: 0.7742 (mp10) REVERT: A 213 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8157 (mm-30) REVERT: A 216 GLU cc_start: 0.8878 (mp0) cc_final: 0.8571 (mp0) REVERT: B 105 GLU cc_start: 0.8065 (tt0) cc_final: 0.7749 (tp30) REVERT: B 190 ASP cc_start: 0.7937 (p0) cc_final: 0.7734 (p0) REVERT: C 227 GLU cc_start: 0.7311 (mm-30) cc_final: 0.6916 (mt-10) REVERT: D 78 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7035 (mp0) REVERT: D 196 MET cc_start: 0.3381 (OUTLIER) cc_final: 0.2950 (ptm) REVERT: E 9 LYS cc_start: 0.9111 (mttm) cc_final: 0.8856 (mttm) REVERT: E 14 GLU cc_start: 0.8851 (mp0) cc_final: 0.8509 (mp0) REVERT: E 109 LYS cc_start: 0.8469 (mttt) cc_final: 0.8239 (pttp) REVERT: E 258 THR cc_start: 0.8363 (OUTLIER) cc_final: 0.8086 (p) REVERT: E 275 GLU cc_start: 0.8337 (tp30) cc_final: 0.8121 (tt0) REVERT: F 42 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8499 (tp30) REVERT: F 105 ARG cc_start: 0.7875 (mtt180) cc_final: 0.7593 (mtt180) REVERT: F 201 LYS cc_start: 0.8923 (mttp) cc_final: 0.8651 (mmtm) REVERT: G 16 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7801 (pp) REVERT: L 9 LYS cc_start: 0.6820 (mtpp) cc_final: 0.6326 (mmtt) REVERT: L 19 THR cc_start: 0.7304 (OUTLIER) cc_final: 0.7013 (p) REVERT: L 243 ILE cc_start: 0.8347 (pt) cc_final: 0.8080 (pt) REVERT: L 299 LYS cc_start: 0.8988 (tppp) cc_final: 0.8352 (tmmt) outliers start: 48 outliers final: 29 residues processed: 234 average time/residue: 0.4088 time to fit residues: 139.4173 Evaluate side-chains 227 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 193 time to evaluate : 2.281 ------------------------------------------------------------------------------- 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 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 101 ASN Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 306 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 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 G residue 244 LEU 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 99 optimal weight: 0.5980 chunk 125 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 132 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 145 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 chunk 142 optimal weight: 0.6980 chunk 122 optimal weight: 30.0000 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 ASN ** D 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 250 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 = 0.130911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.086028 restraints weight = 27848.177| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 2.16 r_work: 0.2832 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20347 Z= 0.209 Angle : 0.539 8.271 27948 Z= 0.284 Chirality : 0.042 0.263 3136 Planarity : 0.004 0.057 3336 Dihedral : 19.324 171.355 3631 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.05 % Allowed : 9.38 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.17), residues: 2276 helix: 2.04 (0.18), residues: 843 sheet: 0.68 (0.25), residues: 367 loop : 0.07 (0.19), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 119 HIS 0.006 0.001 HIS E 57 PHE 0.013 0.001 PHE L 6 TYR 0.012 0.001 TYR G 51 ARG 0.003 0.000 ARG A 229 *********************** 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 252 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 213 time to evaluate : 1.997 Fit side-chains REVERT: A 149 MET cc_start: 0.8808 (ptm) cc_final: 0.8473 (ptm) REVERT: A 208 GLN cc_start: 0.7949 (mp10) cc_final: 0.7731 (mp10) REVERT: A 210 LYS cc_start: 0.8632 (mtmm) cc_final: 0.8246 (mttp) REVERT: A 213 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8102 (mm-30) REVERT: A 216 GLU cc_start: 0.8914 (mp0) cc_final: 0.8304 (mp0) REVERT: A 328 MET cc_start: 0.8947 (mtt) cc_final: 0.8745 (mtt) REVERT: C 227 GLU cc_start: 0.7153 (mm-30) cc_final: 0.6825 (mt-10) REVERT: D 78 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7015 (mp0) REVERT: D 196 MET cc_start: 0.3681 (ptm) cc_final: 0.3469 (mtm) REVERT: E 9 LYS cc_start: 0.9088 (mttm) cc_final: 0.8738 (mttm) REVERT: E 14 GLU cc_start: 0.8832 (mp0) cc_final: 0.8467 (mp0) REVERT: E 109 LYS cc_start: 0.8465 (mttt) cc_final: 