Starting phenix.real_space_refine on Tue Jan 14 12:12:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s35_19688/01_2025/8s35_19688.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s35_19688/01_2025/8s35_19688.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8s35_19688/01_2025/8s35_19688.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s35_19688/01_2025/8s35_19688.map" model { file = "/net/cci-nas-00/data/ceres_data/8s35_19688/01_2025/8s35_19688.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s35_19688/01_2025/8s35_19688.cif" } resolution = 2.9 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= -0.003 sd= 0.016 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 111 5.49 5 S 93 5.16 5 C 15470 2.51 5 N 4404 2.21 5 O 5003 1.98 5 H 23571 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 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: 48653 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 5227 Classifications: {'peptide': 342} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 327} Chain: "B" Number of atoms: 5247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 5247 Classifications: {'peptide': 342} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 327} Chain: "C" Number of atoms: 5247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 5247 Classifications: {'peptide': 342} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 327} Chain: "D" Number of atoms: 5144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 5144 Classifications: {'peptide': 335} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 320} Chain breaks: 1 Chain: "E" Number of atoms: 3702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 3702 Classifications: {'peptide': 250} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 235} Chain breaks: 2 Chain: "F" Number of atoms: 3625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 3625 Classifications: {'peptide': 235} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 215} Chain: "G" Number of atoms: 4209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 4209 Classifications: {'peptide': 263} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 246} Chain: "H" Number of atoms: 1187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 1187 Classifications: {'RNA': 37} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 12, 'rna3p_pyr': 11} Link IDs: {'rna2p': 13, 'rna3p': 23} Chain: "I" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 1160 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain: "J" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 953 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Unresolved chain links: 1 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 3068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 3068 Classifications: {'peptide': 203} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 191} Chain breaks: 3 Chain: "M" Number of atoms: 9883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 624, 9883 Classifications: {'peptide': 624} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 26, 'TRANS': 597} 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 28652 SG CYS G 30 48.216 79.684 20.202 1.00184.26 S ATOM 28684 SG CYS G 33 45.855 77.176 20.587 1.00180.69 S ATOM 29064 SG CYS G 58 45.308 79.454 17.585 1.00185.26 S ATOM 29112 SG CYS G 61 44.393 80.628 20.967 1.00179.26 S Time building chain proxies: 17.28, per 1000 atoms: 0.36 Number of scatterers: 48653 At special positions: 0 Unit cell: (102.3, 134.2, 190.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 93 16.00 P 111 15.00 O 5003 8.00 N 4404 7.00 C 15470 6.00 H 23571 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 10.01 Conformation dependent library (CDL) restraints added in 2.9 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 58 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 61 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 30 " Number of angles added : 6 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5374 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 30 sheets defined 44.1% alpha, 17.2% beta 32 base pairs and 49 stacking pairs defined. Time for finding SS restraints: 18.61 Creating SS restraints... Processing helix chain 'A' and resid 44 through 65 removed outlier: 3.591A pdb=" N ILE A 48 " --> pdb=" O PRO A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 85 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 Processing helix chain 'A' and resid 154 through 160 Processing helix chain 'A' and resid 161 through 197 removed outlier: 3.969A pdb=" N GLN A 184 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS A 197 " --> pdb=" O LYS A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 209 removed outlier: 3.611A pdb=" N ILE A 209 " --> pdb=" O ALA A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 225 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 334 removed outlier: 3.543A pdb=" N PHE A 326 " --> pdb=" O GLY A 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 65 removed outlier: 3.518A pdb=" N ILE B 48 " --> pdb=" O PRO B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 85 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 160 removed outlier: 3.500A 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 224 removed outlier: 4.044A pdb=" N GLU B 206 " --> pdb=" O ASP B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 275 removed outlier: 3.685A pdb=" N ALA B 274 " --> pdb=" O ILE B 270 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU B 275 " --> pdb=" O ARG B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 285 Processing helix chain 'B' and resid 322 through 335 removed outlier: 3.703A pdb=" N PHE B 326 " --> pdb=" O GLY B 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 65 removed outlier: 3.567A 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 101 through 110 removed outlier: 3.940A pdb=" N GLU C 105 " --> pdb=" O ASN C 101 " (cutoff:3.500A) 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: 3.730A pdb=" N GLU C 158 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 194 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 225 removed outlier: 3.827A pdb=" N ALA C 205 " --> pdb=" O LYS C 201 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU C 206 " --> pdb=" O ASP C 202 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 275 removed outlier: 3.510A pdb=" N ALA C 274 " --> pdb=" O ILE C 270 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU C 275 " --> pdb=" O ARG C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 335 removed outlier: 3.548A pdb=" N PHE C 326 " --> pdb=" O GLY C 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 65 removed outlier: 3.621A 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 101 through 110 removed outlier: 4.334A pdb=" N GLU D 105 " --> pdb=" O ASN D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 117 Processing helix chain 'D' and resid 148 through 153 removed outlier: 3.633A pdb=" N ARG D 152 " --> pdb=" O ILE D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 159 Processing helix chain 'D' and resid 161 through 196 removed outlier: 3.747A 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 275 removed outlier: 3.858A pdb=" N GLU D 275 " --> pdb=" O ARG D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 285 Processing helix chain 'D' and resid 322 through 335 removed outlier: 3.615A pdb=" N PHE D 326 " --> pdb=" O GLY D 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 65 removed outlier: 3.914A 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 98 through 110 removed outlier: 4.190A pdb=" N ALA E 102 " --> pdb=" O GLY E 98 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ALA E 104 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 4.137A 