Starting phenix.real_space_refine on Mon Jan 13 19:02:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s36_19689/01_2025/8s36_19689.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s36_19689/01_2025/8s36_19689.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/8s36_19689/01_2025/8s36_19689.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s36_19689/01_2025/8s36_19689.map" model { file = "/net/cci-nas-00/data/ceres_data/8s36_19689/01_2025/8s36_19689.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s36_19689/01_2025/8s36_19689.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= -0.002 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 107 5.49 5 S 89 5.16 5 C 14959 2.51 5 N 4250 2.21 5 O 4843 1.98 5 H 23099 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: 47348 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 5252 Classifications: {'peptide': 342} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 327} Chain: "B" Number of atoms: 5252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 5252 Classifications: {'peptide': 342} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 327} Chain: "C" Number of atoms: 5252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 5252 Classifications: {'peptide': 342} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 327} Chain: "D" Number of atoms: 5251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 5251 Classifications: {'peptide': 342} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 327} Chain: "E" Number of atoms: 3720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 3720 Classifications: {'peptide': 249} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 234} 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': 6, 'rna3p_pur': 12, 'rna3p_pyr': 12} Link IDs: {'rna2p': 13, 'rna3p': 23} Chain: "I" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 1230 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain: "J" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 1019 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "L" Number of atoms: 3113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 3113 Classifications: {'peptide': 204} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 192} Chain breaks: 3 Chain: "M" Number of atoms: 8237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 8237 Classifications: {'peptide': 519} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 23, 'TRANS': 495} 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 28812 SG CYS G 30 48.621 77.609 20.219 1.00199.52 S ATOM 28844 SG CYS G 33 46.327 74.874 20.665 1.00189.20 S ATOM 29224 SG CYS G 58 45.519 77.382 17.942 1.00188.71 S ATOM 29272 SG CYS G 61 44.996 78.605 21.283 1.00157.27 S Time building chain proxies: 16.81, per 1000 atoms: 0.36 Number of scatterers: 47348 At special positions: 0 Unit cell: (103.4, 133.1, 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 89 16.00 P 107 15.00 O 4843 8.00 N 4250 7.00 C 14959 6.00 H 23099 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: 9.54 Conformation dependent library (CDL) restraints added in 2.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN G 301 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 58 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 30 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 33 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 61 " Number of angles added : 6 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5198 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 29 sheets defined 43.1% alpha, 17.2% beta 34 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 16.66 Creating SS restraints... Processing helix chain 'A' and resid 44 through 65 removed outlier: 3.654A pdb=" N ILE A 48 " --> pdb=" O PRO A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 84 Processing helix chain 'A' and resid 103 through 110 Processing helix chain 'A' and resid 110 through 116 Processing helix chain 'A' and resid 148 through 153 Processing helix chain 'A' and resid 154 through 158 Processing helix chain 'A' and resid 161 through 199 removed outlier: 3.674A pdb=" N ARG A 167 " --> pdb=" O ASP A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 225 removed outlier: 3.762A pdb=" N LYS A 225 " --> pdb=" O ARG A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 273 Processing helix chain 'A' and resid 281 through 285 Processing helix chain 'A' and resid 322 through 335 Processing helix chain 'B' and resid 44 through 65 removed outlier: 3.532A pdb=" N ILE B 48 " --> pdb=" O PRO B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 84 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 Processing helix chain 'B' and resid 161 through 196 Processing helix chain 'B' and resid 200 through 224 removed outlier: 3.862A pdb=" N ALA B 205 " --> pdb=" O LYS B 201 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLU B 206 " --> pdb=" O ASP B 202 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU B 214 " --> pdb=" O LYS B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 275 removed outlier: 3.613A pdb=" N ALA B 274 " --> pdb=" O ILE B 270 " (cutoff:3.500A) removed outlier: 3.922A 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 Processing helix chain 'C' and resid 44 through 65 Processing helix chain 'C' and resid 75 through 85 Processing helix chain 'C' and resid 101 through 110 removed outlier: 4.842A 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 Processing helix chain 'C' and resid 161 through 197 removed outlier: 3.977A pdb=" N LYS C 197 " --> pdb=" O LYS C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 225 removed outlier: 3.747A pdb=" N LYS C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 275 removed outlier: 3.749A pdb=" N GLU C 275 " --> pdb=" O ARG C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 removed outlier: 4.217A pdb=" N CYS C 286 " --> pdb=" O ASN C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 334 removed outlier: 3.713A pdb=" N PHE C 326 " --> pdb=" O GLY C 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 65 removed outlier: 3.607A pdb=" N ILE D 48 " --> pdb=" O PRO D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 83 Processing helix chain 'D' and resid 101 through 110 removed outlier: 4.488A 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 Processing helix chain 'D' and resid 154 through 160 Processing helix chain 'D' and resid 161 through 198 removed outlier: 3.824A pdb=" N ALA D 195 " --> pdb=" O ALA D 191 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS D 197 " --> pdb=" O LYS D 193 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER D 198 " --> pdb=" O LYS D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 226 removed outlier: 4.223A pdb=" N GLU D 206 " --> pdb=" O ASP D 202 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLN D 226 " --> pdb=" O LYS D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 273 Processing helix chain 'D' and resid 281 through 285 Processing helix chain 'D' and resid 322 through 335 removed outlier: 3.689A pdb=" N PHE D 326 " --> pdb=" O GLY D 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 65 removed outlier: 3.737A pdb=" N ILE E 48 " --> pdb=" O PRO E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 84 Processing helix chain 'E' and resid 96 through 100 Processing helix chain 'E' and resid 101 through 110 removed outlier: 4.179A 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 282 through 286 removed outlier: 4.286A pdb=" N CYS E 286 " --> pdb=" O ASN E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 335 removed outlier: 3.659A 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 54 removed outlier: 3.722A pdb=" N VAL F 46 " --> pdb=" O GLU F 42 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE F 53 " --> pdb=" O ARG F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 150 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: 