0.8216 (pttp) REVERT: E 119 TRP cc_start: 0.9051 (t-100) cc_final: 0.8816 (t-100) REVERT: E 258 THR cc_start: 0.8323 (OUTLIER) cc_final: 0.8050 (p) REVERT: E 275 GLU cc_start: 0.8333 (tp30) cc_final: 0.8114 (tt0) REVERT: E 334 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8379 (pp20) REVERT: F 3 ASN cc_start: 0.7167 (p0) cc_final: 0.6900 (t0) REVERT: F 42 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8506 (tp30) REVERT: F 166 GLU cc_start: 0.9083 (tp30) cc_final: 0.8816 (tt0) REVERT: F 201 LYS cc_start: 0.8933 (mttp) cc_final: 0.8680 (mmtm) REVERT: G 16 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7639 (pp) REVERT: L 19 THR cc_start: 0.7090 (OUTLIER) cc_final: 0.6806 (p) REVERT: L 124 LYS cc_start: 0.8849 (mmtp) cc_final: 0.8628 (mttp) REVERT: L 137 GLN cc_start: 0.8512 (mp10) cc_final: 0.8175 (mm-40) REVERT: L 249 SER cc_start: 0.8362 (t) cc_final: 0.7958 (m) REVERT: L 288 LEU cc_start: 0.8488 (tt) cc_final: 0.8214 (mm) REVERT: L 299 LYS cc_start: 0.8984 (tppp) cc_final: 0.8366 (tmmt) outliers start: 39 outliers final: 20 residues processed: 240 average time/residue: 0.4048 time to fit residues: 140.3067 Evaluate side-chains 220 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 195 time to evaluate : 1.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 109 LYS Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 253 SER Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 89 TRP Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain L residue 19 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 177 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 chunk 156 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 208 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 19 optimal weight: 9.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 226 GLN ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 ASN ** D 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN G 251 HIS L 250 HIS L 256 ASN L 281 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.127678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.083555 restraints weight = 28078.671| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 2.49 r_work: 0.2768 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 20347 Z= 0.403 Angle : 0.610 10.998 27948 Z= 0.318 Chirality : 0.045 0.272 3136 Planarity : 0.004 0.053 3336 Dihedral : 19.388 172.873 3631 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.37 % Allowed : 9.96 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.17), residues: 2276 helix: 1.94 (0.18), residues: 842 sheet: 0.56 (0.25), residues: 362 loop : -0.02 (0.19), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 293 HIS 0.007 0.001 HIS E 57 PHE 0.017 0.002 PHE A 80 TYR 0.013 0.002 TYR G 9 ARG 0.006 0.001 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 200 time to evaluate : 2.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 ARG cc_start: 0.9131 (mmt90) cc_final: 0.8786 (mmt-90) REVERT: A 149 MET cc_start: 0.8832 (ptm) cc_final: 0.8467 (ptm) REVERT: A 213 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8135 (mm-30) REVERT: A 216 GLU cc_start: 0.8931 (mt-10) cc_final: 0.8263 (mp0) REVERT: A 302 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8625 (pt0) REVERT: A 328 MET cc_start: 0.9064 (mtt) cc_final: 0.8820 (mtt) REVERT: C 171 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7299 (tp) REVERT: C 227 GLU cc_start: 0.7438 (mm-30) cc_final: 0.7112 (mt-10) REVERT: D 78 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.6949 (mp0) REVERT: D 196 MET cc_start: 0.3465 (OUTLIER) cc_final: 0.2913 (ptm) REVERT: E 14 GLU cc_start: 0.8826 (mp0) cc_final: 0.8484 (mp0) REVERT: E 106 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8601 (tp) REVERT: E 109 LYS cc_start: 0.8483 (mttt) cc_final: 0.8246 (pttp) REVERT: E 258 THR cc_start: 0.8376 (OUTLIER) cc_final: 0.8111 (p) REVERT: E 330 LYS cc_start: 0.9140 (tppt) cc_final: 0.8874 (tptp) REVERT: E 334 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8440 (pp20) REVERT: F 84 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.7926 (tmt) REVERT: F 105 ARG cc_start: 0.7874 (mtt180) cc_final: 0.7057 (mtt180) REVERT: F 201 LYS cc_start: 0.8943 (mttp) cc_final: 