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: 3.718A 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 52 removed outlier: 3.615A pdb=" N GLU F 52 " --> pdb=" O ALA F 48 " (cutoff:3.500A) 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 235 removed outlier: 4.235A pdb=" N GLY F 235 " --> pdb=" O SER F 231 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 12 removed outlier: 3.627A pdb=" N SER G 7 " --> pdb=" O HIS G 3 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL G 8 " --> pdb=" O PRO G 4 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 20 removed outlier: 3.697A pdb=" N LEU G 16 " --> pdb=" O THR G 13 " (cutoff:3.500A) Proline residue: G 18 - end of helix Processing helix chain 'G' and resid 36 through 40 removed outlier: 3.508A pdb=" N GLU G 39 " --> pdb=" O ALA G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 63 removed outlier: 3.853A 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 108 through 115 Processing helix chain 'G' and resid 116 through 123 removed outlier: 4.071A pdb=" N PHE G 120 " --> pdb=" O PRO G 116 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP G 121 " --> pdb=" O GLU G 117 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N HIS G 122 " --> pdb=" O HIS G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 140 Processing helix chain 'G' and resid 155 through 163 Processing helix chain 'G' and resid 184 through 187 Processing helix chain 'G' and resid 191 through 203 removed outlier: 3.929A 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 246 Processing helix chain 'G' and resid 249 through 261 Processing helix chain 'L' and resid 44 through 64 removed outlier: 3.678A pdb=" N ILE L 48 " --> pdb=" O PRO L 44 " (cutoff:3.500A) Processing helix chain 'L' and resid 101 through 103 No H-bonds generated for 'chain 'L' and resid 101 through 103' Processing helix chain 'L' and resid 104 through 110 Processing helix chain 'L' and resid 110 through 116 Processing helix chain 'L' and resid 258 through 275 removed outlier: 3.776A pdb=" N ALA L 274 " --> pdb=" O ILE L 270 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU L 275 " --> pdb=" O ARG L 271 " (cutoff:3.500A) Processing helix chain 'L' and resid 322 through 334 removed outlier: 4.178A pdb=" N GLU L 334 " --> pdb=" O LYS L 330 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 10 removed outlier: 3.678A pdb=" N PHE M 7 " --> pdb=" O THR M 3 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU M 8 " --> pdb=" O SER M 4 " (cutoff:3.500A) Processing helix chain 'M' and resid 15 through 31 Processing helix chain 'M' and resid 50 through 60 removed outlier: 3.899A pdb=" N LYS M 60 " --> pdb=" O LEU M 56 " (cutoff:3.500A) Processing helix chain 'M' and resid 72 through 80 removed outlier: 3.610A pdb=" N HIS M 77 " --> pdb=" O HIS M 73 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE M 80 " --> pdb=" O MET M 76 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 95 Processing helix chain 'M' and resid 113 through 120 removed outlier: 3.698A pdb=" N GLY M 117 " --> pdb=" O GLU M 113 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU M 120 " --> pdb=" O ARG M 116 " (cutoff:3.500A) Processing helix chain 'M' and resid 128 through 138 removed outlier: 4.531A pdb=" N VAL M 132 " --> pdb=" O ASP M 128 " (cutoff:3.500A) Processing helix chain 'M' and resid 142 through 147 Processing helix chain 'M' and resid 171 through 182 removed outlier: 3.780A pdb=" N SER M 182 " --> pdb=" O LEU M 178 " (cutoff:3.500A) Processing helix chain 'M' and resid 189 through 196 removed outlier: 3.786A pdb=" N VAL M 193 " --> pdb=" O THR M 189 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASP M 196 " --> pdb=" O MET M 192 " (cutoff:3.500A) Processing helix chain 'M' and resid 216 through 228 removed outlier: 4.392A pdb=" N GLU M 225 " --> pdb=" O VAL M 221 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N VAL M 226 " --> pdb=" O ASP M 222 " (cutoff:3.500A) Processing helix chain 'M' and resid 234 through 241 Processing helix chain 'M' and resid 246 through 265 removed outlier: 3.603A pdb=" N VAL M 250 " --> pdb=" O PRO M 246 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N HIS M 251 " --> pdb=" O ARG M 247 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N VAL M 252 " --> pdb=" O ASN M 248 " (cutoff:3.500A) Processing helix chain 'M' and resid 272 through 291 removed outlier: 3.712A pdb=" N ARG M 291 " --> pdb=" O SER M 287 " (cutoff:3.500A) Processing helix chain 'M' and resid 295 through 316 removed outlier: 4.227A pdb=" N GLY M 316 " --> pdb=" O LEU M 312 " (cutoff:3.500A) Processing helix chain 'M' and resid 341 through 350 removed outlier: 3.773A pdb=" N TRP M 350 " --> pdb=" O TYR M 346 " (cutoff:3.500A) Processing helix chain 'M' and resid 370 through 377 Processing helix chain 'M' and resid 380 through 384 removed outlier: 3.898A pdb=" N ILE M 384 " --> pdb=" O SER M 381 " (cutoff:3.500A) Processing helix chain 'M' and resid 414 through 417 Processing helix chain 'M' and resid 420 through 433 Processing helix chain 'M' and resid 444 through 455 Processing helix chain 'M' and resid 470 through 481 removed outlier: 3.982A pdb=" N ILE M 474 " --> pdb=" O ALA M 470 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU M 480 " --> pdb=" O LYS M 476 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS M 481 " --> pdb=" O GLN M 477 " (cutoff:3.500A) Processing helix chain 'M' and resid 519 through 534 Processing helix chain 'M' and resid 538 through 564 Processing helix chain 'M' and resid 592 through 599 Processing helix chain 'M' and resid 600 through 602 No H-bonds generated for 'chain 'M' and resid 600 through 602' Processing helix chain 'M' and resid 603 through 609 Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 132 removed outlier: 6.200A pdb=" N VAL A 125 " --> pdb=" O LYS A 255 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LYS A 255 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ILE A 127 " --> pdb=" O SER A 253 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N SER A 253 " --> pdb=" O ILE A 127 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ASN A 129 " --> pdb=" O ARG A 251 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG A 251 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N GLU A 247 " --> pdb=" O THR A 12 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N THR A 12 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N SER A 249 " --> pdb=" O ILE A 10 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ILE A 10 " --> pdb=" O SER A 249 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ARG A 251 " --> pdb=" O GLY A 8 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N GLY A 8 " --> pdb=" O ARG A 251 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N SER A 253 " --> pdb=" O PHE A 6 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N PHE A 6 " --> pdb=" O SER A 253 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LYS A 255 " --> pdb=" O LEU A 4 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU A 4 " --> pdb=" O LYS A 255 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N THR A 3 " --> pdb=" O TRP A 298 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N TRP A 298 " --> pdb=" O THR A 3 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N THR A 297 " --> pdb=" O THR A 307 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N THR A 307 " --> pdb=" O THR A 297 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 17 Processing sheet with id=AA3, first strand: chain 'B' and resid 125 through 127 Processing sheet with id=AA4, first strand: chain 'B' and resid 125 through 127 removed outlier: 6.749A pdb=" N GLU B 247 " --> pdb=" O THR B 12 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N THR B 12 " --> pdb=" O GLU B 247 