Starting phenix.real_space_refine on Sun Aug 9 01:43:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9srw_55160/08_2026/9srw_55160.cif Found real_map, /net/cci-nas-00/data/ceres_data/9srw_55160/08_2026/9srw_55160.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9srw_55160/08_2026/9srw_55160.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9srw_55160/08_2026/9srw_55160.map" model { file = "/net/cci-nas-00/data/ceres_data/9srw_55160/08_2026/9srw_55160.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9srw_55160/08_2026/9srw_55160.cif" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 6 6.06 5 S 64 5.16 5 C 9760 2.51 5 N 2658 2.21 5 O 2862 1.98 5 H 15488 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30838 Number of models: 1 Model: "" Number of chains: 12 Chain: "E" Number of atoms: 3376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3376 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 14, 'TRANS': 198} Chain breaks: 1 Chain: "A" Number of atoms: 6017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 6017 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 13, 'TRANS': 374} Chain breaks: 1 Chain: "B" Number of atoms: 6023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 6023 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 13, 'TRANS': 374} Chain breaks: 1 Chain: "F" Number of atoms: 3376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3376 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 14, 'TRANS': 198} Chain breaks: 1 Chain: "C" Number of atoms: 6017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 6017 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 13, 'TRANS': 374} Chain breaks: 1 Chain: "D" Number of atoms: 6023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 6023 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 13, 'TRANS': 374} Chain breaks: 1 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" 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 7149 SG CYS A 257 85.500 77.336 70.246 1.00 81.08 S ATOM 7180 SG CYS A 259 89.063 77.731 71.566 1.00 78.44 S ATOM 7235 SG CYS A 264 87.784 80.097 68.852 1.00 65.11 S ATOM 13169 SG CYS B 257 101.025 94.565 47.585 1.00 64.14 S ATOM 13201 SG CYS B 259 98.607 92.208 45.787 1.00 57.29 S ATOM 13257 SG CYS B 264 98.217 92.797 49.574 1.00 43.79 S ATOM 22565 SG CYS C 257 69.835 114.054 70.254 1.00 81.08 S ATOM 22596 SG CYS C 259 66.270 113.660 71.571 1.00 78.44 S ATOM 22651 SG CYS C 264 67.554 111.289 68.863 1.00 65.11 S ATOM 28585 SG CYS D 257 54.348 96.771 47.608 1.00 64.14 S ATOM 28617 SG CYS D 259 56.767 99.126 45.809 1.00 57.29 S ATOM 28673 SG CYS D 264 57.153 98.544 49.597 1.00 43.79 S Time building chain proxies: 4.35, per 1000 atoms: 0.14 Number of scatterers: 30838 At special positions: 0 Unit cell: (156.389, 192.392, 88.8829, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 6 29.99 S 64 16.00 O 2862 8.00 N 2658 7.00 C 9760 6.00 H 15488 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.85 Conformation dependent library (CDL) restraints added in 876.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" ND1 HIS A 247 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 259 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 264 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 257 " pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" ND1 HIS B 247 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 259 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 264 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 257 " pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" ND1 HIS C 247 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 259 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 264 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 257 " pdb=" ZN D 501 " pdb="ZN ZN D 501 " - pdb=" ND1 HIS D 247 " pdb="ZN ZN D 501 " - pdb=" SG CYS D 259 " pdb="ZN ZN D 501 " - pdb=" SG CYS D 264 " pdb="ZN ZN D 501 " - pdb=" SG CYS D 257 " pdb=" ZN E 301 " pdb="ZN ZN E 301 " - pdb=" NE2 HIS E 152 " pdb="ZN ZN E 301 " - pdb=" NE2 HIS E 148 " pdb=" ZN F 301 " pdb="ZN ZN F 301 " - pdb=" NE2 HIS F 152 " pdb="ZN ZN F 301 " - pdb=" NE2 HIS F 148 " Number of angles added : 12 