0.8697 (mmtm) REVERT: G 16 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7930 (pp) REVERT: G 228 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.8008 (tp30) REVERT: L 19 THR cc_start: 0.7106 (OUTLIER) cc_final: 0.6821 (p) REVERT: L 49 ARG cc_start: 0.8077 (ttt90) cc_final: 0.7851 (ttt90) REVERT: L 124 LYS cc_start: 0.8895 (mmtp) cc_final: 0.8688 (mttp) REVERT: L 137 GLN cc_start: 0.8476 (mp10) cc_final: 0.7988 (mm-40) outliers start: 45 outliers final: 24 residues processed: 233 average time/residue: 0.3994 time to fit residues: 135.1649 Evaluate side-chains 226 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 191 time to evaluate : 2.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 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 101 ASN 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 106 LEU Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 253 SER Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 89 TRP Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain L residue 19 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 167 optimal weight: 1.9990 chunk 200 optimal weight: 0.6980 chunk 121 optimal weight: 20.0000 chunk 107 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 22 optimal weight: 7.9990 chunk 225 optimal weight: 10.0000 chunk 113 optimal weight: 1.9990 chunk 131 optimal weight: 0.1980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 GLN ** D 101 ASN ** 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 = 0.3628 r_free = 0.3628 target = 0.130790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.085901 restraints weight = 27799.443| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 2.16 r_work: 0.2835 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20347 Z= 0.191 Angle : 0.539 9.887 27948 Z= 0.283 Chirality : 0.042 0.280 3136 Planarity : 0.004 0.047 3336 Dihedral : 19.293 175.544 3631 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.90 % Allowed : 11.01 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.17), residues: 2276 helix: 2.13 (0.18), residues: 839 sheet: 0.56 (0.25), residues: 361 loop : 0.09 (0.19), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 119 HIS 0.008 0.001 HIS E 57 PHE 0.012 0.001 PHE L 6 TYR 0.012 0.001 TYR G 9 ARG 0.005 0.000 ARG A 229 *********************** 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: 36 poor density : 209 time to evaluate : 2.010 Fit side-chains REVERT: A 30 ARG cc_start: 0.9076 (mmt90) cc_final: 0.8741 (mmt-90) REVERT: A 210 LYS cc_start: 0.8472 (mtmm) cc_final: 0.8197 (mttp) REVERT: A 213 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8120 (mm-30) REVERT: A 216 GLU cc_start: 0.8931 (mt-10) cc_final: 0.8215 (mp0) REVERT: A 328 MET cc_start: 0.8941 (mtt) cc_final: 0.8725 (mtt) REVERT: B 213 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8602 (pp20) REVERT: B 217 LYS cc_start: 0.8633 (ptpt) cc_final: 0.8327 (ptpt) REVERT: C 227 GLU cc_start: 0.7265 (mm-30) cc_final: 0.6941 (mt-10) REVERT: D 78 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.6887 (mp0) REVERT: D 196 MET cc_start: 0.3589 (ptm) cc_final: 0.3341 (mtm) REVERT: E 14 GLU cc_start: 0.8831 (mp0) cc_final: 0.8476 (mp0) REVERT: E 109 LYS cc_start: 0.8459 (mttt) cc_final: 0.8209 (pttp) REVERT: E 258 THR cc_start: 0.8266 (OUTLIER) cc_final: 0.8004 (p) REVERT: E 290 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8323 (pt0) REVERT: E 330 LYS cc_start: 0.9154 (tppt) cc_final: 0.8911 (tptp) REVERT: E 334 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8421 (pp20) REVERT: F 3 ASN cc_start: 0.7064 (p0) cc_final: 0.6773 (t0) REVERT: F 42 GLU cc_start: 0.8779 (mm-30) cc_final: 0.8515 (tp30) REVERT: F 84 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.8009 (tmt) REVERT: F 166 GLU cc_start: 0.9098 (tp30) cc_final: 0.8843 (tt0) REVERT: F 201 LYS cc_start: 0.8922 (mttp) cc_final: 0.8692 (mmtm) REVERT: G 16 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7672 (pp) REVERT: G 191 ASP cc_start: 0.9092 (t0) cc_final: 0.8857 (t0) REVERT: L 19 THR cc_start: 0.7066 (OUTLIER) cc_final: 0.6786 (p) REVERT: L 49 ARG cc_start: 0.8080 (ttt90) cc_final: 0.7877 (ttt90) REVERT: L 124 LYS cc_start: 0.8814 (mmtp) cc_final: 0.8302 (mttt) REVERT: L 137 GLN cc_start: 0.8589 (mp10) cc_final: 0.8144 (mm-40) REVERT: L 288 LEU cc_start: 0.8473 (tt) cc_final: 0.8200 (mm) outliers start: 36 outliers final: 19 residues processed: 237 average time/residue: 0.3972 time to fit residues: 136.4157 Evaluate side-chains 212 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 186 time to evaluate : 2.062 ------------------------------------------------------------------------------- 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 B residue 321 THR 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 253 SER Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 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 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 4 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 0 optimal weight: 0.5980 chunk 219 optimal weight: 1.9990 chunk 218 optimal weight: 2.9990 chunk 118 optimal weight: 9.9990 chunk 116 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 GLN ** D 101 ASN ** 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 = 0.3615 r_free = 0.3615 target = 0.129797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.084836 restraints weight = 27740.384| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 2.15 r_work: 0.2814 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20347 Z= 0.246 Angle : 0.551 9.427 27948 Z= 0.287 Chirality : 0.042 0.308 3136 Planarity : 0.004 0.047 3336 Dihedral : 19.258 178.953 3631 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.00 % Allowed : 11.01 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.17), residues: 2276 helix: 2.13 (0.18), residues: 844 sheet: 0.58 (0.24), residues: 363 loop : 0.11 (0.19), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 119 HIS 0.008 0.001 HIS E 57 PHE 0.016 0.001 PHE L 37 TYR 0.010 0.001 TYR L 239 ARG 0.007 0.000 ARG A 229 *********************** 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 239 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 201 time to evaluate : 2.078 Fit side-chains revert: symmetry clash REVERT: A 213 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8102 (mm-30) REVERT: A 216 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8287 (mp0) REVERT: A 328 MET cc_start: 0.9009 (mtt) cc_final: 0.8789 (mtt) REVERT: C 227 GLU cc_start: 0.7286 (mm-30) cc_final: 0.6899 (mt-10) REVERT: D 78 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.6934 (mp0) REVERT: D 196 MET cc_start: 0.3422 (ptm) cc_final: 0.3088 (ptm) REVERT: E 9 LYS cc_start: 0.8901 (mttm) cc_final: 0.8549 (mtpp) REVERT: E 14 GLU cc_start: 0.8843 (mp0) cc_final: 0.8490 (mp0) REVERT: E 106 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8513 (tp) REVERT: E 109 LYS cc_start: 0.8457 (mttt) cc_final: 0.8212 (pttp) REVERT: E 258 THR cc_start: 0.8380 (OUTLIER) cc_final: 0.8098 (p) REVERT: E 290 GLU cc_start: 0.8598 (tm-30) cc_final: 0.8354 (pt0) REVERT: E 330 LYS cc_start: 0.9158 (tppt) cc_final: 0.8918 (tptp) REVERT: E 334 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8445 (pp20) REVERT: F 3 ASN cc_start: 0.7099 (p0) cc_final: 0.6805 (t0) REVERT: F 84 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.8018 (tmt) REVERT: F 87 ASP cc_start: 0.8906 (m-30) cc_final: 0.8693 (m-30) REVERT: F 166 GLU cc_start: 0.9112 (tp30) cc_final: 0.8813 (tt0) REVERT: F 201 LYS cc_start: 0.8912 (mttp) cc_final: 0.8681 (mmtm) REVERT: G 16 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7718 (pp) REVERT: G 132 GLN cc_start: 0.8891 (mt0) cc_final: 0.8365 (mt0) REVERT: G 191 ASP cc_start: 0.9171 (t0) cc_final: 0.8956 (t0) REVERT: L 19 THR cc_start: 0.7059 (OUTLIER) cc_final: 0.6784 (p) REVERT: L 49 ARG cc_start: 0.8010 (ttt90) cc_final: 0.7795 (ttt90) REVERT: L 124 LYS cc_start: 0.8855 (mmtp) cc_final: 0.8413 (mttt) REVERT: L 288 LEU cc_start: 0.8533 (tt) cc_final: 0.8231 (mm) outliers start: 38 outliers final: 21 residues processed: 231 average time/residue: 0.3869 time to fit residues: 129.8477 Evaluate side-chains 216 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 188 time to evaluate : 2.