4.100A pdb=" N GLY F 235 " --> pdb=" O SER F 231 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 12 Processing helix chain 'G' and resid 13 through 20 removed outlier: 3.800A pdb=" N LEU G 17 " --> pdb=" O SER G 14 " (cutoff:3.500A) Proline residue: G 18 - end of helix Processing helix chain 'G' and resid 36 through 40 removed outlier: 3.861A pdb=" N GLU G 39 " --> pdb=" O ALA G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 63 removed outlier: 3.856A pdb=" N THR G 63 " --> pdb=" O ARG G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 66 No H-bonds generated for 'chain 'G' and resid 64 through 66' Processing helix chain 'G' and resid 68 through 73 Processing helix chain 'G' and resid 85 through 89 removed outlier: 3.784A pdb=" N TRP G 89 " --> pdb=" O PHE G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 115 Processing helix chain 'G' and resid 116 through 123 removed outlier: 3.921A pdb=" N PHE G 120 " --> pdb=" O PRO G 116 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP G 121 " --> pdb=" O GLU G 117 " (cutoff:3.500A) removed outlier: 3.933A 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 191 through 203 removed outlier: 3.622A 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 245 removed outlier: 3.832A pdb=" N LEU G 245 " --> pdb=" O PRO G 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 249 through 263 Processing helix chain 'L' and resid 44 through 64 removed outlier: 3.741A pdb=" N ILE L 48 " --> pdb=" O PRO L 44 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 110 removed outlier: 3.724A pdb=" N LYS L 109 " --> pdb=" O GLU L 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 110 through 116 Processing helix chain 'L' and resid 258 through 273 removed outlier: 3.923A pdb=" N LEU L 264 " --> pdb=" O GLU L 260 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE L 265 " --> pdb=" O GLU L 261 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE L 266 " --> pdb=" O ALA L 262 " (cutoff:3.500A) Processing helix chain 'L' and resid 322 through 336 removed outlier: 3.760A pdb=" N ASN L 335 " --> pdb=" O ALA L 331 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLN L 336 " --> pdb=" O PHE L 332 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 9 Processing helix chain 'M' and resid 15 through 31 removed outlier: 3.792A pdb=" N ASP M 20 " --> pdb=" O LYS M 16 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR M 21 " --> pdb=" O VAL M 17 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN M 31 " --> pdb=" O GLY M 27 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 50 Processing helix chain 'M' and resid 51 through 59 Processing helix chain 'M' and resid 78 through 84 removed outlier: 3.685A pdb=" N ARG M 84 " --> pdb=" O PHE M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 94 removed outlier: 3.952A pdb=" N ILE M 90 " --> pdb=" O LEU M 86 " (cutoff:3.500A) Processing helix chain 'M' and resid 114 through 119 Processing helix chain 'M' and resid 129 through 137 removed outlier: 4.166A pdb=" N LEU M 133 " --> pdb=" O THR M 129 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU M 134 " --> pdb=" O VAL M 130 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA M 137 " --> pdb=" O LEU M 133 " (cutoff:3.500A) Processing helix chain 'M' and resid 142 through 150 removed outlier: 4.518A pdb=" N PHE M 146 " --> pdb=" O PRO M 142 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU M 147 " --> pdb=" O LEU M 143 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU M 148 " --> pdb=" O VAL M 144 " (cutoff:3.500A) Processing helix chain 'M' and resid 173 through 183 removed outlier: 3.573A pdb=" N ARG M 177 " --> pdb=" O ILE M 173 " (cutoff:3.500A) Processing helix chain 'M' and resid 190 through 199 removed outlier: 3.883A pdb=" N CYS M 197 " --> pdb=" O VAL M 193 " (cutoff:3.500A) Processing helix chain 'M' and resid 216 through 223 Processing helix chain 'M' and resid 224 through 227 Processing helix chain 'M' and resid 339 through 350 removed outlier: 3.684A pdb=" N VAL M 343 " --> pdb=" O ILE M 339 " (cutoff:3.500A) Processing helix chain 'M' and resid 365 through 370 Processing helix chain 'M' and resid 370 through 377 removed outlier: 3.728A pdb=" N LEU M 377 " --> pdb=" O LEU M 373 " (cutoff:3.500A) 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: 3.994A pdb=" N ILE M 474 " --> pdb=" O ALA M 470 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU M 480 " --> pdb=" O LYS M 476 " (cutoff:3.500A) removed outlier: 4.042A 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 removed outlier: 3.826A pdb=" N GLU M 596 " --> pdb=" O ARG M 593 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE M 598 " --> pdb=" O LEU M 595 " (cutoff:3.500A) 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 127 Processing sheet with id=AA2, first strand: chain 'A' and resid 125 through 127 removed outlier: 4.116A pdb=" N ASN A 256 " --> pdb=" O ARG A 2 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ARG A 2 " --> pdb=" O ASN A 256 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N THR A 3 " --> pdb=" O TRP A 298 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N TRP A 298 " --> pdb=" O THR A 3 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N THR A 297 " --> pdb=" O THR A 307 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N THR A 307 " --> pdb=" O THR A 297 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 16 through 17 Processing sheet with id=AA4, first strand: chain 'B' and resid 125 through 127 Processing sheet with id=AA5, first strand: chain 'B' and resid 125 through 127 removed outlier: 7.017A pdb=" N GLU B 247 " --> pdb=" O THR B 12 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N THR B 12 " --> pdb=" O GLU B 247 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N SER B 249 " --> pdb=" O ILE B 10 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE B 10 " --> pdb=" O SER B 249 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ARG B 251 " --> pdb=" O GLY B 8 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N GLY B 8 " --> pdb=" O ARG B 251 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N SER B 253 " --> pdb=" O PHE B 6 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N PHE B 6 " --> pdb=" O SER B 253 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N LYS B 255 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU B 4 " --> pdb=" O LYS B 255 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N THR B 297 " --> pdb=" O THR B 307 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N THR B 307 " --> pdb=" O THR B 297 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 16 through 17 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: 7.196A pdb=" N GLU C 247 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N THR C 12 " --> pdb=" O GLU C 247 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N SER C 249 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILE C 10 " --> pdb=" O SER C 249 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ARG C 251 " --> pdb=" O GLY C 8 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N GLY C 8 " --> pdb=" O ARG C 251 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N SER C 253 " --> pdb=" O PHE C 6 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N PHE C 6 " --> pdb=" O SER C 253 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LYS C 255 " --> pdb=" O LEU C 4 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU C 4 " --> pdb=" O LYS C 255 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N THR C 297 " --> pdb=" O THR C 307 " (cutoff:3.500A) removed outlier: 5.409A 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 removed outlier: 3.756A pdb=" N GLY C 144 " --> pdb=" O ILE C 236 " (cutoff:3.500A) 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: 7.135A pdb=" N GLU D 247 " --> pdb=" O THR D 12 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N