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 18 sheets defined 56.1% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'E' and resid 18 through 23 Processing helix chain 'E' and resid 25 through 29 removed outlier: 3.762A pdb=" N THR E 29 " --> pdb=" O PRO E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 50 removed outlier: 3.814A pdb=" N ARG E 45 " --> pdb=" O THR E 41 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLN E 48 " --> pdb=" O GLU E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 74 Processing helix chain 'E' and resid 75 through 80 removed outlier: 4.410A pdb=" N LEU E 79 " --> pdb=" O PRO E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 85 removed outlier: 3.685A pdb=" N LEU E 84 " --> pdb=" O LEU E 81 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASP E 85 " --> pdb=" O GLU E 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 81 through 85' Processing helix chain 'E' and resid 131 through 138 removed outlier: 3.532A pdb=" N PHE E 138 " --> pdb=" O ILE E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 155 Processing helix chain 'E' and resid 172 through 195 Processing helix chain 'E' and resid 196 through 199 removed outlier: 3.501A pdb=" N ALA E 199 " --> pdb=" O GLU E 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 196 through 199' Processing helix chain 'E' and resid 202 through 207 removed outlier: 3.667A pdb=" N SER E 207 " --> pdb=" O TYR E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 223 removed outlier: 3.550A pdb=" N PHE E 221 " --> pdb=" O SER E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 227 Processing helix chain 'E' and resid 231 through 243 Processing helix chain 'E' and resid 245 through 251 Processing helix chain 'A' and resid 9 through 29 Processing helix chain 'A' and resid 32 through 41 Processing helix chain 'A' and resid 45 through 57 Processing helix chain 'A' and resid 123 through 139 Processing helix chain 'A' and resid 140 through 142 No H-bonds generated for 'chain 'A' and resid 140 through 142' Processing helix chain 'A' and resid 177 through 187 Processing helix chain 'A' and resid 195 through 206 Processing helix chain 'A' and resid 244 through 248 Processing helix chain 'A' and resid 265 through 270 Processing helix chain 'A' and resid 270 through 284 removed outlier: 3.995A pdb=" N GLN A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 292 removed outlier: 3.556A pdb=" N GLY A 292 " --> pdb=" O MET A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 307 Processing helix chain 'A' and resid 308 through 334 Processing helix chain 'A' and resid 342 through 346 removed outlier: 3.706A pdb=" N LYS A 346 " --> pdb=" O PRO A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 362 Proline residue: A 353 - end of helix Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 382 through 385 removed outlier: 4.250A pdb=" N ALA A 385 " --> pdb=" O GLY A 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 382 through 385' Processing helix chain 'A' and resid 386 through 396 removed outlier: 3.839A pdb=" N VAL A 390 " --> pdb=" O GLY A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 404 Processing helix chain 'B' and resid 9 through 29 removed outlier: 3.676A pdb=" N GLN B 15 " --> pdb=" O ASP B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 40 Processing helix chain 'B' and resid 43 through 57 Processing helix chain 'B' and resid 123 through 140 Processing helix chain 'B' and resid 141 through 143 No H-bonds generated for 'chain 'B' and resid 141 through 143' Processing helix chain 'B' and resid 177 through 187 Processing helix chain 'B' and resid 195 through 206 Processing helix chain 'B' and resid 244 through 248 removed outlier: 3.622A pdb=" N THR B 248 " --> pdb=" O ILE B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 270 Processing helix chain 'B' and resid 270 through 283 removed outlier: 3.984A pdb=" N ASN B 283 " --> pdb=" O GLN B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 307 Processing helix chain 'B' and resid 308 through 334 removed outlier: 3.778A pdb=" N ILE B 325 " --> pdb=" O HIS B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 346 Processing helix chain 'B' and resid 347 through 362 Proline