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N SER B 249 " --> pdb=" O ILE B 10 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ILE B 10 " --> pdb=" O SER B 249 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ARG B 251 " --> pdb=" O GLY B 8 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N GLY B 8 " --> pdb=" O ARG B 251 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N SER B 253 " --> pdb=" O PHE B 6 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N PHE B 6 " --> pdb=" O SER B 253 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N LYS B 255 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU B 4 " --> pdb=" O LYS B 255 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N THR B 297 " --> pdb=" O THR B 307 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N THR B 307 " --> pdb=" O THR B 297 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 138 through 142 Processing sheet with id=AA6, first strand: chain 'B' and resid 145 through 146 Processing sheet with id=AA7, first strand: chain 'C' and resid 125 through 127 Processing sheet with id=AA8, first strand: chain 'C' and resid 125 through 127 removed outlier: 6.991A pdb=" N GLU C 247 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N THR C 12 " --> pdb=" O GLU C 247 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N SER C 249 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE C 10 " --> pdb=" O SER C 249 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ARG C 251 " --> pdb=" O GLY C 8 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N GLY C 8 " --> pdb=" O ARG C 251 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N SER C 253 " --> pdb=" O PHE C 6 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N PHE C 6 " --> pdb=" O SER C 253 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N LYS C 255 " --> pdb=" O LEU C 4 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU C 4 " --> pdb=" O LYS C 255 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR C 297 " --> pdb=" O THR C 307 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N THR C 307 " --> pdb=" O THR C 297 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 16 through 17 Processing sheet with id=AB1, first strand: chain 'C' and resid 144 through 146 Processing sheet with id=AB2, first strand: chain 'D' and resid 125 through 127 Processing sheet with id=AB3, first strand: chain 'D' and resid 125 through 127 removed outlier: 3.952A pdb=" N ASN D 256 " --> pdb=" O ARG D 2 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N ARG D 2 " --> pdb=" O ASN D 256 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N THR D 297 " --> pdb=" O THR D 307 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N THR D 307 " --> pdb=" O THR D 297 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 138 through 141 Processing sheet with id=AB5, first strand: chain 'E' and resid 125 through 127 Processing sheet with id=AB6, first strand: chain 'E' and resid 125 through 127 removed outlier: 6.779A pdb=" N GLU E 247 " --> pdb=" O THR E 12 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N THR E 12 " --> pdb=" O GLU E 247 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N SER E 249 " --> pdb=" O ILE E 10 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE E 10 " --> pdb=" O SER E 249 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ARG E 251 " --> pdb=" O GLY E 8 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N GLY E 8 " --> pdb=" O ARG E 251 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N SER E 253 " --> pdb=" O PHE E 6 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N PHE E 6 " --> pdb=" O SER E 253 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N LYS E 255 " --> pdb=" O LEU E 4 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU E 4 " --> pdb=" O LYS E 255 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N THR E 297 " --> pdb=" O THR E 307 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N THR E 307 " --> pdb=" O THR E 297 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 138 through 141 Processing sheet with id=AB8, first strand: chain 'F' and resid 167 through 174 removed outlier: 5.699A pdb=" N ASN F 169 " --> pdb=" O SER F 12 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N SER F 12 " --> pdb=" O ASN F 169 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS F 5 " --> pdb=" O GLY F 139 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY F 139 " --> pdb=" O LYS F 5 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 56 through 57 Processing sheet with id=AC1, first strand: chain 'F' and resid 79 through 86 Processing sheet with id=AC2, first strand: chain 'F' and resid 103 through 104 Processing sheet with id=AC3, first strand: chain 'F' and resid 182 through 183 Processing sheet with id=AC4, first strand: chain 'F' and resid 191 through 192 removed outlier: 3.639A pdb=" N LEU F 216 " --> pdb=" O SER F 204 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 24 through 25 Processing sheet with id=AC6, first strand: chain 'G' and resid 124 through 127 removed outlier: 4.164A pdb=" N GLU G 124 " --> pdb=" O SER G 103 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA G 107 " --> pdb=" O ILE G 126 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N LEU G 146 " --> pdb=" O TYR G 173 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N CYS G 175 " --> pdb=" O LEU G 146 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N TYR G 148 " --> pdb=" O CYS G 175 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 125 through 132 removed outlier: 6.032A pdb=" N VAL L 125 " --> pdb=" O LYS L 255 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LYS L 255 " --> pdb=" O VAL L 125 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ILE L 127 " --> pdb=" O SER L 253 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N SER L 253 " --> pdb=" O ILE L 127 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ASN L 129 " --> pdb=" O ARG L 251 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ARG L 251 " --> pdb=" O ASN L 129 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASN L 256 " --> pdb=" O ARG L 2 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ARG L 2 " --> pdb=" O ASN L 256 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N THR L 297 " --> pdb=" O THR L 307 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N THR L 307 " --> pdb=" O THR L 297 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU L 310 " --> pdb=" O THR L 321 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 139 through 141 Processing sheet with id=AC9, first strand: chain 'M' and resid 100 through 102 removed outlier: 6.656A pdb=" N SER M 101 " --> pdb=" O VAL M 187 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL M 67 " --> pdb=" O ILE M 213 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ASP M 215 " --> pdb=" O VAL M 67 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ALA M 69 " --> pdb=" O ASP M 215 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU M 212 " --> pdb=" O LEU M 354 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N THR M 356 " --> pdb=" O LEU M 212 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ILE M 214 " --> pdb=" O THR M 356 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER M 357 " --> pdb=" O ILE M 38 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N VAL M 35 " --> pdb=" O ILE M 386 " (cutoff:3.500A) removed outlier: 8.929A pdb=" N LYS M 388 " --> pdb=" O VAL M 35 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU M 37 " --> pdb=" O LYS M 388 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N PHE M 390 " --> pdb=" O LEU M 37 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N SER M 39 " --> pdb=" O PHE M 390 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 230 through 233 Processing sheet with id=AD2, first strand: chain 'M' and resid 462 through 464 removed outlier: 6.293A pdb=" N TYR M 463 " --> pdb=" O ILE M 486 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ALA M 438 " --> pdb=" O LEU M 485 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N SER M 487 " --> pdb=" O ALA M 438 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL M 440 " --> pdb=" O SER M 487 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU M 508 " --> pdb=" O ILE M 576 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N SER M 397 " --> pdb=" O VAL M 573 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ILE M 575 " --> pdb=" O SER M 397 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LYS M 399 " --> pdb=" O ILE M 575 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ILE M 577 " --> pdb=" O LYS M 399 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N THR M 401 " --> pdb=" O ILE M 577 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 411 through 413 1094 hydrogen bonds defined for protein. 