THR D 12 " --> pdb=" O GLU D 247 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N SER D 249 " --> pdb=" O ILE D 10 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE D 10 " --> pdb=" O SER D 249 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ARG D 251 " --> pdb=" O GLY D 8 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N GLY D 8 " --> pdb=" O ARG D 251 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N SER D 253 " --> pdb=" O PHE D 6 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N PHE D 6 " --> pdb=" O SER D 253 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N LYS D 255 " --> pdb=" O LEU D 4 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU D 4 " --> pdb=" O LYS D 255 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N THR D 297 " --> pdb=" O THR D 307 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N THR D 307 " --> pdb=" O THR D 297 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 139 through 142 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: 7.179A pdb=" N GLU E 247 " --> pdb=" O THR E 12 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N THR E 12 " --> pdb=" O GLU E 247 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N SER E 249 " --> pdb=" O ILE E 10 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE E 10 " --> pdb=" O SER E 249 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ARG E 251 " --> pdb=" O GLY E 8 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N GLY E 8 " --> pdb=" O ARG E 251 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N SER E 253 " --> pdb=" O PHE E 6 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N PHE E 6 " --> pdb=" O SER E 253 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N LYS E 255 " --> pdb=" O LEU E 4 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LEU E 4 " --> pdb=" O LYS E 255 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N THR E 297 " --> pdb=" O THR E 307 " (cutoff:3.500A) removed outlier: 5.136A 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: 5.512A pdb=" N ASN F 169 " --> pdb=" O SER F 12 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N SER F 12 " --> pdb=" O ASN F 169 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS F 5 " --> pdb=" O GLY F 139 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N PHE F 70 " --> pdb=" O GLN F 227 " (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 80 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 Processing sheet with id=AC5, first strand: chain 'G' and resid 45 through 48 Processing sheet with id=AC6, first strand: chain 'G' and resid 124 through 127 removed outlier: 4.138A pdb=" N GLU G 124 " --> pdb=" O SER G 103 " (cutoff:3.500A) removed outlier: 8.808A pdb=" N LEU G 146 " --> pdb=" O TYR G 173 " (cutoff:3.500A) removed outlier: 8.928A pdb=" N CYS G 175 " --> pdb=" O LEU G 146 " (cutoff:3.500A) removed outlier: 6.817A 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: 5.477A pdb=" N ARG L 251 " --> pdb=" O GLY L 128 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ALA L 130 " --> pdb=" O SER L 249 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N SER L 249 " --> pdb=" O ALA L 130 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N GLU L 247 " --> pdb=" O PRO L 132 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N THR L 3 " --> pdb=" O TRP L 298 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TRP L 298 " --> pdb=" O THR L 3 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY L 309 " --> pdb=" O VAL L 295 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N THR L 297 " --> pdb=" O THR L 307 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N THR L 307 " --> pdb=" O THR L 297 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 138 through 141 Processing sheet with id=AC9, first strand: chain 'M' and resid 185 through 189 removed outlier: 7.009A pdb=" N LEU M 212 " --> pdb=" O LEU M 354 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N THR M 356 " --> pdb=" O LEU M 212 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE M 214 " --> pdb=" O THR M 356 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LYS M 34 " --> pdb=" O ALA M 353 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N LEU M 355 " --> pdb=" O LYS M 34 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ALA M 36 " --> pdb=" O LEU M 355 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N SER M 357 " --> pdb=" O ALA M 36 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE M 38 " --> pdb=" O SER M 357 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL M 35 " --> pdb=" O SER M 385 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ARG M 387 " --> pdb=" O VAL M 35 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N LEU M 37 " --> pdb=" O ARG M 387 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ILE M 389 " --> pdb=" O LEU M 37 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N SER M 39 " --> pdb=" O ILE M 389 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 462 through 464 Processing sheet with id=AD2, first strand: chain 'M' and resid 411 through 413 removed outlier: 3.653A pdb=" N ASP M 413 " --> pdb=" O ILE M 418 " (cutoff:3.500A) 1035 hydrogen bonds defined for protein. 2892 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 93 hydrogen bonds 186 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 15.89 Time building geometry restraints manager: 11.51 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: 23082 1.03 - 1.23: 133 1.23 - 1.43: 10506 1.43 - 1.62: 14178 1.62 - 1.82: 157 Bond restraints: 48056 Sorted by residual: bond pdb=" CB LYS A 217 " pdb=" CG LYS A 217 " ideal model delta sigma weight residual 1.520 1.570 -0.050 3.00e-02 1.11e+03 2.78e+00 bond pdb=" C3' DC I -9 " pdb=" O3' DC I -9 " ideal model delta sigma weight residual 1.422 1.470 -0.048 3.00e-02 1.11e+03 2.57e+00 bond pdb=" CA ASN L 136 " pdb=" CB ASN L 136 " ideal model delta sigma weight residual 1.522 1.550 -0.028 1.86e-02 2.89e+03 2.28e+00 bond pdb=" CB GLU G 22 " pdb=" CG GLU G 22 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.13e+00 bond pdb=" CB ASP B 323 " pdb=" CG ASP B 323 " ideal model delta sigma weight residual 1.516 1.550 -0.034 2.50e-02 1.60e+03 1.88e+00 ... (remaining 48051 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 86446 2.78 - 5.55: 470 5.55 - 8.33: 24 8.33 - 11.10: 9 11.10 - 13.88: 6 Bond angle restraints: 86955 Sorted by residual: angle pdb=" CB MET D 81 " pdb=" CG MET D 81 " pdb=" SD MET D 81 " ideal model delta sigma weight residual 112.70 126.58 -13.88 3.00e+00 1.11e-01 2.14e+01 angle pdb=" CA LYS A 217 " pdb=" CB LYS A 217 " pdb=" CG LYS A 217 " ideal model delta sigma weight residual 114.10 123.21 -9.11 2.00e+00 2.50e-01 2.08e+01 angle pdb=" CB MET A 140 " pdb=" CG MET A 140 " pdb=" SD MET A 140 " ideal model delta sigma weight residual 112.70 125.99 -13.29 3.00e+00 1.11e-01 1.96e+01 angle pdb=" CB MET A 81 " pdb=" CG MET A 81 " pdb=" SD MET A 81 " ideal model delta sigma weight residual 112.70 125.45 -12.75 3.00e+00 1.11e-01 1.80e+01 angle pdb=" CB MET M 521 " pdb=" CG MET M 521 " pdb=" SD MET M 521 " ideal model delta sigma weight residual 112.70 125.26 -12.56 3.00e+00 1.11e-01 1.75e+01 ... (remaining 86950 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 21246 35.91 - 71.83: 1031 71.83 - 107.74: 40 107.74 - 143.66: 1 143.66 - 179.57: 6 Dihedral angle restraints: 22324 sinusoidal: 12970 harmonic: 9354 Sorted by residual: dihedral pdb=" O4' U H 30 " pdb=" C1' U H 30 " pdb=" N1 U H 30 " pdb=" C2 U H 30 " ideal model delta sinusoidal sigma weight residual 200.00 33.12 166.88 1 1.50e+01 4.44e-03 8.42e+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 -80.89 -79.11 1 1.50e+01 4.44e-03 3.46e+01 dihedral pdb=" CA HIS M 77 " pdb=" C HIS M 77 " pdb=" N GLN M 78 " pdb=" CA GLN M 78 " ideal model delta harmonic sigma weight residual 180.00 151.64 28.36 0 5.00e+00 4.00e-02 3.22e+01 ... (remaining 22321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 3020 0.047 - 0.095: 644 0.095 - 0.142: 184 0.142 - 0.189: 9 0.189 - 0.236: 1 Chirality restraints: 3858 Sorted by residual: chirality pdb=" CB VAL M 195 " pdb=" CA VAL M 195 " pdb=" CG1 VAL M 195 " pdb=" CG2 VAL M 195 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CB ILE C 100 " pdb=" CA ILE C 100 " pdb=" CG1 ILE C 100 " pdb=" CG2 ILE C 100 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.53e-01 chirality pdb=" CA LYS A 201 " pdb=" N LYS A 201 " pdb=" C LYS A 201 " pdb=" CB LYS A 201 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.18 2.00e-01 2.50e+01 7.67e-01 ... (remaining 3855 not shown) Planarity restraints: 6864 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 215 " 0.023 2.00e-02 2.50e+03 4.72e-02 2.23e+01 pdb=" CG ASP A 215 " -0.082 2.00e-02 2.50e+03 pdb=" OD1 ASP A 215 " 0.029 2.00e-02 2.50e+03 pdb=" OD2 ASP A 215 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN L 137 " 0.016 2.00e-02 2.50e+03 3.13e-02 9.82e+00 pdb=" C GLN L 137 " -0.054 2.00e-02 2.50e+03 pdb=" O GLN L 137 " 0.020 2.00e-02 2.50e+03 pdb=" N TRP L 138 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 294 " -0.014 2.00e-02 2.50e+03 2.94e-02 8.64e+00 pdb=" C THR E 294 " 0.051 2.00e-02 2.50e+03 pdb=" O THR E 294 " -0.019 2.00e-02 2.50e+03 pdb=" N VAL E 295 " -0.017 2.00e-02 2.50e+03 ... (remaining 6861 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 2235 2.17 - 2.77: 93712 2.77 - 3.38: 142236 3.38 - 3.99: 188527 3.99 - 4.60: 286955 Nonbonded interactions: 713665 Sorted by model distance: nonbonded pdb=" O THR D 12 " pdb=" H GLY D 245 " model vdw 1.558 2.450 nonbonded pdb=" OE1 GLU A 206 " pdb=" H GLU A 206 " model vdw 1.569 2.450 nonbonded pdb=" OE1 GLU F 75 " pdb=" H GLU F 75 " model vdw 1.577 2.450 nonbonded pdb=" H ALA E 282 " pdb=" OP1 G H 27 " model vdw 1.578 2.450 nonbonded pdb=" O THR A 12 " pdb=" H GLY A 245 " model vdw 1.585 2.450 ... (remaining 713660 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 196 or (resid 197 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ or name HA o \ r name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name H \ E2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 198 through 342)) selection = (chain 'B' and (resid 1 through 196 or (resid 197 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ or name HA o \ r name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name H \ E2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 198 through 342)) selection = (chain 'C' and (resid 1 through 196 or (resid 197 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ or name HA o \ r name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name H \ E2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 198 through 342)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.180 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: 0.630 Extract box with map and model: 1.280 Check model and map are aligned: 0.270 Set scattering table: 0.340 Process input model: 102.360 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.120 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:9.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 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 0.050 24957 Z= 0.225 Angle : 0.729 13.880 34254 Z= 0.384 Chirality : 0.043 0.236 3858 Planarity : 0.006 0.073 4095 Dihedral : 18.438 179.571 9664 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 0.50 % Favored : 99.43 % Rotamer: Outliers : 0.81 % Allowed : 13.52 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.15), residues: 2810 helix: -0.32 (0.16), residues: 1036 sheet: -0.53 (0.25), residues: 402 loop : -1.12 (0.16), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 372 HIS 0.007 0.001 HIS C 281 PHE 0.021 0.001 PHE E 37 TYR 0.017 0.001 TYR M 478 ARG 0.008 0.000 ARG B 212 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 380 is missing expected H atoms. Skipping. Evaluate side-chains 180 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 161 time to evaluate : 2.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 MET cc_start: 0.9285 (mmm) cc_final: 0.9081 (mmm) REVERT: A 157 MET cc_start: 0.9391 (mmm) cc_final: 0.9176 (mmm) REVERT: C 81 MET cc_start: 0.8202 (tpp) cc_final: 0.7827 (tpp) REVERT: D 140 MET cc_start: 0.9433 (mmm) cc_final: 0.9209 (mmm) REVERT: D 157 MET cc_start: 0.9382 (mmm) cc_final: 0.8872 (mmm) REVERT: F 32 GLU cc_start: 0.9436 (tp30) cc_final: 0.8464 (tp30) REVERT: F 92 GLU cc_start: 0.8463 (tm-30) cc_final: 0.8232 (tm-30) REVERT: F 145 GLU cc_start: 0.8923 (tp30) cc_final: 0.8645 (tp30) REVERT: G 189 MET cc_start: 0.8809 (tpp) cc_final: 0.8386 (mmm) REVERT: L 249 SER cc_start: 0.9283 (m) cc_final: 0.9032 (p) REVERT: L 252 MET cc_start: 0.7394 (mpp) cc_final: 0.7003 (mpp) REVERT: L 293 TRP cc_start: 0.8988 (m-90) cc_final: 0.8481 (m-90) REVERT: M 198 MET cc_start: 0.8647 (mmt) cc_final: 0.8339 (mpm) REVERT: M 535 TYR cc_start: 0.9128 (m-80) cc_final: 0.8788 (m-80) outliers start: 19 outliers final: 15 residues processed: 175 average time/residue: 2.3107 time to fit residues: 472.4697 Evaluate side-chains 173 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 158 time to evaluate : 2.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 170 ASP Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain L residue 299 LYS Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 79 ILE Chi-restraints excluded: chain M residue 101 SER Chi-restraints excluded: chain M residue 222 ASP Chi-restraints excluded: chain M residue 226 VAL Chi-restraints excluded: chain M residue 336 ASN Chi-restraints excluded: chain M residue 347 CYS Chi-restraints excluded: chain M residue 370 MET Chi-restraints excluded: chain M residue 524 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 244 optimal weight: 1.9990 chunk 219 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 147 optimal weight: 6.9990 chunk 117 optimal weight: 10.0000 chunk 226 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 137 optimal weight: 0.9980 chunk 168 optimal weight: 5.9990 chunk 262 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 GLN ** D 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 ASN L 281 HIS L 285 ASN ** M 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 190 HIS ** 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 = 0.3527 r_free = 0.3527 target = 0.059389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.041670 restraints weight = 303574.638| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 3.96 r_work: 0.2819 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 24957 Z= 0.397 Angle : 0.647 8.635 34254 Z= 0.350 Chirality : 0.043 0.164 3858 Planarity : 0.005 0.066 4095 Dihedral : 18.662 178.891 4400 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.52 % Favored : 96.41 % Rotamer: Outliers : 1.48 % Allowed : 12.97 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: -0.17 (0.16), residues: 2810 helix: 0.96 (0.16), residues: 1045 sheet: -0.65 (0.25), residues: 405 loop : -0.74 (0.17), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 372 HIS 0.006 0.001 HIS F 152 PHE 0.011 0.001 PHE D 332 TYR 0.013 0.002 TYR F 132 ARG 0.005 0.001 ARG L 63 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 380 is missing expected H atoms. Skipping. Evaluate side-chains 189 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 154 time to evaluate : 2.