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 321 THR 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 D residue 318 VAL Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 253 SER Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain 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 198 optimal weight: 4.9990 chunk 180 optimal weight: 0.5980 chunk 175 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 162 optimal weight: 0.7980 chunk 135 optimal weight: 3.9990 chunk 149 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 GLN ** D 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 281 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.130956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.086112 restraints weight = 27886.959| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 2.16 r_work: 0.2832 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20347 Z= 0.209 Angle : 0.546 10.254 27948 Z= 0.283 Chirality : 0.042 0.314 3136 Planarity : 0.004 0.048 3336 Dihedral : 19.190 170.678 3631 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.74 % Allowed : 11.28 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.17), residues: 2276 helix: 2.22 (0.18), residues: 834 sheet: 0.58 (0.24), residues: 370 loop : 0.17 (0.19), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 119 HIS 0.009 0.001 HIS E 57 PHE 0.012 0.001 PHE L 6 TYR 0.007 0.001 TYR L 239 ARG 0.007 0.000 ARG A 229 *********************** 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 239 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 206 time to evaluate : 2.098 Fit side-chains revert: symmetry clash REVERT: A 30 ARG cc_start: 0.9119 (mmt90) cc_final: 0.8771 (mmt-90) REVERT: A 106 LEU cc_start: 0.8861 (tp) cc_final: 0.8611 (tp) REVERT: A 210 LYS cc_start: 0.8612 (mtmm) cc_final: 0.8275 (mttp) REVERT: A 213 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8136 (mm-30) REVERT: A 216 GLU cc_start: 0.8939 (mt-10) cc_final: 0.8277 (mp0) REVERT: A 328 MET cc_start: 0.8948 (mtt) cc_final: 0.8700 (mtt) REVERT: C 99 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7034 (mt-10) REVERT: C 184 GLN cc_start: 0.8090 (tp40) cc_final: 0.7750 (tp-100) REVERT: C 227 GLU cc_start: 0.7144 (mm-30) cc_final: 0.6933 (mt-10) REVERT: D 78 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.6932 (mp0) REVERT: D 196 MET cc_start: 0.3310 (ptm) cc_final: 0.3055 (ptm) REVERT: E 9 LYS cc_start: 0.8882 (mttm) cc_final: 0.8652 (mttm) REVERT: E 14 GLU cc_start: 0.8823 (mp0) cc_final: 0.8485 (mp0) REVERT: E 109 LYS cc_start: 0.8448 (mttt) cc_final: 0.8201 (pttp) REVERT: E 258 THR cc_start: 0.8336 (OUTLIER) cc_final: 0.8043 (p) REVERT: E 290 GLU cc_start: 0.8569 (tm-30) cc_final: 0.8332 (pt0) REVERT: F 42 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8518 (tp30) REVERT: F 166 GLU cc_start: 0.9099 (tp30) cc_final: 0.8877 (tt0) REVERT: F 201 LYS cc_start: 0.8914 (mttp) cc_final: 0.8689 (mmtm) REVERT: G 16 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7659 (pp) REVERT: G 191 ASP cc_start: 0.9147 (t0) cc_final: 0.8923 (t0) REVERT: L 124 LYS cc_start: 0.8859 (mmtp) cc_final: 0.8196 (mttp) REVERT: L 261 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.7974 (pt0) REVERT: L 288 LEU cc_start: 0.8516 (tt) cc_final: 0.8226 (mm) outliers start: 33 outliers final: 19 residues processed: 231 average time/residue: 0.3997 time to fit residues: 133.6523 Evaluate side-chains 222 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 199 time to evaluate : 2.221 ------------------------------------------------------------------------------- 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 19 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 253 SER Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 253 SER Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 199 optimal weight: 4.9990 chunk 192 optimal weight: 0.0770 chunk 211 optimal weight: 5.9990 chunk 193 optimal weight: 0.9990 chunk 168 optimal weight: 0.0570 chunk 55 optimal weight: 0.4980 chunk 153 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 203 optimal weight: 0.5980 chunk 144 optimal weight: 7.9990 chunk 214 optimal weight: 4.9990 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 HIS ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 GLN ** D 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3655 r_free = 0.3655 target = 