residue: B 353 - end of helix Processing helix chain 'B' and resid 364 through 369 Processing helix chain 'B' and resid 384 through 396 removed outlier: 4.263A pdb=" N ALA B 388 " --> pdb=" O MET B 384 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU B 389 " --> pdb=" O ALA B 385 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL B 390 " --> pdb=" O GLY B 386 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA B 393 " --> pdb=" O LEU B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 405 removed outlier: 3.921A pdb=" N ARG B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 23 Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.762A pdb=" N THR F 29 " --> pdb=" O PRO F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 50 removed outlier: 3.815A pdb=" N ARG F 45 " --> pdb=" O THR F 41 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLN F 48 " --> pdb=" O GLU F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 74 Processing helix chain 'F' and resid 75 through 80 removed outlier: 4.410A pdb=" N LEU F 79 " --> pdb=" O PRO F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 85 removed outlier: 3.686A pdb=" N LEU F 84 " --> pdb=" O LEU F 81 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASP F 85 " --> pdb=" O GLU F 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 81 through 85' Processing helix chain 'F' and resid 131 through 138 removed outlier: 3.532A pdb=" N PHE F 138 " --> pdb=" O ILE F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 155 Processing helix chain 'F' and resid 172 through 195 Processing helix chain 'F' and resid 196 through 199 Processing helix chain 'F' and resid 202 through 207 removed outlier: 3.668A pdb=" N SER F 207 " --> pdb=" O TYR F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 223 removed outlier: 3.551A pdb=" N PHE F 221 " --> pdb=" O SER F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 227 Processing helix chain 'F' and resid 231 through 243 Processing helix chain 'F' and resid 245 through 251 Processing helix chain 'C' and resid 9 through 29 Processing helix chain 'C' and resid 32 through 41 Processing helix chain 'C' and resid 45 through 57 Processing helix chain 'C' and resid 123 through 139 Processing helix chain 'C' and resid 140 through 142 No H-bonds generated for 'chain 'C' and resid 140 through 142' Processing helix chain 'C' and resid 177 through 187 Processing helix chain 'C' and resid 195 through 206 Processing helix chain 'C' and resid 244 through 248 Processing helix chain 'C' and resid 265 through 270 Processing helix chain 'C' and resid 270 through 284 removed outlier: 3.995A pdb=" N GLN C 284 " --> pdb=" O LEU C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 292 removed outlier: 3.556A pdb=" N GLY C 292 " --> pdb=" O MET C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 307 Processing helix chain 'C' and resid 308 through 334 Processing helix chain 'C' and resid 342 through 346 removed outlier: 3.706A pdb=" N LYS C 346 " --> pdb=" O PRO C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 362 Proline residue: C 353 - end of helix Processing helix chain 'C' and resid 364 through 369 Processing helix chain 'C' and resid 382 through 385 removed outlier: 4.251A pdb=" N ALA C 385 " --> pdb=" O GLY C 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 382 through 385' Processing helix chain 'C' and resid 386 through 396 removed outlier: 3.839A pdb=" N VAL C 390 " --> pdb=" O GLY C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 404 Processing helix chain 'D' and resid 9 through 29 removed outlier: 3.675A pdb=" N GLN D 15 " --> pdb=" O ASP D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 40 Processing helix chain 'D' and resid 43 through 57 Processing helix chain 'D' and resid 123 through 140 Processing helix chain 'D' and resid 141 through 143 No H-bonds generated for 'chain 'D' and resid 141 through 143' Processing helix chain 'D' and resid 177 through 187 Processing helix chain 'D' and resid 195 through 206 Processing helix chain 'D' and resid 244 through 248 removed outlier: 3.622A pdb=" N THR D 248 " --> pdb=" O ILE D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 270 Processing helix chain 'D' and