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.9260 (tpp) cc_final: 0.8980 (tpp) REVERT: A 140 MET cc_start: 0.9408 (mmm) cc_final: 0.9187 (mmm) REVERT: B 1 MET cc_start: 0.9194 (mtt) cc_final: 0.8915 (mtt) REVERT: B 212 ARG cc_start: 0.9250 (ttp80) cc_final: 0.8991 (tmm160) REVERT: C 87 ASP cc_start: 0.8780 (OUTLIER) cc_final: 0.8481 (t70) REVERT: C 212 ARG cc_start: 0.9396 (mmm-85) cc_final: 0.9165 (mmm-85) REVERT: C 286 CYS cc_start: 0.9750 (m) cc_final: 0.9521 (m) REVERT: F 32 GLU cc_start: 0.9500 (tp30) cc_final: 0.8626 (tp30) REVERT: F 52 GLU cc_start: 0.9364 (mt-10) cc_final: 0.8523 (tp30) REVERT: F 145 GLU cc_start: 0.8978 (tp30) cc_final: 0.8723 (tp30) REVERT: F 201 LYS cc_start: 0.9393 (mppt) cc_final: 0.9132 (mppt) REVERT: G 189 MET cc_start: 0.8782 (tpp) cc_final: 0.8309 (mmm) REVERT: L 249 SER cc_start: 0.9325 (m) cc_final: 0.9111 (p) REVERT: M 192 MET cc_start: 0.9515 (mtt) cc_final: 0.9212 (mtt) REVERT: M 198 MET cc_start: 0.8818 (mmt) cc_final: 0.8375 (mpm) REVERT: M 450 MET cc_start: 0.9152 (mtm) cc_final: 0.8934 (mtm) outliers start: 35 outliers final: 15 residues processed: 182 average time/residue: 2.2661 time to fit residues: 485.3629 Evaluate side-chains 160 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 2.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain L residue 299 LYS Chi-restraints excluded: chain M residue 79 ILE Chi-restraints excluded: chain M residue 101 SER Chi-restraints excluded: chain M residue 149 GLU Chi-restraints excluded: chain M residue 158 THR Chi-restraints excluded: chain M residue 222 ASP Chi-restraints excluded: chain M residue 226 VAL Chi-restraints excluded: chain M residue 336 ASN Chi-restraints excluded: chain M residue 347 CYS Chi-restraints excluded: chain M residue 370 MET Chi-restraints excluded: chain M residue 524 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 22 optimal weight: 7.9990 chunk 221 optimal weight: 0.0980 chunk 206 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 157 optimal weight: 0.8980 chunk 263 optimal weight: 2.9990 chunk 248 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 227 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 ASN ** M 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 184 ASN ** 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 = 0.3551 r_free = 0.3551 target = 0.060040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.042485 restraints weight = 303217.182| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 3.94 r_work: 0.2836 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 24957 Z= 0.252 Angle : 0.586 8.921 34254 Z= 0.313 Chirality : 0.041 0.153 3858 Planarity : 0.004 0.060 4095 Dihedral : 18.642 178.207 4395 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.31 % Favored : 96.65 % Rotamer: Outliers : 1.19 % Allowed : 14.03 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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 (0.16), residues: 2810 helix: 1.29 (0.16), residues: 1052 sheet: -0.75 (0.25), residues: 393 loop : -0.62 (0.17), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 372 HIS 0.005 0.001 HIS C 29 PHE 0.010 0.001 PHE B 43 TYR 0.013 0.001 TYR M 478 ARG 0.004 0.000 ARG L 63 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 380 is missing expected H atoms. Skipping. Evaluate side-chains 180 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 2.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.9293 (tpp) cc_final: 0.9048 (tpp) REVERT: A 140 MET cc_start: 0.9399 (mmm) cc_final: 0.9111 (mmm) REVERT: B 1 MET cc_start: 0.9144 (mtt) cc_final: 0.8830 (mtt) REVERT: C 87 ASP cc_start: 0.8643 (OUTLIER) cc_final: 0.8387 (t70) REVERT: C 212 ARG cc_start: 0.9399 (mmm-85) cc_final: 0.9163 (mmm-85) REVERT: C 286 CYS cc_start: 0.9718 (m) cc_final: 0.9473 (m) REVERT: D 81 MET cc_start: 0.9148 (tpp) cc_final: 0.8931 (tpp) REVERT: D 157 MET cc_start: 0.9389 (mmm) cc_final: 0.9096 (mmt) REVERT: F 32 GLU cc_start: 0.9477 (tp30) cc_final: 0.8586 (tp30) REVERT: F 52 GLU cc_start: 0.9346 (mt-10) cc_final: 0.8518 (tp30) REVERT: F 145 GLU cc_start: 0.8992 (tp30) cc_final: 0.8745 (tp30) REVERT: F 201 LYS cc_start: 0.9414 (mppt) cc_final: 0.9151 (mppt) REVERT: G 189 MET cc_start: 0.8767 (tpp) cc_final: 0.8315 (mmm) REVERT: L 249 SER cc_start: 0.9321 (m) cc_final: 0.9100 (p) REVERT: L 252 MET cc_start: 0.7606 (mpp) cc_final: 0.7352 (mpp) REVERT: M 192 MET cc_start: 0.9519 (mtt) cc_final: 0.9220 (mtt) REVERT: M 198 MET cc_start: 0.8870 (mmt) cc_final: 0.8562 (mpm) REVERT: M 398 MET cc_start: 0.8651 (tmm) cc_final: 0.8382 (tmm) outliers start: 28 outliers final: 18 residues processed: 176 average time/residue: 2.2356 time to fit residues: 464.0048 Evaluate side-chains 162 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 2.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain E residue 38 ASN Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain L residue 129 ASN Chi-restraints excluded: chain L residue 299 LYS Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 79 ILE Chi-restraints excluded: chain M residue 101 SER Chi-restraints excluded: chain M residue 149 GLU Chi-restraints excluded: chain M residue 158 THR Chi-restraints excluded: chain M residue 222 ASP Chi-restraints excluded: chain M residue 226 VAL Chi-restraints excluded: chain M residue 336 ASN Chi-restraints excluded: chain M residue 370 MET Chi-restraints excluded: chain M residue 524 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 271 optimal weight: 6.9990 chunk 208 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 264 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 119 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 192 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 184 ASN ** 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 = 0.3541 r_free = 0.3541 target = 0.059632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.042040 restraints weight = 304270.571| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 3.91 r_work: 0.2823 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 24957 Z= 0.264 Angle : 0.578 8.209 34254 Z= 0.308 Chirality : 0.041 0.152 3858 Planarity : 0.004 0.070 4095 Dihedral : 18.645 178.311 4394 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.81 % Favored : 96.16 % Rotamer: Outliers : 1.48 % Allowed : 13.95 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 2810 helix: 1.50 (0.16), residues: 1056 sheet: -0.93 (0.25), residues: 403 loop : -0.60 (0.17), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 350 HIS 0.004 0.001 HIS E 54 PHE 0.010 0.001 PHE B 43 TYR 0.011 0.001 TYR M 478 ARG 0.013 0.000 ARG B 212 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 380 is missing expected H atoms. Skipping. Evaluate side-chains 181 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 146 time to evaluate : 2.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.9255 (tpp) cc_final: 0.8971 (tpp) REVERT: A 140 MET cc_start: 0.9405 (mmm) cc_final: 0.8932 (mmm) REVERT: B 1 MET cc_start: 0.9152 (mtt) cc_final: 0.8821 (mtt) REVERT: C 87 ASP cc_start: 0.8708 (OUTLIER) cc_final: 0.8433 (t70) REVERT: C 140 MET cc_start: 0.9250 (mmm) cc_final: 0.8947 (mmm) REVERT: C 212 ARG cc_start: 0.9422 (mmm-85) cc_final: 0.9182 (mmm-85) REVERT: C 286 CYS cc_start: 0.9756 (m) cc_final: 0.9491 (m) REVERT: C 321 THR cc_start: 0.9492 (OUTLIER) cc_final: 0.9230 (p) REVERT: D 81 MET cc_start: 0.9149 (tpp) cc_final: 0.8938 (tpp) REVERT: D 157 MET cc_start: 0.9358 (mmm) cc_final: 0.9112 (mmt) REVERT: F 32 GLU cc_start: 0.9479 (tp30) cc_final: 0.8583 (tp30) REVERT: F 52 GLU cc_start: 0.9332 (mt-10) cc_final: 0.8518 (tp30) REVERT: F 122 MET cc_start: 0.9194 (tpp) cc_final: 0.8941 (tpp) REVERT: F 145 GLU cc_start: 0.9010 (tp30) cc_final: 0.8776 (tp30) REVERT: F 201 LYS cc_start: 0.9403 (mppt) cc_final: 0.9129 (mppt) REVERT: G 189 MET cc_start: 0.8740 (tpp) cc_final: 0.8411 (tpt) REVERT: L 249 SER cc_start: 0.9328 (m) cc_final: 0.9109 (p) REVERT: L 252 MET cc_start: 0.7550 (mpp) cc_final: 0.7304 (mpp) REVERT: M 192 MET cc_start: 0.9532 (mtt) cc_final: 0.9232 (mtt) REVERT: M 198 MET cc_start: 0.8908 (mmt) cc_final: 0.8385 (mpm) REVERT: M 216 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.8718 (pm20) REVERT: M 450 MET cc_start: 0.9177 (mtp) cc_final: 0.8901 (mtm) outliers start: 35 outliers final: 23 residues processed: 176 average time/residue: 2.3244 time to fit residues: 478.1955 Evaluate side-chains 167 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 2.