3066 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 88 hydrogen bonds 176 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 49 stacking parallelities Total time for adding SS restraints: 16.43 Time building geometry restraints manager: 12.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 23553 1.03 - 1.23: 89 1.23 - 1.43: 10922 1.43 - 1.62: 14655 1.62 - 1.82: 163 Bond restraints: 49382 Sorted by residual: bond pdb=" CB MET M 121 " pdb=" CG MET M 121 " ideal model delta sigma weight residual 1.520 1.585 -0.065 3.00e-02 1.11e+03 4.70e+00 bond pdb=" C3' DC J 3 " pdb=" O3' DC J 3 " ideal model delta sigma weight residual 1.422 1.475 -0.053 3.00e-02 1.11e+03 3.12e+00 bond pdb=" CB GLU M 524 " pdb=" CG GLU M 524 " ideal model delta sigma weight residual 1.520 1.567 -0.047 3.00e-02 1.11e+03 2.44e+00 bond pdb=" C3' DC I -9 " pdb=" O3' DC I -9 " ideal model delta sigma weight residual 1.422 1.467 -0.045 3.00e-02 1.11e+03 2.23e+00 bond pdb=" C1' DC J 5 " pdb=" N1 DC J 5 " ideal model delta sigma weight residual 1.490 1.535 -0.045 3.00e-02 1.11e+03 2.21e+00 ... (remaining 49377 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.53: 88886 3.53 - 7.07: 245 7.07 - 10.60: 11 10.60 - 14.14: 6 14.14 - 17.67: 1 Bond angle restraints: 89149 Sorted by residual: angle pdb=" CB MET M 121 " pdb=" CG MET M 121 " pdb=" SD MET M 121 " ideal model delta sigma weight residual 112.70 130.37 -17.67 3.00e+00 1.11e-01 3.47e+01 angle pdb=" CA MET M 121 " pdb=" CB MET M 121 " pdb=" CG MET M 121 " ideal model delta sigma weight residual 114.10 124.37 -10.27 2.00e+00 2.50e-01 2.64e+01 angle pdb=" CB MET C 81 " pdb=" CG MET C 81 " pdb=" SD MET C 81 " ideal model delta sigma weight residual 112.70 126.53 -13.83 3.00e+00 1.11e-01 2.13e+01 angle pdb=" CB MET A 140 " pdb=" CG MET A 140 " pdb=" SD MET A 140 " ideal model delta sigma weight residual 112.70 125.88 -13.18 3.00e+00 1.11e-01 1.93e+01 angle pdb=" CB MET A 81 " pdb=" CG MET A 81 " pdb=" SD MET A 81 " ideal model delta sigma weight residual 112.70 125.85 -13.15 3.00e+00 1.11e-01 1.92e+01 ... (remaining 89144 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 21840 35.98 - 71.95: 1095 71.95 - 107.93: 61 107.93 - 143.91: 5 143.91 - 179.89: 10 Dihedral angle restraints: 23011 sinusoidal: 13337 harmonic: 9674 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 232.00 52.11 179.89 1 1.70e+01 3.46e-03 6.64e+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 -74.96 -85.04 1 1.50e+01 4.44e-03 3.90e+01 dihedral pdb=" O4' C H 1 " pdb=" C1' C H 1 " pdb=" N1 C H 1 " pdb=" C2 C H 1 " ideal model delta sinusoidal sigma weight residual -160.00 -87.17 -72.83 1 1.50e+01 4.44e-03 3.01e+01 ... (remaining 23008 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2606 0.034 - 0.067: 899 0.067 - 0.101: 308 0.101 - 0.134: 145 0.134 - 0.168: 24 Chirality restraints: 3982 Sorted by residual: chirality pdb=" CA TRP L 293 " pdb=" N TRP L 293 " pdb=" C TRP L 293 " pdb=" CB TRP L 293 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.05e-01 chirality pdb=" CA ILE M 513 " pdb=" N ILE M 513 " pdb=" C ILE M 513 " pdb=" CB ILE M 513 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.40e-01 chirality pdb=" CA ILE D 131 " pdb=" N ILE D 131 " pdb=" C ILE D 131 " pdb=" CB ILE D 131 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.79e-01 ... (remaining 3979 not shown) Planarity restraints: 7075 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET M 121 " -0.013 2.00e-02 2.50e+03 2.57e-02 6.62e+00 pdb=" C MET M 121 " 0.044 2.00e-02 2.50e+03 pdb=" O MET M 121 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP M 122 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL M 52 " -0.039 5.00e-02 4.00e+02 5.97e-02 5.71e+00 pdb=" N PRO M 53 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO M 53 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO M 53 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP L 293 " 0.029 2.00e-02 2.50e+03 1.11e-02 4.89e+00 pdb=" CG TRP L 293 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP L 293 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP L 293 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP L 293 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP L 293 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP L 293 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 293 " 0.016 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 293 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP L 293 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 TRP L 293 " 0.002 2.00e-02 2.50e+03 pdb=" HE1 TRP L 293 " 0.002 2.00e-02 2.50e+03 pdb=" HE3 TRP L 293 " -0.005 2.00e-02 2.50e+03 pdb=" HZ2 TRP L 293 " 0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP L 293 " -0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP L 293 " 0.000 2.00e-02 2.50e+03 ... (remaining 7072 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 3351 2.20 - 2.80: 100996 2.80 - 3.40: 142825 3.40 - 4.00: 190861 4.00 - 4.60: 289002 Nonbonded interactions: 727035 Sorted by model distance: nonbonded pdb=" OE1 GLU M 225 " pdb=" H GLU M 225 " model vdw 1.599 2.450 nonbonded pdb=" O THR C 12 " pdb=" H GLY C 245 " model vdw 1.620 2.450 nonbonded pdb=" O THR D 12 " pdb=" H GLY D 245 " model vdw 1.622 2.450 nonbonded pdb=" H HIS C 281 " pdb=" OP2 A H 15 " model vdw 1.625 2.450 nonbonded pdb=" H HIS M 33 " pdb=" O ARG M 351 " model vdw 1.629 2.450 ... (remaining 727030 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 342)) selection = (chain 'B' and (resid 1 through 52 or (resid 53 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)) or resid 54 through 56 or (resid 57 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ )) or resid 58 through 197 or resid 205 through 342)) selection = (chain 'C' and (resid 1 through 52 or (resid 53 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)) or resid 54 through 56 or (resid 57 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ )) or resid 58 through 197 or resid 205 through 342)) selection = (chain 'D' and (resid 1 through 52 or (resid 53 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)) or resid 54 through 56 or (resid 57 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ )) or resid 58 through 342)) } 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: 1.840 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: 0.670 Extract box with map and model: 1.460 Check model and map are aligned: 0.270 Set scattering table: 0.350 Process input model: 107.600 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.130 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:10.