resid 270 through 283 removed outlier: 3.775A pdb=" N ASN D 283 " --> pdb=" O GLN D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 307 Processing helix chain 'D' and resid 308 through 334 removed outlier: 3.778A pdb=" N ILE D 325 " --> pdb=" O HIS D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 346 Processing helix chain 'D' and resid 347 through 362 Proline residue: D 353 - end of helix Processing helix chain 'D' and resid 364 through 369 Processing helix chain 'D' and resid 384 through 396 removed outlier: 4.264A pdb=" N ALA D 388 " --> pdb=" O MET D 384 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU D 389 " --> pdb=" O ALA D 385 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL D 390 " --> pdb=" O GLY D 386 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA D 393 " --> pdb=" O LEU D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 405 removed outlier: 3.921A pdb=" N ARG D 402 " --> pdb=" O SER D 398 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 51 through 53 Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 63 Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 115 removed outlier: 6.596A pdb=" N LEU A 108 " --> pdb=" O ASP A 103 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ASP A 103 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE A 98 " --> pdb=" O ARG A 91 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG A 102 " --> pdb=" O TYR A 87 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N HIS A 86 " --> pdb=" O SER A 148 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N ALA A 150 " --> pdb=" O HIS A 86 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU A 88 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N THR A 152 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LEU A 90 " --> pdb=" O THR A 152 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 153 " --> pdb=" O GLN A 193 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 156 through 158 removed outlier: 7.025A pdb=" N ILE A 156 " --> pdb=" O HIS A 165 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 233 through 234 removed outlier: 5.948A pdb=" N ILE A 338 " --> pdb=" O GLU A 374 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 60 through 62 Processing sheet with id=AA7, first strand: chain 'B' and resid 108 through 115 removed outlier: 6.667A pdb=" N LEU B 108 " --> pdb=" O ASP B 103 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ASP B 103 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N HIS B 86 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE B 149 " --> pdb=" O HIS B 86 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU B 88 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ILE B 151 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU B 90 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N LEU B 153 " --> pdb=" O LEU B 90 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ILE B 92 " --> pdb=" O LEU B 153 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 156 through 158 removed outlier: 6.984A pdb=" N ILE B 156 " --> pdb=" O HIS B 165 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 233 through 234 removed outlier: 6.478A pdb=" N ILE B 216 " --> pdb=" O LEU B 339 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N GLY B 341 " --> pdb=" O ILE B 216 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL B 218 " --> pdb=" O GLY B 341 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 51 through 53 Processing sheet with id=AB2, first strand: chain 'C' and resid 60 through 63 Processing sheet with id=AB3, first strand: chain 'C' and resid 108 through 115 removed outlier: 6.596A pdb=" N LEU C 108 " --> pdb=" O ASP C 103 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ASP C 103 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE C 98 " --> pdb=" O ARG C 91 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG C 102 " --> pdb=" O TYR C 87 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N HIS C 86 " --> pdb=" O SER C 148 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N ALA C 150 " --> pdb=" O HIS C 86 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU C 88 " --> pdb=" O ALA C 150 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N