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 107 ARG Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain E residue 38 ASN Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain L residue 129 ASN Chi-restraints excluded: chain L residue 299 LYS Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 79 ILE Chi-restraints excluded: chain M residue 101 SER Chi-restraints excluded: chain M residue 149 GLU Chi-restraints excluded: chain M residue 158 THR Chi-restraints excluded: chain M residue 161 MET Chi-restraints excluded: chain M residue 216 GLU Chi-restraints excluded: chain M residue 226 VAL Chi-restraints excluded: chain M residue 336 ASN Chi-restraints excluded: chain M residue 370 MET Chi-restraints excluded: chain M residue 524 GLU Chi-restraints excluded: chain M residue 613 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 232 optimal weight: 9.9990 chunk 178 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 216 optimal weight: 8.9990 chunk 266 optimal weight: 4.9990 chunk 203 optimal weight: 5.9990 chunk 286 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 224 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 237 ASN ** M 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 412 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.057608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.039876 restraints weight = 308562.480| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 3.86 r_work: 0.2764 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 24957 Z= 0.481 Angle : 0.660 7.305 34254 Z= 0.357 Chirality : 0.044 0.187 3858 Planarity : 0.004 0.046 4095 Dihedral : 18.737 177.228 4392 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.34 % Favored : 95.62 % Rotamer: Outliers : 1.44 % Allowed : 14.96 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: -0.03 (0.16), residues: 2810 helix: 1.37 (0.16), residues: 1053 sheet: -0.98 (0.24), residues: 400 loop : -0.80 (0.17), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 350 HIS 0.008 0.001 HIS F 152 PHE 0.060 0.002 PHE A 80 TYR 0.012 0.002 TYR M 478 ARG 0.009 0.000 ARG B 212 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 380 is missing expected H atoms. Skipping. Evaluate side-chains 177 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 143 time to evaluate : 2.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.9115 (tpp) cc_final: 0.8860 (tpp) REVERT: A 140 MET cc_start: 0.9342 (mmm) cc_final: 0.8768 (mmm) REVERT: B 1 MET cc_start: 0.9189 (mtt) cc_final: 0.8895 (mtt) REVERT: B 215 ASP cc_start: 0.9463 (m-30) cc_final: 0.9028 (m-30) REVERT: C 87 ASP cc_start: 0.8745 (OUTLIER) cc_final: 0.8491 (t70) REVERT: C 157 MET cc_start: 0.9231 (mmm) cc_final: 0.8850 (mmm) REVERT: C 212 ARG cc_start: 0.9407 (mmm-85) cc_final: 0.9184 (mmm-85) REVERT: C 286 CYS cc_start: 0.9756 (m) cc_final: 0.9507 (m) REVERT: C 321 THR cc_start: 0.9466 (OUTLIER) cc_final: 0.9217 (p) REVERT: D 81 MET cc_start: 0.9132 (tpp) cc_final: 0.8879 (tpp) REVERT: F 32 GLU cc_start: 0.9515 (tp30) cc_final: 0.8641 (tp30) REVERT: F 52 GLU cc_start: 0.9356 (mt-10) cc_final: 0.8487 (tm-30) REVERT: F 122 MET cc_start: 0.9199 (tpp) cc_final: 0.8845 (tpp) REVERT: F 145 GLU cc_start: 0.9017 (tp30) cc_final: 0.8772 (tp30) REVERT: F 201 LYS cc_start: 0.9405 (mppt) cc_final: 0.9142 (mppt) REVERT: G 189 MET cc_start: 0.8778 (tpp) cc_final: 0.8347 (mmm) REVERT: L 249 SER cc_start: 0.9364 (m) cc_final: 0.9148 (p) REVERT: M 192 MET cc_start: 0.9530 (mtt) cc_final: 0.9252 (mtt) REVERT: M 198 MET cc_start: 0.8944 (mmt) cc_final: 0.8544 (mpm) outliers start: 34 outliers final: 18 residues processed: 173 average time/residue: 2.2372 time to fit residues: 454.8458 Evaluate side-chains 157 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 2.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain L residue 129 ASN Chi-restraints excluded: chain L residue 299 LYS Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 79 ILE Chi-restraints excluded: chain M residue 101 SER Chi-restraints excluded: chain M residue 158 THR Chi-restraints excluded: chain M residue 226 VAL Chi-restraints excluded: chain M residue 336 ASN Chi-restraints excluded: chain M residue 370 MET Chi-restraints excluded: chain M residue 524 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 266 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 146 optimal weight: 0.8980 chunk 284 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 206 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 184 ASN ** 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 = 0.3527 r_free = 0.3527 target = 0.059480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.041766 restraints weight = 301813.547| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 3.94 r_work: 0.2820 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24957 Z= 0.193 Angle : 0.577 7.502 34254 Z= 0.305 Chirality : 0.041 0.159 3858 Planarity : 0.004 0.084 4095 Dihedral : 18.679 178.019 4391 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.95 % Favored : 96.01 % Rotamer: Outliers : 1.40 % Allowed : 14.88 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.16), residues: 2810 helix: 1.54 (0.16), residues: 1051 sheet: -1.05 (0.25), residues: 393 loop : -0.61 (0.17), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 350 HIS 0.004 0.001 HIS D 281 PHE 0.016 0.001 PHE A 80 TYR 0.010 0.001 TYR M 478 ARG 0.017 0.000 ARG B 212 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 380 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 2.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.9101 (tpp) cc_final: 0.8879 (tpp) REVERT: A 140 MET cc_start: 0.9284 (mmm) cc_final: 0.8695 (mmm) REVERT: B 1 MET cc_start: 0.9167 (mtt) cc_final: 0.8805 (mtt) REVERT: B 140 MET cc_start: 0.9315 (mmm) cc_final: 0.8654 (mmm) REVERT: B 215 ASP cc_start: 0.9457 (m-30) cc_final: 0.9033 (m-30) REVERT: C 212 ARG cc_start: 0.9389 (mmm-85) cc_final: 0.9152 (mmm-85) REVERT: C 286 CYS cc_start: 0.9745 (m) cc_final: 0.9472 (m) REVERT: D 81 MET cc_start: 0.9109 (tpp) cc_final: 0.8832 (tpp) REVERT: D 157 MET cc_start: 0.9348 (mmm) cc_final: 0.9119 (mmm) REVERT: F 13 SER cc_start: 0.9325 (OUTLIER) cc_final: 0.8874 (t) REVERT: F 32 GLU cc_start: 0.9450 (tp30) cc_final: 0.8593 (tp30) REVERT: F 52 GLU cc_start: 0.9312 (mt-10) cc_final: 0.8473 (tm-30) REVERT: F 122 MET cc_start: 0.9163 (tpp) cc_final: 0.8846 (tpp) REVERT: F 145 GLU cc_start: 0.8927 (tp30) cc_final: 0.8700 (tp30) REVERT: F 201 LYS cc_start: 0.9421 (mppt) cc_final: 0.9189 (mppt) REVERT: G 189 MET cc_start: 0.8756 (tpp) cc_final: 0.8439 (tpt) REVERT: L 249 SER cc_start: 0.9352 (m) cc_final: 0.9127 (p) REVERT: M 192 MET cc_start: 0.9518 (mtt) cc_final: 0.9231 (mtt) REVERT: M 198 MET cc_start: 0.8979 (mmt) cc_final: 0.8595 (mpm) outliers start: 33 outliers final: 22 residues processed: 174 average time/residue: 2.2064 time to fit residues: 451.3376 Evaluate side-chains 160 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 2.