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 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 : 0.004 0.065 25811 Z= 0.248 Angle : 0.727 17.674 35415 Z= 0.377 Chirality : 0.043 0.168 3982 Planarity : 0.005 0.060 4238 Dihedral : 18.953 179.886 9978 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Rotamer: Outliers : 0.82 % Allowed : 13.87 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: -0.29 (0.15), residues: 2906 helix: 0.75 (0.15), residues: 1150 sheet: -0.49 (0.25), residues: 421 loop : -0.87 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP L 293 HIS 0.011 0.001 HIS L 250 PHE 0.016 0.001 PHE M 338 TYR 0.018 0.001 TYR F 157 ARG 0.003 0.000 ARG E 49 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 3.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 GLU cc_start: 0.9009 (OUTLIER) cc_final: 0.8639 (mm-30) REVERT: C 1 MET cc_start: 0.8505 (mtp) cc_final: 0.8182 (mtt) REVERT: C 140 MET cc_start: 0.9423 (mmm) cc_final: 0.9107 (mmm) REVERT: C 196 MET cc_start: 0.9006 (mtt) cc_final: 0.8624 (mmt) REVERT: C 286 CYS cc_start: 0.9108 (m) cc_final: 0.8830 (m) REVERT: D 81 MET cc_start: 0.9094 (tpp) cc_final: 0.8686 (tpp) REVERT: E 81 MET cc_start: 0.8837 (tpp) cc_final: 0.8496 (tpt) REVERT: E 261 GLU cc_start: 0.9411 (OUTLIER) cc_final: 0.9199 (mm-30) REVERT: F 60 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8684 (tt) REVERT: F 158 ASP cc_start: 0.8028 (p0) cc_final: 0.7588 (p0) REVERT: G 20 MET cc_start: 0.9376 (mpp) cc_final: 0.9117 (mpt) REVERT: G 150 GLN cc_start: 0.9279 (OUTLIER) cc_final: 0.8094 (tm-30) REVERT: L 114 SER cc_start: 0.9104 (t) cc_final: 0.8859 (m) REVERT: L 138 TRP cc_start: 0.9139 (p90) cc_final: 0.8753 (p-90) REVERT: M 192 MET cc_start: 0.9291 (mmm) cc_final: 0.8978 (mmm) REVERT: M 398 MET cc_start: 0.9344 (ttm) cc_final: 0.8859 (tmm) outliers start: 20 outliers final: 16 residues processed: 162 average time/residue: 2.2369 time to fit residues: 428.9002 Evaluate side-chains 155 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 2.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain E residue 38 ASN Chi-restraints excluded: chain E residue 255 LYS Chi-restraints excluded: chain E residue 261 GLU Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 150 GLN Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 200 GLN Chi-restraints excluded: chain G residue 211 ASP Chi-restraints excluded: chain L residue 281 HIS Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 94 CYS Chi-restraints excluded: chain M residue 357 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 8.9990 chunk 227 optimal weight: 6.9990 chunk 126 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 153 optimal weight: 7.9990 chunk 121 optimal weight: 0.6980 chunk 235 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 chunk 175 optimal weight: 3.9990 chunk 272 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN C 224 GLN E 336 GLN G 118 HIS ** L 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 460 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.061441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.043036 restraints weight = 324368.645| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 4.16 r_work: 0.2829 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.0770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 25811 Z= 0.274 Angle : 0.583 7.581 35415 Z= 0.313 Chirality : 0.041 0.165 3982 Planarity : 0.005 0.081 4238 Dihedral : 19.888 179.231 4556 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.03 % Allowed : 12.76 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: 0.19 (0.16), residues: 2906 helix: 1.42 (0.15), residues: 1144 sheet: -0.83 (0.24), residues: 440 loop : -0.62 (0.17), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 372 HIS 0.005 0.001 HIS C 281 PHE 0.010 0.001 PHE B 332 TYR 0.010 0.001 TYR F 128 ARG 0.006 0.000 ARG M 235 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 2.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 GLU cc_start: 0.9163 (OUTLIER) cc_final: 0.8883 (mm-30) REVERT: B 81 MET cc_start: 0.8711 (tmm) cc_final: 0.8171 (tmm) REVERT: C 1 MET cc_start: 0.8462 (mtp) cc_final: 0.8096 (mtt) REVERT: C 140 MET cc_start: 0.9408 (mmm) cc_final: 0.9089 (mmm) REVERT: C 196 MET cc_start: 0.9030 (mtt) cc_final: 0.8629 (mmt) REVERT: D 81 MET cc_start: 0.9070 (tpp) cc_final: 0.8720 (tpp) REVERT: E 81 MET cc_start: 0.8737 (tpp) cc_final: 0.8350 (tpt) REVERT: E 140 MET cc_start: 0.9415 (mmm) cc_final: 0.9209 (mmm) REVERT: F 60 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8825 (tm) REVERT: F 158 ASP cc_start: 0.8066 (p0) cc_final: 0.7725 (p0) REVERT: G 20 MET cc_start: 0.9314 (mpp) cc_final: 0.8989 (mpt) REVERT: G 150 GLN cc_start: 0.9341 (OUTLIER) cc_final: 0.8130 (tm-30) REVERT: L 114 SER cc_start: 0.9022 (t) cc_final: 0.8736 (m) REVERT: L 138 TRP cc_start: 0.9202 (p90) cc_final: 0.8914 (p-90) REVERT: M 192 MET cc_start: 0.9240 (mmm) cc_final: 0.8865 (mmm) REVERT: M 212 LEU cc_start: 0.9807 (tp) cc_final: 0.9448 (tp) REVERT: M 398 MET cc_start: 0.9267 (ttm) cc_final: 0.8804 (tmm) outliers start: 25 outliers final: 14 residues processed: 157 average time/residue: 2.0273 time to fit residues: 380.8863 Evaluate side-chains 144 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 2.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain D residue 37 PHE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain E residue 38 ASN Chi-restraints excluded: chain E residue 255 LYS Chi-restraints excluded: chain E residue 261 GLU Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 150 GLN Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain L residue 286 CYS Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 94 CYS Chi-restraints excluded: chain M residue 139 TRP Chi-restraints excluded: chain M residue 357 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 50 optimal weight: 3.9990 chunk 111 optimal weight: 9.9990 chunk 126 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 185 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 279 optimal weight: 0.9980 chunk 225 optimal weight: 20.0000 chunk 255 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 275 optimal weight: 3.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN M 73 HIS M 417 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.061469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.043045 restraints weight = 323836.132| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 4.20 r_work: 0.2833 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25811 Z= 0.272 Angle : 0.566 8.567 35415 Z= 0.302 Chirality : 0.041 0.156 3982 Planarity : 0.004 0.061 4238 Dihedral : 19.735 179.136 4538 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.23 % Allowed : 12.76 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.16), residues: 2906 helix: 1.56 (0.15), residues: 1152 sheet: -0.84 (0.24), residues: 455 loop : -0.68 (0.17), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 372 HIS 0.005 0.001 HIS E 54 PHE 0.011 0.001 PHE B 332 TYR 0.015 0.001 TYR L 42 ARG 0.004 0.000 ARG A 251 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 2.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 GLU cc_start: 0.9234 (OUTLIER) cc_final: 0.8908 (mm-30) REVERT: C 1 MET cc_start: 0.8533 (mtp) cc_final: 0.8129 (mtt) REVERT: C 81 MET cc_start: 0.8978 (tpp) cc_final: 0.8755 (tpp) REVERT: C 140 MET cc_start: 0.9400 (mmm) cc_final: 0.9052 (mmm) REVERT: C 196 MET cc_start: 0.8958 (mtt) cc_final: 0.8567 (mmt) REVERT: D 81 MET cc_start: 0.9042 (tpp) cc_final: 0.8697 (tpp) REVERT: E 140 MET cc_start: 0.9383 (mmm) cc_final: 0.9096 (mmm) REVERT: F 60 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8799 (tm) REVERT: G 150 GLN cc_start: 0.9345 (OUTLIER) cc_final: 0.8238 (tm-30) REVERT: M 104 MET cc_start: 0.6960 (OUTLIER) cc_final: 0.6517 (ppp) REVERT: M 192 MET cc_start: 0.9215 (mmm) cc_final: 0.8836 (mmp) REVERT: M 212 LEU cc_start: 0.9820 (tp) cc_final: 0.9441 (tp) REVERT: M 370 MET cc_start: 0.8865 (mpp) cc_final: 0.8623 (mpp) REVERT: M 398 MET cc_start: 0.9305 (ttm) cc_final: 0.8814 (tmm) outliers start: 30 outliers final: 15 residues processed: 150 average time/residue: 2.0025 time to fit residues: 360.2014 Evaluate side-chains 139 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 2.