0.132710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.088179 restraints weight = 27742.894| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.15 r_work: 0.2875 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20347 Z= 0.161 Angle : 0.537 14.813 27948 Z= 0.278 Chirality : 0.042 0.341 3136 Planarity : 0.004 0.048 3336 Dihedral : 19.091 169.960 3631 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.48 % Allowed : 11.91 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.18), residues: 2276 helix: 2.29 (0.18), residues: 836 sheet: 0.63 (0.24), residues: 373 loop : 0.25 (0.19), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 119 HIS 0.009 0.001 HIS E 57 PHE 0.023 0.001 PHE L 6 TYR 0.014 0.001 TYR G 9 ARG 0.006 0.000 ARG A 229 *********************** 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 243 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 215 time to evaluate : 1.906 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 ARG cc_start: 0.9115 (mmt90) cc_final: 0.8759 (mmt-90) REVERT: A 106 LEU cc_start: 0.8821 (tp) cc_final: 0.8600 (tp) REVERT: A 184 GLN cc_start: 0.7923 (tm-30) cc_final: 0.7595 (mm-40) REVERT: A 210 LYS cc_start: 0.8472 (mtmm) cc_final: 0.7989 (mttp) REVERT: A 213 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8113 (mm-30) REVERT: A 216 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8258 (mp0) REVERT: A 328 MET cc_start: 0.8903 (mtt) cc_final: 0.8674 (mtt) REVERT: C 99 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7039 (mt-10) REVERT: C 149 MET cc_start: 0.8228 (ttm) cc_final: 0.7831 (mtp) REVERT: C 153 ASP cc_start: 0.7734 (t0) cc_final: 0.7393 (p0) REVERT: C 184 GLN cc_start: 0.8096 (tp40) cc_final: 0.7692 (tp-100) REVERT: D 78 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.6946 (mp0) REVERT: D 157 MET cc_start: 0.7738 (mmm) cc_final: 0.7352 (mmt) REVERT: D 196 MET cc_start: 0.3285 (ptm) cc_final: 0.3042 (ptm) REVERT: E 9 LYS cc_start: 0.8815 (mttm) cc_final: 0.8552 (mttm) REVERT: E 14 GLU cc_start: 0.8797 (mp0) cc_final: 0.8453 (mp0) REVERT: E 106 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8455 (tp) REVERT: E 109 LYS cc_start: 0.8454 (mttt) cc_final: 0.8201 (pttp) REVERT: E 136 ASN cc_start: 0.8566 (m-40) cc_final: 0.7981 (t0) REVERT: E 258 THR cc_start: 0.8285 (OUTLIER) cc_final: 0.7982 (p) REVERT: E 283 ASN cc_start: 0.7842 (p0) cc_final: 0.7533 (p0) REVERT: E 290 GLU cc_start: 0.8533 (tm-30) cc_final: 0.8312 (pt0) REVERT: E 334 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8214 (pp20) REVERT: F 105 ARG cc_start: 0.7763 (mtt180) cc_final: 0.7093 (mtt180) REVERT: F 201 LYS cc_start: 0.8906 (mttp) cc_final: 0.8685 (mmtm) REVERT: G 16 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7532 (pp) REVERT: G 228 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7899 (tp30) REVERT: L 9 LYS cc_start: 0.6082 (mtpp) cc_final: 0.5871 (mmtt) REVERT: L 124 LYS cc_start: 0.8836 (mmtp) cc_final: 0.8273 (mttp) REVERT: L 288 LEU cc_start: 0.8472 (tt) cc_final: 0.8206 (mm) outliers start: 28 outliers final: 18 residues processed: 236 average time/residue: 0.3905 time to fit residues: 134.3406 Evaluate side-chains 226 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 202 time to evaluate : 2.101 ------------------------------------------------------------------------------- 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 253 SER Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 253 SER Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain F residue 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 228 GLU Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain L residue 254 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 78 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 204 optimal weight: 0.4980 chunk 37 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 112 optimal weight: 8.