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain L residue 129 ASN Chi-restraints excluded: chain L residue 299 LYS Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 76 MET Chi-restraints excluded: chain M residue 79 ILE Chi-restraints excluded: chain M residue 101 SER Chi-restraints excluded: chain M residue 149 GLU Chi-restraints excluded: chain M residue 158 THR Chi-restraints excluded: chain M residue 222 ASP Chi-restraints excluded: chain M residue 226 VAL Chi-restraints excluded: chain M residue 336 ASN Chi-restraints excluded: chain M residue 370 MET Chi-restraints excluded: chain M residue 377 LEU Chi-restraints excluded: chain M residue 524 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 256 optimal weight: 9.9990 chunk 259 optimal weight: 7.9990 chunk 71 optimal weight: 0.0370 chunk 127 optimal weight: 2.9990 chunk 247 optimal weight: 10.0000 chunk 149 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 248 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 203 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.5662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 190 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 = 0.3520 r_free = 0.3520 target = 0.059142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.041410 restraints weight = 303589.673| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 3.89 r_work: 0.2813 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24957 Z= 0.238 Angle : 0.583 9.558 34254 Z= 0.307 Chirality : 0.041 0.157 3858 Planarity : 0.004 0.044 4095 Dihedral : 18.653 178.083 4391 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.99 % Favored : 95.94 % Rotamer: Outliers : 1.27 % Allowed : 15.60 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.27 (0.16), residues: 2810 helix: 1.63 (0.16), residues: 1048 sheet: -0.99 (0.25), residues: 397 loop : -0.56 (0.17), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 350 HIS 0.004 0.001 HIS D 281 PHE 0.011 0.001 PHE B 43 TYR 0.010 0.001 TYR F 157 ARG 0.008 0.000 ARG B 212 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 380 is missing expected H atoms. Skipping. Evaluate side-chains 175 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 2.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 MET cc_start: 0.9271 (mmm) cc_final: 0.8665 (mmm) REVERT: B 1 MET cc_start: 0.9204 (mtt) cc_final: 0.8882 (mtt) REVERT: B 211 VAL cc_start: 0.9396 (OUTLIER) cc_final: 0.9136 (p) REVERT: B 215 ASP cc_start: 0.9464 (m-30) cc_final: 0.9017 (m-30) REVERT: C 157 MET cc_start: 0.9238 (mmm) cc_final: 0.8848 (mmm) REVERT: C 212 ARG cc_start: 0.9395 (mmm-85) cc_final: 0.9161 (mmm-85) REVERT: C 286 CYS cc_start: 0.9755 (m) cc_final: 0.9488 (m) REVERT: C 290 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8367 (tm-30) REVERT: C 321 THR cc_start: 0.9487 (OUTLIER) cc_final: 0.9255 (p) REVERT: D 81 MET cc_start: 0.9119 (tpp) cc_final: 0.8827 (tpp) REVERT: F 13 SER cc_start: 0.9346 (OUTLIER) cc_final: 0.8909 (t) REVERT: F 32 GLU cc_start: 0.9454 (tp30) cc_final: 0.8598 (tp30) REVERT: F 92 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8359 (tm-30) REVERT: F 122 MET cc_start: 0.9172 (tpp) cc_final: 0.8867 (tpp) REVERT: F 145 GLU cc_start: 0.8910 (tp30) cc_final: 0.8682 (tp30) REVERT: F 201 LYS cc_start: 0.9422 (mppt) cc_final: 0.9187 (mppt) REVERT: G 189 MET cc_start: 0.8750 (tpp) cc_final: 0.8432 (tpt) REVERT: L 249 SER cc_start: 0.9359 (m) cc_final: 0.9135 (p) REVERT: M 198 MET cc_start: 0.9009 (mmt) cc_final: 0.8795 (mpm) outliers start: 30 outliers final: 21 residues processed: 171 average time/residue: 2.2636 time to fit residues: 454.1846 Evaluate side-chains 165 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 3.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain L residue 129 ASN Chi-restraints excluded: chain L residue 299 LYS Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 76 MET Chi-restraints excluded: chain M residue 79 ILE Chi-restraints excluded: chain M residue 101 SER Chi-restraints excluded: chain M residue 149 GLU Chi-restraints excluded: chain M residue 158 THR Chi-restraints excluded: chain M residue 222 ASP Chi-restraints excluded: chain M residue 226 VAL Chi-restraints excluded: chain M residue 336 ASN Chi-restraints excluded: chain M residue 370 MET Chi-restraints excluded: chain M residue 377 LEU Chi-restraints excluded: chain M residue 524 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 161 optimal weight: 1.9990 chunk 172 optimal weight: 0.9980 chunk 218 optimal weight: 10.0000 chunk 139 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 chunk 269 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 chunk 184 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 281 HIS ** D 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 190 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 = 0.3536 r_free = 0.3536 target = 0.059451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.041847 restraints weight = 303968.377| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 3.88 r_work: 0.2822 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24957 Z= 0.232 Angle : 0.586 10.014 34254 Z= 0.307 Chirality : 0.041 0.155 3858 Planarity : 0.004 0.092 4095 Dihedral : 18.647 178.098 4391 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.20 % Favored : 95.73 % Rotamer: Outliers : 1.23 % Allowed : 16.07 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.32 (0.16), residues: 2810 helix: 1.68 (0.16), residues: 1047 sheet: -0.97 (0.25), residues: 402 loop : -0.54 (0.17), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 89 HIS 0.004 0.001 HIS C 281 PHE 0.011 0.001 PHE B 150 TYR 0.011 0.001 TYR F 157 ARG 0.016 0.000 ARG B 212 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 380 is missing expected H atoms. Skipping. Evaluate side-chains 175 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 2.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 MET cc_start: 0.9251 (mmm) cc_final: 0.8650 (mmm) REVERT: B 1 MET cc_start: 0.9189 (mtt) cc_final: 0.8859 (mtt) REVERT: B 211 VAL cc_start: 0.9397 (OUTLIER) cc_final: 0.9146 (p) REVERT: B 215 ASP cc_start: 0.9468 (m-30) cc_final: 0.9042 (m-30) REVERT: C 157 MET cc_start: 0.9232 (mmm) cc_final: 0.8844 (mmm) REVERT: C 212 ARG cc_start: 0.9392 (mmm-85) cc_final: 0.9154 (mmm-85) REVERT: C 286 CYS cc_start: 0.9727 (m) cc_final: 0.9468 (m) REVERT: C 290 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8359 (tm-30) REVERT: C 321 THR cc_start: 0.9487 (OUTLIER) cc_final: 0.9259 (p) REVERT: D 81 MET cc_start: 0.9118 (tpp) cc_final: 0.8811 (tpp) REVERT: F 13 SER cc_start: 0.9320 (OUTLIER) cc_final: 0.8876 (t) REVERT: F 32 GLU cc_start: 0.9461 (tp30) cc_final: 0.8581 (tp30) REVERT: F 52 GLU cc_start: 0.9318 (mt-10) cc_final: 0.8566 (tm-30) REVERT: F 122 MET cc_start: 0.9168 (tpp) cc_final: 0.8867 (tpp) REVERT: F 145 GLU cc_start: 0.8901 (tp30) cc_final: 0.8673 (tp30) REVERT: F 201 LYS cc_start: 0.9426 (mppt) cc_final: 0.9191 (mppt) REVERT: G 189 MET cc_start: 0.8741 (tpp) cc_final: 0.8278 (mmm) REVERT: L 249 SER cc_start: 0.9375 (m) cc_final: 0.9155 (p) REVERT: M 192 MET cc_start: 0.9433 (mtt) cc_final: 0.9141 (mtt) outliers start: 29 outliers final: 20 residues processed: 172 average time/residue: 2.3163 time to fit residues: 465.4555 Evaluate side-chains 165 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 2.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain L residue 129 ASN Chi-restraints excluded: chain L residue 299 LYS Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 76 MET Chi-restraints excluded: chain M residue 79 ILE Chi-restraints excluded: chain M residue 101 SER Chi-restraints excluded: chain M residue 158 THR Chi-restraints excluded: chain M residue 222 ASP Chi-restraints excluded: chain M residue 226 VAL Chi-restraints excluded: chain M residue 336 ASN Chi-restraints excluded: chain M residue 370 MET Chi-restraints excluded: chain M residue 377 LEU Chi-restraints excluded: chain M residue 524 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 43 optimal weight: 6.9990 chunk 222 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 148 optimal weight: 0.9990 chunk 163 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 229 optimal weight: 4.9990 chunk 209 optimal weight: 5.9990 chunk 250 optimal weight: 10.