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain D residue 37 PHE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain E residue 261 GLU Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 150 GLN Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain L residue 286 CYS Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 94 CYS Chi-restraints excluded: chain M residue 104 MET Chi-restraints excluded: chain M residue 139 TRP Chi-restraints excluded: chain M residue 357 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 83 optimal weight: 5.9990 chunk 218 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 200 optimal weight: 5.9990 chunk 257 optimal weight: 10.0000 chunk 283 optimal weight: 7.9990 chunk 236 optimal weight: 10.0000 chunk 147 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN D 184 GLN ** E 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.060577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.042050 restraints weight = 325952.105| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 4.17 r_work: 0.2800 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 25811 Z= 0.331 Angle : 0.585 9.369 35415 Z= 0.312 Chirality : 0.041 0.155 3982 Planarity : 0.004 0.060 4238 Dihedral : 19.731 179.144 4529 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.31 % Allowed : 13.25 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: 0.23 (0.16), residues: 2906 helix: 1.61 (0.15), residues: 1156 sheet: -0.99 (0.24), residues: 433 loop : -0.72 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 372 HIS 0.006 0.001 HIS E 54 PHE 0.013 0.001 PHE B 332 TYR 0.011 0.001 TYR F 128 ARG 0.004 0.000 ARG M 231 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 2.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.8543 (mtp) cc_final: 0.8151 (mtt) REVERT: C 140 MET cc_start: 0.9374 (mmm) cc_final: 0.9025 (mmm) REVERT: C 196 MET cc_start: 0.8957 (mtt) cc_final: 0.8521 (mmt) REVERT: C 286 CYS cc_start: 0.9362 (m) cc_final: 0.9102 (m) REVERT: D 81 MET cc_start: 0.9036 (tpp) cc_final: 0.8785 (tpp) REVERT: E 81 MET cc_start: 0.8474 (tpt) cc_final: 0.8151 (tpp) REVERT: F 60 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8785 (tm) REVERT: G 150 GLN cc_start: 0.9376 (OUTLIER) cc_final: 0.8226 (tm-30) REVERT: G 210 MET cc_start: 0.9227 (tpp) cc_final: 0.8816 (tmm) REVERT: M 104 MET cc_start: 0.7285 (ptp) cc_final: 0.7015 (ppp) REVERT: M 192 MET cc_start: 0.9157 (mmm) cc_final: 0.8735 (mmp) REVERT: M 212 LEU cc_start: 0.9818 (tp) cc_final: 0.9434 (tp) REVERT: M 398 MET cc_start: 0.9269 (ttm) cc_final: 0.8819 (tmm) outliers start: 32 outliers final: 20 residues processed: 152 average time/residue: 1.9584 time to fit residues: 358.2379 Evaluate side-chains 138 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 2.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain D residue 37 PHE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain E residue 261 GLU Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 150 GLN Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain L residue 286 CYS Chi-restraints excluded: chain M residue 94 CYS Chi-restraints excluded: chain M residue 139 TRP Chi-restraints excluded: chain M residue 210 MET Chi-restraints excluded: chain M residue 357 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 200 optimal weight: 5.9990 chunk 282 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 197 optimal weight: 4.9990 chunk 170 optimal weight: 0.6980 chunk 150 optimal weight: 6.9990 chunk 12 optimal weight: 0.6980 chunk 188 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 287 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 5 ASN ** E 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 57 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.059841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.041029 restraints weight = 327286.120| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 4.17 r_work: 0.2773 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 25811 Z= 0.381 Angle : 0.606 8.901 35415 Z= 0.324 Chirality : 0.041 0.153 3982 Planarity : 0.004 0.054 4238 Dihedral : 19.782 179.129 4527 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.56 % Allowed : 13.83 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: 0.12 (0.16), residues: 2906 helix: 1.57 (0.15), residues: 1158 sheet: -1.14 (0.23), residues: 430 loop : -0.82 (0.17), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 372 HIS 0.006 0.001 HIS E 54 PHE 0.016 0.001 PHE M 7 TYR 0.019 0.001 TYR G 157 ARG 0.004 0.000 ARG M 231 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 119 time to evaluate : 2.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 140 MET cc_start: 0.9267 (mmm) cc_final: 0.8673 (mmm) REVERT: C 1 MET cc_start: 0.8555 (mtp) cc_final: 0.8222 (mtt) REVERT: C 81 MET cc_start: 0.9078 (tpp) cc_final: 0.8842 (tpp) REVERT: C 140 MET cc_start: 0.9377 (mmm) cc_final: 0.9020 (mmm) REVERT: C 196 MET cc_start: 0.8947 (mtt) cc_final: 0.8526 (mmt) REVERT: D 81 MET cc_start: 0.9028 (tpp) cc_final: 0.8758 (tpp) REVERT: F 60 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8786 (tm) REVERT: F 145 GLU cc_start: 0.9259 (OUTLIER) cc_final: 0.8899 (tm-30) REVERT: G 150 GLN cc_start: 0.9390 (OUTLIER) cc_final: 0.8485 (tm-30) REVERT: G 189 MET cc_start: 0.8574 (tmm) cc_final: 0.8360 (tmm) REVERT: M 192 MET cc_start: 0.9160 (mmm) cc_final: 0.8715 (mmp) REVERT: M 370 MET cc_start: 0.9007 (mpp) cc_final: 0.8747 (mpp) REVERT: M 398 MET cc_start: 0.9233 (ttm) cc_final: 0.8893 (tmm) outliers start: 38 outliers final: 22 residues processed: 150 average time/residue: 2.1265 time to fit residues: 379.4896 Evaluate side-chains 140 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 2.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain D residue 37 PHE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain E residue 2 ARG Chi-restraints excluded: chain E residue 261 GLU Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 150 GLN Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain L residue 286 CYS Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 94 CYS Chi-restraints excluded: chain M residue 139 TRP Chi-restraints excluded: chain M residue 210 MET Chi-restraints excluded: chain M residue 357 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 118 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 289 optimal weight: 0.9980 chunk 140 optimal weight: 4.9990 chunk 124 optimal weight: 8.9990 chunk 159 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 278 optimal weight: 5.9990 chunk 222 optimal weight: 9.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.059559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.040672 restraints weight = 327406.438| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 4.11 r_work: 0.2745 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 25811 Z= 0.350 Angle : 0.597 11.042 35415 Z= 0.317 Chirality : 0.041 0.171 3982 Planarity : 0.004 0.053 4238 Dihedral : 19.805 179.240 4524 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.68 % Allowed : 13.99 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: 0.13 (0.16), residues: 2906 helix: 1.62 (0.15), residues: 1158 sheet: -1.23 (0.23), residues: 431 loop : -0.81 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 372 HIS 0.006 0.001 HIS E 54 PHE 0.014 0.001 PHE B 332 TYR 0.012 0.001 TYR L 42 ARG 0.003 0.000 ARG M 231 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 115 time to evaluate : 2.