THR C 152 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LEU C 90 " --> pdb=" O THR C 152 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU C 153 " --> pdb=" O GLN C 193 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 156 through 158 removed outlier: 7.024A pdb=" N ILE C 156 " --> pdb=" O HIS C 165 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 233 through 234 removed outlier: 5.949A pdb=" N ILE C 338 " --> pdb=" O GLU C 374 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 60 through 62 Processing sheet with id=AB7, first strand: chain 'D' and resid 108 through 115 removed outlier: 6.667A pdb=" N LEU D 108 " --> pdb=" O ASP D 103 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ASP D 103 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N HIS D 86 " --> pdb=" O THR D 147 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE D 149 " --> pdb=" O HIS D 86 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU D 88 " --> pdb=" O ILE D 149 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ILE D 151 " --> pdb=" O LEU D 88 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU D 90 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N LEU D 153 " --> pdb=" O LEU D 90 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ILE D 92 " --> pdb=" O LEU D 153 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 156 through 158 removed outlier: 6.984A pdb=" N ILE D 156 " --> pdb=" O HIS D 165 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 233 through 234 removed outlier: 6.478A pdb=" N ILE D 216 " --> pdb=" O LEU D 339 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N GLY D 341 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL D 218 " --> pdb=" O GLY D 341 " (cutoff:3.500A) 809 hydrogen bonds defined for protein. 2304 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.96 Time building geometry restraints manager: 3.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 15468 1.03 - 1.23: 22 1.23 - 1.42: 6366 1.42 - 1.61: 9158 1.61 - 1.81: 102 Bond restraints: 31116 Sorted by residual: bond pdb=" N GLN C 12 " pdb=" H GLN C 12 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" N GLN A 12 " pdb=" H GLN A 12 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" N VAL D 31 " pdb=" CA VAL D 31 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.20e-02 6.94e+03 9.69e+00 bond pdb=" N VAL B 31 " pdb=" CA VAL B 31 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.20e-02 6.94e+03 9.61e+00 bond pdb=" N TYR D 253 " pdb=" CA TYR D 253 " ideal model delta sigma weight residual 1.458 1.488 -0.031 1.22e-02 6.72e+03 6.38e+00 ... (remaining 31111 not shown) Histogram of bond angle deviations from ideal: 0.00 - 13.21: 56422 13.21 - 26.41: 2 26.41 - 39.62: 0 39.62 - 52.82: 0 52.82 - 66.03: 2 Bond angle restraints: 56426 Sorted by residual: angle pdb=" C ASP B 11 " pdb=" N GLN B 12 " pdb=" H GLN B 12 " ideal model delta sigma weight residual 124.32 58.29 66.03 3.00e+00 1.11e-01 4.84e+02 angle pdb=" C ASP D 11 " pdb=" N GLN D 12 " pdb=" H GLN D 12 " ideal model delta sigma weight residual 124.32 58.31 66.01 3.00e+00 1.11e-01 4.84e+02 angle pdb=" N ARG B 281 " pdb=" CA ARG B 281 " pdb=" CB ARG B 281 " ideal model delta sigma weight residual 110.53 102.86 7.67 1.49e+00 4.50e-01 2.65e+01 angle pdb=" C ASP C 11 " pdb=" N GLN C 12 " pdb=" H GLN C 12 " ideal model delta sigma weight residual 125.00 110.91 14.09 3.00e+00 1.11e-01 2.21e+01 angle pdb=" C ASP A 11 " pdb=" N GLN A 12 " pdb=" H GLN A 12 " ideal model delta sigma weight residual 125.00 110.91 14.09 3.00e+00 1.11e-01 2.21e+01 ... (remaining 56421 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 12853 17.87 - 35.73: 1166 35.73 - 53.60: 362 53.60 - 71.47: 106 71.47 - 89.34: 33 Dihedral angle restraints: 14520 sinusoidal: 8012 harmonic: 6508 Sorted by residual: dihedral pdb=" CA PRO E 54 " pdb=" C PRO E 54 " pdb=" N LEU E 55 " pdb=" CA LEU E 55 " ideal model delta harmonic sigma weight residual 180.00 -161.96 -18.04 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA PRO F 54 " pdb=" C PRO F 54 " pdb=" N LEU F 55 " pdb=" CA LEU F 55 " ideal model delta harmonic sigma weight residual -180.00 -161.99 -18.01 