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 ASN ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 GLN ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 HIS ** E 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 ASN L 281 HIS L 336 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.127214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.081565 restraints weight = 27969.907| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 2.17 r_work: 0.2761 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2617 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 20347 Z= 0.456 Angle : 0.651 15.425 27948 Z= 0.335 Chirality : 0.047 0.360 3136 Planarity : 0.004 0.048 3336 Dihedral : 19.254 173.397 3631 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.63 % Allowed : 11.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.17), residues: 2276 helix: 1.91 (0.18), residues: 848 sheet: 0.50 (0.24), residues: 367 loop : 0.10 (0.19), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 119 HIS 0.011 0.001 HIS D 284 PHE 0.022 0.002 PHE L 6 TYR 0.013 0.002 TYR L 239 ARG 0.007 0.001 ARG A 229 ********************** 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 227 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 196 time to evaluate : 2.055 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 ARG cc_start: 0.9124 (mmt90) cc_final: 0.8783 (mmt-90) REVERT: A 184 GLN cc_start: 0.7935 (tm-30) cc_final: 0.7565 (mm-40) REVERT: A 210 LYS cc_start: 0.8571 (mtmm) cc_final: 0.8070 (mttp) REVERT: A 213 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8117 (mm-30) REVERT: A 216 GLU cc_start: 0.8927 (mt-10) cc_final: 0.8243 (mp0) REVERT: A 328 MET cc_start: 0.9056 (mtt) cc_final: 0.8851 (mtt) REVERT: B 105 GLU cc_start: 0.8156 (tt0) cc_final: 0.7839 (tp30) REVERT: C 184 GLN cc_start: 0.8148 (tp40) cc_final: 0.7766 (tp-100) REVERT: D 78 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7033 (mp0) REVERT: D 196 MET cc_start: 0.3465 (ptm) cc_final: 0.3257 (ptm) REVERT: E 14 GLU cc_start: 0.8811 (mp0) cc_final: 0.8526 (mp0) REVERT: E 106 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8600 (tp) REVERT: E 109 LYS cc_start: 0.8483 (mttt) cc_final: 0.8252 (pttp) REVERT: E 258 THR cc_start: 0.8394 (OUTLIER) cc_final: 0.8094 (p) REVERT: E 290 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8382 (pt0) REVERT: F 166 GLU cc_start: 0.9080 (tt0) cc_final: 0.8859 (tt0) REVERT: F 201 LYS cc_start: 0.8937 (mttp) cc_final: 0.8705 (mmtm) REVERT: G 228 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7993 (tp30) outliers start: 31 outliers final: 21 residues processed: 221 average time/residue: 0.4058 time to fit residues: 129.4800 Evaluate side-chains 206 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 180 time to evaluate : 2.129 ------------------------------------------------------------------------------- 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 D residue 318 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 89 TRP Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain L residue 254 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 99 optimal weight: 0.5980 chunk 89 optimal weight: 9.9990 chunk 2 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 152 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 206 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 100 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 ASN ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 GLN ** D 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 HIS ** E 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 150 HIS L 281 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.130978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.086805 restraints weight = 27807.971| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.45 r_work: 0.2821 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20347 Z= 0.201 Angle : 0.570 16.094 27948 Z= 0.294 Chirality : 0.043 0.334 3136 Planarity : 0.004 0.048 3336 Dihedral : 19.160 169.996 3631 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.21 % Allowed : 12.33 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.18), residues: 2276 helix: 2.16 (0.18), residues: 835 sheet: 0.33 (0.24), residues: 382 loop : 0.23 (0.19), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 119 HIS 0.009 0.001 HIS E 57 PHE 0.024 0.001 PHE L 6 TYR 0.010 0.001 TYR F 128 ARG 0.007 0.000 ARG A 229 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11571.08 seconds wall clock time: 205 minutes 20.73 seconds (12320.73 seconds total)