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 140 MET cc_start: 0.9236 (mmm) cc_final: 0.8686 (mmm) REVERT: C 81 MET cc_start: 0.9128 (tpp) cc_final: 0.8888 (tpp) REVERT: C 140 MET cc_start: 0.9358 (mmm) cc_final: 0.8988 (mmm) REVERT: C 196 MET cc_start: 0.8946 (mtt) cc_final: 0.8524 (mmt) REVERT: C 286 CYS cc_start: 0.9352 (m) cc_final: 0.9104 (m) REVERT: D 81 MET cc_start: 0.9081 (tpp) cc_final: 0.8780 (tpp) REVERT: E 81 MET cc_start: 0.8876 (tpp) cc_final: 0.8569 (tpp) REVERT: F 60 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8829 (tm) REVERT: F 145 GLU cc_start: 0.9242 (OUTLIER) cc_final: 0.8884 (tm-30) REVERT: G 150 GLN cc_start: 0.9432 (OUTLIER) cc_final: 0.8487 (tm-30) REVERT: M 192 MET cc_start: 0.9175 (mmm) cc_final: 0.8728 (mmp) REVERT: M 210 MET cc_start: 0.9349 (OUTLIER) cc_final: 0.9098 (mpp) REVERT: M 370 MET cc_start: 0.9202 (mpp) cc_final: 0.8785 (mpp) REVERT: M 398 MET cc_start: 0.9172 (ttm) cc_final: 0.8930 (tmm) REVERT: M 624 CYS cc_start: 0.8054 (t) cc_final: 0.7757 (p) outliers start: 41 outliers final: 26 residues processed: 149 average time/residue: 1.9722 time to fit residues: 353.4653 Evaluate side-chains 144 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 3.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain D residue 37 PHE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain E residue 2 ARG Chi-restraints excluded: chain E residue 261 GLU Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 150 GLN Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 206 SER Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain L residue 281 HIS Chi-restraints excluded: chain L residue 284 HIS Chi-restraints excluded: chain L residue 286 CYS Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 94 CYS Chi-restraints excluded: chain M residue 104 MET Chi-restraints excluded: chain M residue 139 TRP Chi-restraints excluded: chain M residue 210 MET Chi-restraints excluded: chain M residue 357 SER Chi-restraints excluded: chain M residue 374 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 153 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 277 optimal weight: 10.0000 chunk 199 optimal weight: 0.5980 chunk 105 optimal weight: 0.8980 chunk 168 optimal weight: 3.9990 chunk 298 optimal weight: 0.6980 chunk 285 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.060318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.041560 restraints weight = 323270.001| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 4.13 r_work: 0.2772 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25811 Z= 0.233 Angle : 0.570 11.469 35415 Z= 0.298 Chirality : 0.041 0.154 3982 Planarity : 0.004 0.052 4238 Dihedral : 19.818 179.763 4524 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.48 % Allowed : 14.49 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: 0.21 (0.16), residues: 2906 helix: 1.70 (0.16), residues: 1165 sheet: -1.33 (0.23), residues: 431 loop : -0.72 (0.17), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 372 HIS 0.005 0.001 HIS D 281 PHE 0.010 0.001 PHE M 283 TYR 0.012 0.001 TYR L 42 ARG 0.003 0.000 ARG C 2 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 122 time to evaluate : 3.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 140 MET cc_start: 0.9191 (mmm) cc_final: 0.8613 (mmm) REVERT: C 140 MET cc_start: 0.9369 (mmm) cc_final: 0.8983 (mmm) REVERT: C 196 MET cc_start: 0.8929 (mtt) cc_final: 0.8506 (mmt) REVERT: C 286 CYS cc_start: 0.9342 (m) cc_final: 0.9082 (m) REVERT: D 81 MET cc_start: 0.9091 (tpp) cc_final: 0.8811 (tpp) REVERT: E 81 MET cc_start: 0.8869 (tpp) cc_final: 0.8548 (tpp) REVERT: F 60 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8831 (tm) REVERT: F 145 GLU cc_start: 0.9220 (OUTLIER) cc_final: 0.8856 (tm-30) REVERT: G 150 GLN cc_start: 0.9431 (OUTLIER) cc_final: 0.8530 (tm-30) REVERT: G 210 MET cc_start: 0.9142 (OUTLIER) cc_final: 0.8845 (tmm) REVERT: M 210 MET cc_start: 0.9353 (OUTLIER) cc_final: 0.9086 (mpp) REVERT: M 370 MET cc_start: 0.9233 (mpp) cc_final: 0.8840 (mpp) REVERT: M 398 MET cc_start: 0.9145 (ttm) cc_final: 0.8926 (tmm) REVERT: M 624 CYS cc_start: 0.8042 (t) cc_final: 0.7761 (p) outliers start: 36 outliers final: 23 residues processed: 150 average time/residue: 2.0578 time to fit residues: 370.5572 Evaluate side-chains 144 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 116 time to evaluate : 2.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain D residue 37 PHE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain E residue 261 GLU Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 150 GLN Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain L residue 281 HIS Chi-restraints excluded: chain L residue 284 HIS Chi-restraints excluded: chain L residue 286 CYS Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 94 CYS Chi-restraints excluded: chain M residue 104 MET Chi-restraints excluded: chain M residue 139 TRP Chi-restraints excluded: chain M residue 210 MET Chi-restraints excluded: chain M residue 357 SER Chi-restraints excluded: chain M residue 374 CYS Chi-restraints excluded: chain M residue 400 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 140 optimal weight: 7.9990 chunk 178 optimal weight: 3.9990 chunk 234 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 120 optimal weight: 9.9990 chunk 106 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 268 optimal weight: 6.9990 chunk 279 optimal weight: 0.8980 chunk 292 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.059777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.040861 restraints weight = 325410.111| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 4.14 r_work: 0.2756 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 25811 Z= 0.298 Angle : 0.590 12.284 35415 Z= 0.309 Chirality : 0.041 0.154 3982 Planarity : 0.004 0.049 4238 Dihedral : 19.815 179.878 4523 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.35 % Allowed : 14.81 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: 0.21 (0.16), residues: 2906 helix: 1.70 (0.15), residues: 1166 sheet: -1.29 (0.23), residues: 431 loop : -0.75 (0.17), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 293 HIS 0.005 0.001 HIS E 54 PHE 0.012 0.001 PHE B 332 TYR 0.010 0.001 TYR L 42 ARG 0.009 0.000 ARG E 2 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 117 time to evaluate : 2.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 140 MET cc_start: 0.9199 (mmm) cc_final: 0.8638 (mmm) REVERT: C 81 MET cc_start: 0.9126 (tpp) cc_final: 0.8905 (tpp) REVERT: C 140 MET cc_start: 0.9360 (mmm) cc_final: 0.8973 (mmm) REVERT: C 196 MET cc_start: 0.8932 (mtt) cc_final: 0.8510 (mmt) REVERT: D 81 MET cc_start: 0.9097 (tpp) cc_final: 0.8814 (tpp) REVERT: E 81 MET cc_start: 0.8866 (tpp) cc_final: 0.8505 (tpp) REVERT: F 60 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8837 (tm) REVERT: F 145 GLU cc_start: 0.9197 (OUTLIER) cc_final: 0.8862 (tm-30) REVERT: G 82 THR cc_start: 0.9479 (OUTLIER) cc_final: 0.9256 (p) REVERT: G 150 GLN cc_start: 0.9420 (OUTLIER) cc_final: 0.8537 (tm-30) REVERT: G 210 MET cc_start: 0.9094 (OUTLIER) cc_final: 0.8813 (tmm) REVERT: M 210 MET cc_start: 0.9370 (OUTLIER) cc_final: 0.9112 (mpp) REVERT: M 370 MET cc_start: 0.9258 (mpp) cc_final: 0.8891 (mpp) REVERT: M 398 MET cc_start: 0.9137 (ttm) cc_final: 0.8769 (tmm) REVERT: M 624 CYS cc_start: 0.8077 (t) cc_final: 0.7868 (p) outliers start: 33 outliers final: 21 residues processed: 142 average time/residue: 2.0770 time to fit residues: 355.9407 Evaluate side-chains 141 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 2.