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CG ARG D 324 " pdb=" CD ARG D 324 " pdb=" NE ARG D 324 " pdb=" CZ ARG D 324 " ideal model delta sinusoidal sigma weight residual -90.00 -39.94 -50.06 2 1.50e+01 4.44e-03 1.25e+01 ... (remaining 14517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1999 0.048 - 0.096: 360 0.096 - 0.144: 118 0.144 - 0.192: 5 0.192 - 0.240: 4 Chirality restraints: 2486 Sorted by residual: chirality pdb=" CA TYR B 253 " pdb=" N TYR B 253 " pdb=" C TYR B 253 " pdb=" CB TYR B 253 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA TYR D 253 " pdb=" N TYR D 253 " pdb=" C TYR D 253 " pdb=" CB TYR D 253 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CG LEU F 17 " pdb=" CB LEU F 17 " pdb=" CD1 LEU F 17 " pdb=" CD2 LEU F 17 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 2483 not shown) Planarity restraints: 4624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 281 " 0.897 9.50e-02 1.11e+02 3.45e-01 7.50e+02 pdb=" NE ARG B 281 " 0.200 2.00e-02 2.50e+03 pdb=" CZ ARG B 281 " 0.042 2.00e-02 2.50e+03 pdb=" NH1 ARG B 281 " -0.032 2.00e-02 2.50e+03 pdb=" NH2 ARG B 281 " -0.034 2.00e-02 2.50e+03 pdb="HH11 ARG B 281 " -0.307 2.00e-02 2.50e+03 pdb="HH12 ARG B 281 " 0.196 2.00e-02 2.50e+03 pdb="HH21 ARG B 281 " -0.255 2.00e-02 2.50e+03 pdb="HH22 ARG B 281 " 0.150 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP D 11 " -0.074 2.00e-02 2.50e+03 2.43e-01 5.92e+02 pdb=" N GLN D 12 " 0.414 2.00e-02 2.50e+03 pdb=" CA GLN D 12 " -0.138 2.00e-02 2.50e+03 pdb=" H GLN D 12 " -0.201 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 11 " 0.075 2.00e-02 2.50e+03 2.43e-01 5.91e+02 pdb=" N GLN B 12 " -0.414 2.00e-02 2.50e+03 pdb=" CA GLN B 12 " 0.138 2.00e-02 2.50e+03 pdb=" H GLN B 12 " 0.201 2.00e-02 2.50e+03 ... (remaining 4621 not shown) Histogram of nonbonded interaction distances: 0.84 - 1.59: 32 1.59 - 2.34: 9924 2.34 - 3.10: 95763 3.10 - 3.85: 125808 3.85 - 4.60: 206051 Warning: very small nonbonded interaction distances. Nonbonded interactions: 437578 Sorted by model distance: nonbonded pdb=" HA SER A 287 " pdb=" HZ3 LYS D 255 " model vdw 0.840 1.816 nonbonded pdb=" HZ3 LYS B 255 " pdb=" HA SER C 287 " model vdw 0.860 1.816 nonbonded pdb=" HZ2 LYS B 255 " pdb=" CB SER C 287 " model vdw 0.890 2.200 nonbonded pdb=" HB2 SER A 287 " pdb=" CD LYS D 255 " model vdw 0.911 2.920 nonbonded pdb=" HZ1 LYS B 255 " pdb=" C SER C 287 " model vdw 0.916 2.200 ... (remaining 437573 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: 0.04 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' 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=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.730 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: 0.190 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 33.770 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.080 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:6.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 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 : 0.011 0.962 15650 Z= 1.048 Angle : 0.595 7.667 21224 Z= 0.332 Chirality : 0.042 0.240 2486 Planarity : 0.007 0.244 2738 Dihedral : 16.684 89.335 5736 Min Nonbonded Distance : 1.575 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.17 % Favored : 94.73 % Rotamer: Outliers : 1.02 % Allowed : 22.58 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.19), residues: 1954 helix: 1.04 (0.18), residues: 932 sheet: -0.55 (0.31), residues: 272 loop : -1.02 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 52 TYR 0.012 0.001 TYR A 22 PHE 0.008 0.001 PHE D 135 TRP 0.006 0.001 TRP E 19 HIS 0.005 0.001 HIS C 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.17 (15628) covalent geometry : angle 0.59516 / 0.33 (21212) hydrogen bonds : bond 0.17142 / 11.04 ( 809) hydrogen bonds : angle 7.05765 / 5.11 ( 2304) metal coordination : bond 0.00824 / 0.58 ( 20) metal coordination : angle 0.82346 / 0.49 ( 12) Misc. bond : bond 0.91517 / 46.17 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 391 time to evaluate : 0.831 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: E 225 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7624 (mp0) REVERT: A 52 ARG cc_start: 0.7680 (ttp-170) cc_final: 