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 190 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 = 0.3521 r_free = 0.3521 target = 0.059136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.041411 restraints weight = 303286.088| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 3.89 r_work: 0.2815 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 24957 Z= 0.249 Angle : 0.603 10.511 34254 Z= 0.315 Chirality : 0.041 0.155 3858 Planarity : 0.004 0.054 4095 Dihedral : 18.638 177.943 4391 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.31 % Favored : 95.62 % Rotamer: Outliers : 1.14 % Allowed : 16.32 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.33 (0.16), residues: 2810 helix: 1.68 (0.16), residues: 1048 sheet: -0.88 (0.25), residues: 382 loop : -0.55 (0.17), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 89 HIS 0.004 0.001 HIS B 250 PHE 0.010 0.001 PHE B 150 TYR 0.011 0.001 TYR F 157 ARG 0.014 0.000 ARG B 212 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 380 is missing expected H atoms. Skipping. Evaluate side-chains 168 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 2.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.9208 (mtt) cc_final: 0.8880 (mtt) REVERT: B 211 VAL cc_start: 0.9441 (OUTLIER) cc_final: 0.9217 (p) REVERT: B 215 ASP cc_start: 0.9470 (m-30) cc_final: 0.9042 (m-30) REVERT: C 157 MET cc_start: 0.9216 (mmm) cc_final: 0.8859 (mmm) REVERT: C 212 ARG cc_start: 0.9388 (mmm-85) cc_final: 0.9154 (mmm-85) REVERT: C 286 CYS cc_start: 0.9732 (m) cc_final: 0.9473 (m) REVERT: C 290 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.8364 (tm-30) REVERT: C 321 THR cc_start: 0.9480 (OUTLIER) cc_final: 0.9253 (p) REVERT: D 81 MET cc_start: 0.9129 (tpp) cc_final: 0.8820 (tpp) REVERT: F 13 SER cc_start: 0.9321 (OUTLIER) cc_final: 0.8871 (t) REVERT: F 32 GLU cc_start: 0.9457 (tp30) cc_final: 0.8572 (tp30) REVERT: F 92 GLU cc_start: 0.8899 (tm-30) cc_final: 0.8488 (tm-30) REVERT: F 122 MET cc_start: 0.9173 (tpp) cc_final: 0.8870 (tpp) REVERT: F 145 GLU cc_start: 0.8880 (tp30) cc_final: 0.8649 (tp30) REVERT: F 201 LYS cc_start: 0.9427 (mppt) cc_final: 0.9193 (mppt) REVERT: G 189 MET cc_start: 0.8733 (tpp) cc_final: 0.8365 (mmm) REVERT: L 249 SER cc_start: 0.9384 (m) cc_final: 0.9166 (p) REVERT: M 192 MET cc_start: 0.9444 (mtt) cc_final: 0.9136 (mtt) outliers start: 27 outliers final: 22 residues processed: 165 average time/residue: 2.1568 time to fit residues: 419.9622 Evaluate side-chains 166 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 2.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain E residue 339 ASP Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain L residue 129 ASN Chi-restraints excluded: chain L residue 299 LYS Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 76 MET Chi-restraints excluded: chain M residue 101 SER Chi-restraints excluded: chain M residue 158 THR Chi-restraints excluded: chain M residue 222 ASP Chi-restraints excluded: chain M residue 226 VAL Chi-restraints excluded: chain M residue 336 ASN Chi-restraints excluded: chain M residue 370 MET Chi-restraints excluded: chain M residue 377 LEU Chi-restraints excluded: chain M residue 524 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 20 optimal weight: 5.9990 chunk 263 optimal weight: 0.0010 chunk 121 optimal weight: 4.9990 chunk 250 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 244 optimal weight: 3.9990 chunk 145 optimal weight: 5.9990 chunk 182 optimal weight: 0.7980 chunk 159 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 overall best weight: 2.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 190 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 = 0.3531 r_free = 0.3531 target = 0.059094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.041430 restraints weight = 306378.464| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 3.90 r_work: 0.2803 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 24957 Z= 0.290 Angle : 0.618 10.817 34254 Z= 0.323 Chirality : 0.041 0.154 3858 Planarity : 0.004 0.057 4095 Dihedral : 18.634 177.591 4389 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.48 % Favored : 95.44 % Rotamer: Outliers : 1.14 % Allowed : 16.36 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.27 (0.16), residues: 2810 helix: 1.67 (0.16), residues: 1047 sheet: -0.96 (0.25), residues: 402 loop : -0.60 (0.17), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP M 139 HIS 0.005 0.001 HIS E 54 PHE 0.018 0.001 PHE E 340 TYR 0.011 0.001 TYR F 157 ARG 0.013 0.000 ARG B 212 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 380 is missing expected H atoms. Skipping. Evaluate side-chains 168 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 2.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 MET cc_start: 0.9222 (mmm) cc_final: 0.8572 (mmm) REVERT: B 1 MET cc_start: 0.9181 (mtt) cc_final: 0.8845 (mtt) REVERT: B 211 VAL cc_start: 0.9439 (OUTLIER) cc_final: 0.9225 (p) REVERT: B 215 ASP cc_start: 0.9473 (m-30) cc_final: 0.9051 (m-30) REVERT: C 157 MET cc_start: 0.9244 (mmm) cc_final: 0.8899 (mmm) REVERT: C 212 ARG cc_start: 0.9418 (mmm-85) cc_final: 0.9191 (mmm-85) REVERT: C 286 CYS cc_start: 0.9746 (m) cc_final: 0.9487 (m) REVERT: C 290 GLU cc_start: 0.8979 (OUTLIER) cc_final: 0.8401 (tm-30) REVERT: C 321 THR cc_start: 0.9465 (OUTLIER) cc_final: 0.9232 (p) REVERT: D 81 MET cc_start: 0.9111 (tpp) cc_final: 0.8797 (tpp) REVERT: F 13 SER cc_start: 0.9356 (OUTLIER) cc_final: 0.8903 (t) REVERT: F 32 GLU cc_start: 0.9454 (tp30) cc_final: 0.8590 (tp30) REVERT: F 52 GLU cc_start: 0.9339 (mt-10) cc_final: 0.8608 (tm-30) REVERT: F 92 GLU cc_start: 0.8912 (tm-30) cc_final: 0.8499 (tm-30) REVERT: F 122 MET cc_start: 0.9207 (tpp) cc_final: 0.8997 (tpp) REVERT: F 145 GLU cc_start: 0.8934 (tp30) cc_final: 0.8675 (tp30) REVERT: F 201 LYS cc_start: 0.9424 (mppt) cc_final: 0.9147 (mppt) REVERT: G 189 MET cc_start: 0.8749 (tpp) cc_final: 0.8380 (mmm) REVERT: L 249 SER cc_start: 0.9388 (m) cc_final: 0.9171 (p) REVERT: M 192 MET cc_start: 0.9481 (mtt) cc_final: 0.9174 (mtt) REVERT: M 447 GLU cc_start: 0.9717 (tt0) cc_final: 0.9412 (tt0) outliers start: 27 outliers final: 19 residues processed: 164 average time/residue: 2.2089 time to fit residues: 426.7624 Evaluate side-chains 161 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 2.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 95 PHE Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain L residue 129 ASN Chi-restraints excluded: chain L residue 299 LYS Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 76 MET Chi-restraints excluded: chain M residue 101 SER Chi-restraints excluded: chain M residue 158 THR Chi-restraints excluded: chain M residue 222 ASP Chi-restraints excluded: chain M residue 226 VAL Chi-restraints excluded: chain M residue 370 MET Chi-restraints excluded: chain M residue 377 LEU Chi-restraints excluded: chain M residue 524 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 218 optimal weight: 9.9990 chunk 281 optimal weight: 3.9990 chunk 184 optimal weight: 3.9990 chunk 274 optimal weight: 3.9990 chunk 283 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 127 optimal weight: 0.9990 chunk 213 optimal weight: 4.9990 chunk 149 optimal weight: 0.5980 chunk 201 optimal weight: 3.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 190 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 = 0.059081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.041398 restraints weight = 306442.771| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 3.89 r_work: 0.2805 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24957 Z= 0.279 Angle : 0.615 12.081 34254 Z= 0.321 Chirality : 0.041 0.156 3858 Planarity : 0.004 0.051 4095 Dihedral : 18.641 177.542 4387 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.41 % Favored : 95.48 % Rotamer: Outliers : 0.97 % Allowed : 16.53 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.27 (0.16), residues: 2810 helix: 1.65 (0.16), residues: 1049 sheet: -0.98 (0.25), residues: 408 loop : -0.58 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 89 HIS 0.004 0.001 HIS C 281 PHE 0.011 0.001 PHE B 150 TYR 0.011 0.001 TYR F 157 ARG 0.012 0.000 ARG B 212 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21085.96 seconds wall clock time: 359 minutes 57.21 seconds (21597.21 seconds total)