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain D residue 37 PHE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 150 GLN Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain L residue 281 HIS Chi-restraints excluded: chain L residue 284 HIS Chi-restraints excluded: chain L residue 286 CYS Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 94 CYS Chi-restraints excluded: chain M residue 104 MET Chi-restraints excluded: chain M residue 139 TRP Chi-restraints excluded: chain M residue 210 MET Chi-restraints excluded: chain M residue 357 SER Chi-restraints excluded: chain M residue 374 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 46 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 225 optimal weight: 10.0000 chunk 109 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 129 optimal weight: 0.4980 chunk 229 optimal weight: 10.0000 chunk 197 optimal weight: 3.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.059576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.040653 restraints weight = 324211.084| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 4.12 r_work: 0.2750 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 25811 Z= 0.307 Angle : 0.595 12.671 35415 Z= 0.312 Chirality : 0.041 0.154 3982 Planarity : 0.004 0.049 4238 Dihedral : 19.826 179.919 4520 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.35 % Allowed : 15.14 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: 0.21 (0.16), residues: 2906 helix: 1.73 (0.15), residues: 1163 sheet: -1.33 (0.23), residues: 418 loop : -0.78 (0.17), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 89 HIS 0.005 0.001 HIS E 54 PHE 0.012 0.001 PHE B 332 TYR 0.010 0.001 TYR L 42 ARG 0.004 0.000 ARG E 2 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 2.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 140 MET cc_start: 0.9351 (mmm) cc_final: 0.8970 (mmm) REVERT: C 196 MET cc_start: 0.8927 (mtt) cc_final: 0.8468 (mmt) REVERT: D 81 MET cc_start: 0.9100 (tpp) cc_final: 0.8822 (tpp) REVERT: E 324 GLU cc_start: 0.9172 (OUTLIER) cc_final: 0.8642 (tm-30) REVERT: F 60 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8843 (tm) REVERT: F 145 GLU cc_start: 0.9191 (OUTLIER) cc_final: 0.8864 (tm-30) REVERT: G 150 GLN cc_start: 0.9407 (OUTLIER) cc_final: 0.8579 (tm-30) REVERT: G 210 MET cc_start: 0.9108 (OUTLIER) cc_final: 0.8807 (tmm) REVERT: M 104 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.7481 (ppp) REVERT: M 192 MET cc_start: 0.9115 (mmm) cc_final: 0.8701 (mmp) REVERT: M 210 MET cc_start: 0.9390 (OUTLIER) cc_final: 0.9094 (mpp) REVERT: M 370 MET cc_start: 0.9344 (mpp) cc_final: 0.8803 (mpp) REVERT: M 398 MET cc_start: 0.9117 (ttm) cc_final: 0.8876 (tmm) REVERT: M 450 MET cc_start: 0.9177 (mmm) cc_final: 0.8939 (mpm) REVERT: M 624 CYS cc_start: 0.8142 (t) cc_final: 0.7923 (p) outliers start: 33 outliers final: 21 residues processed: 144 average time/residue: 2.1669 time to fit residues: 373.5073 Evaluate side-chains 143 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 2.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain D residue 37 PHE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 150 GLN Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain L residue 281 HIS Chi-restraints excluded: chain L residue 284 HIS Chi-restraints excluded: chain L residue 286 CYS Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 94 CYS Chi-restraints excluded: chain M residue 104 MET Chi-restraints excluded: chain M residue 139 TRP Chi-restraints excluded: chain M residue 210 MET Chi-restraints excluded: chain M residue 357 SER Chi-restraints excluded: chain M residue 374 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 147 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 170 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 277 optimal weight: 8.9990 chunk 146 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 254 optimal weight: 20.0000 chunk 103 optimal weight: 0.8980 chunk 134 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.060245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.041197 restraints weight = 324436.932| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 4.19 r_work: 0.2769 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 25811 Z= 0.227 Angle : 0.582 13.211 35415 Z= 0.301 Chirality : 0.040 0.153 3982 Planarity : 0.004 0.049 4238 Dihedral : 19.832 179.680 4520 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.23 % Allowed : 15.18 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: 0.31 (0.16), residues: 2906 helix: 1.83 (0.16), residues: 1158 sheet: -1.36 (0.23), residues: 422 loop : -0.70 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 89 HIS 0.005 0.001 HIS G 3 PHE 0.027 0.001 PHE M 7 TYR 0.010 0.001 TYR L 42 ARG 0.005 0.000 ARG E 2 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 2.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 140 MET cc_start: 0.9179 (mmm) cc_final: 0.8582 (mmm) REVERT: C 140 MET cc_start: 0.9356 (mmm) cc_final: 0.8965 (mmm) REVERT: D 81 MET cc_start: 0.9111 (tpp) cc_final: 0.8874 (tpp) REVERT: F 60 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8844 (tm) REVERT: F 145 GLU cc_start: 0.9148 (OUTLIER) cc_final: 0.8809 (tm-30) REVERT: G 82 THR cc_start: 0.9450 (OUTLIER) cc_final: 0.9237 (p) REVERT: G 150 GLN cc_start: 0.9409 (OUTLIER) cc_final: 0.8593 (tm-30) REVERT: G 210 MET cc_start: 0.9124 (OUTLIER) cc_final: 0.8830 (tmm) REVERT: M 104 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.7284 (ppp) REVERT: M 210 MET cc_start: 0.9377 (OUTLIER) cc_final: 0.9114 (mpp) REVERT: M 370 MET cc_start: 0.9295 (mpp) cc_final: 0.8698 (mpp) REVERT: M 398 MET cc_start: 0.9112 (ttm) cc_final: 0.8857 (tmm) outliers start: 30 outliers final: 20 residues processed: 138 average time/residue: 2.0507 time to fit residues: 340.5344 Evaluate side-chains 141 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 2.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain D residue 37 PHE Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 150 GLN Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain L residue 281 HIS Chi-restraints excluded: chain L residue 284 HIS Chi-restraints excluded: chain L residue 286 CYS Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 94 CYS Chi-restraints excluded: chain M residue 104 MET Chi-restraints excluded: chain M residue 139 TRP Chi-restraints excluded: chain M residue 210 MET Chi-restraints excluded: chain M residue 357 SER Chi-restraints excluded: chain M residue 374 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 224 optimal weight: 10.0000 chunk 248 optimal weight: 30.0000 chunk 233 optimal weight: 10.0000 chunk 152 optimal weight: 3.9990 chunk 211 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 212 optimal weight: 8.9990 chunk 116 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 287 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN ** E 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.058102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.038904 restraints weight = 334257.862| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 4.16 r_work: 0.2694 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.073 25811 Z= 0.520 Angle : 0.694 12.758 35415 Z= 0.368 Chirality : 0.043 0.154 3982 Planarity : 0.004 0.048 4238 Dihedral : 19.887 179.318 4520 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 1.19 % Allowed : 15.51 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: -0.09 (0.15), residues: 2906 helix: 1.52 (0.15), residues: 1163 sheet: -1.30 (0.24), residues: 423 loop : -1.06 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP M 227 HIS 0.008 0.002 HIS E 54 PHE 0.021 0.002 PHE B 332 TYR 0.013 0.002 TYR D 42 ARG 0.005 0.001 ARG M 231 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21959.71 seconds wall clock time: 375 minutes 3.51 seconds (22503.51 seconds total)