0.7471 (ttp80) REVERT: B 167 MET cc_start: 0.7135 (ptm) cc_final: 0.6792 (ptm) REVERT: B 190 VAL cc_start: 0.8042 (m) cc_final: 0.7773 (t) REVERT: B 206 PHE cc_start: 0.8622 (OUTLIER) cc_final: 0.6928 (m-10) REVERT: B 285 SER cc_start: 0.7691 (t) cc_final: 0.7040 (p) REVERT: F 218 GLU cc_start: 0.6900 (mt-10) cc_final: 0.6585 (mt-10) REVERT: F 225 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7546 (mp0) outliers start: 17 outliers final: 7 residues processed: 403 average time/residue: 1.2028 time to fit residues: 540.5389 Evaluate side-chains 346 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 338 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 206 PHE Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 206 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 98 optimal weight: 0.0030 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 overall best weight: 1.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 223 ASN A 284 GLN B 279 GLN B 284 GLN F 186 ASN C 284 GLN D 15 GLN D 284 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.159062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.137715 restraints weight = 66373.490| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 1.72 r_work: 0.3823 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3694 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 15650 Z= 0.225 Angle : 0.627 8.030 21224 Z= 0.329 Chirality : 0.045 0.155 2486 Planarity : 0.005 0.075 2738 Dihedral : 5.246 48.714 2117 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.87 % Allowed : 20.91 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.19), residues: 1954 helix: 0.95 (0.17), residues: 918 sheet: -0.62 (0.29), residues: 296 loop : -0.91 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 23 TYR 0.012 0.002 TYR B 87 PHE 0.019 0.002 PHE B 333 TRP 0.006 0.001 TRP D 199 HIS 0.007 0.002 HIS A 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.22 (15628) covalent geometry : angle 0.62003 / 0.33 (21212) hydrogen bonds : bond 0.05137 / 3.38 ( 809) hydrogen bonds : angle 5.35000 / 3.85 ( 2304) metal coordination : bond 0.01829 / 1.14 ( 20) metal coordination : angle 4.00397 / 2.33 ( 12) Misc. bond : bond 0.01477 / 0.74 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 371 time to evaluate : 0.822 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: E 184 MET cc_start: 0.8422 (mtp) cc_final: 0.8180 (mtp) REVERT: E 190 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7850 (mt-10) REVERT: E 225 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7778 (mp0) REVERT: A 158 ASP cc_start: 0.6922 (t0) cc_final: 0.6592 (t0) REVERT: B 167 MET cc_start: 0.7360 (ptm) cc_final: 0.7090 (ptm) REVERT: B 206 PHE cc_start: 0.8651 (OUTLIER) cc_final: 0.7091 (m-10) REVERT: B 285 SER cc_start: 0.7925 (t) cc_final: 0.7685 (m) REVERT: B 369 GLN cc_start: 0.7497 (pt0) cc_final: 0.7147 (mt0) REVERT: F 218 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6989 (mt-10) REVERT: F 225 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7750 (mp0) REVERT: C 152 THR cc_start: 0.7877 (OUTLIER) cc_final: 0.7522 (m) REVERT: D 22 TYR cc_start: 0.7900 (t80) cc_final: 0.7599 (t80) REVERT: D 206 PHE cc_start: 0.8521 (OUTLIER) cc_final: 0.6750 (m-80) REVERT: D 244 GLU cc_start: 0.8265 (mm-30) cc_final: 0.8058 (mm-30) outliers start: 48 outliers final: 15 residues processed: 396 average time/residue: 1.3814 time to fit residues: 605.0317 Evaluate side-chains 370 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 352 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 206 PHE Chi-restraints excluded: chain B residue 284 GLN Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 30 CYS Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 206 PHE Chi-restraints excluded: chain D residue 284 GLN Chi-restraints excluded: chain D residue 288 SER Chi-restraints excluded: chain D residue 299 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 85 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 171 optimal weight: 0.8980 chunk 138 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 183 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 186 ASN A 223 ASN A 361 GLN B 222 HIS B 233 HIS B 380 ASN F 186 ASN C 284 GLN D 369 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.159100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.137759 restraints weight = 66305.077| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 1.73 r_work: 0.3822 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3694 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 15650 Z= 0.174 Angle : 0.568 12.210 21224 Z= 0.296 Chirality : 0.042 0.152 2486 Planarity : 0.005 0.066 2738 Dihedral : 4.727 40.329 2108 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.81 % Allowed : 21.21 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.19), residues: 1954 helix: 1.04 (0.17), residues: 918 sheet: -0.55 (0.29), residues: 294 loop : -0.84 (0.24), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 23 TYR 0.008 0.001 TYR B 87 PHE 0.012 0.001 PHE F 227 TRP 0.005 0.001 TRP E 19 HIS 0.006 0.001 HIS A 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (15628) covalent geometry : angle 0.56353 / 0.30 (21212) hydrogen bonds : bond 0.04746 / 3.13 ( 809) hydrogen bonds : angle 5.11568 / 3.69 ( 2304) metal coordination : bond 0.01435 / 0.86 ( 20) metal coordination : angle 2.94044 / 1.70 ( 12) Misc. bond : bond 0.02251 / 1.11 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 354 time to evaluate : 0.736 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: E 184 MET cc_start: 0.8440 (mtp) cc_final: 0.8084 (mtp) REVERT: E 225 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7762 (mp0) REVERT: B 324 ARG cc_start: 0.8077 (ttm-80) cc_final: 0.7867 (ttm-80) REVERT: B 369 GLN cc_start: 0.7512 (pt0) cc_final: 0.7113 (mt0) REVERT: F 218 GLU cc_start: 0.7059 (mt-10) cc_final: 0.6755 (mt-10) REVERT: F 225 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7721 (mp0) REVERT: C 281 ARG cc_start: 0.8661 (mtm180) cc_final: 0.8394 (mmm-85) REVERT: D 22 TYR cc_start: 0.7906 (t80) cc_final: 0.7587 (t80) outliers start: 47 outliers final: 25 residues processed: 377 average time/residue: 1.3611 time to fit residues: 565.2359 Evaluate side-chains 372 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 347 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 20 GLN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 155 ASP Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain F residue 30 CYS Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 155 ASP Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 206 PHE Chi-restraints excluded: chain D residue 288 SER Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 374 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 73 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 191 optimal weight: 0.9990 chunk 181 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 361 GLN B 15 GLN B 222 HIS B 233 HIS F 186 ASN ** C 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 GLN D 369 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.159036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.137610 restraints weight = 66053.332| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 1.73 r_work: 0.3820 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3691 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15650 Z= 0.162 Angle : 0.550 7.018 21224 Z= 0.287 Chirality : 0.042 0.152 2486 Planarity : 0.005 0.069 2738 Dihedral : 4.618 39.310 2106 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.45 % Allowed : 21.45 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.19), residues: 1954 helix: 1.17 (0.17), residues: 916 sheet: -0.57 (0.29), residues: 294 loop : -0.82 (0.24), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 23 TYR 0.007 0.001 TYR A 22 PHE 0.011 0.001 PHE C 135 TRP 0.005 0.001 TRP E 19 HIS 0.006 0.001 HIS A 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (15628) covalent geometry : angle 0.54536 / 0.29 (21212) hydrogen bonds : bond 0.04499 / 2.95 ( 809) hydrogen bonds : angle 4.97612 / 3.59 ( 2304) metal coordination : bond 0.01509 / 0.92 ( 20) metal coordination : angle 2.93389 / 1.70 ( 12) Misc. bond : bond 0.02037 / 1.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 357 time to evaluate : 0.679 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: E 184 MET cc_start: 0.8440 (mtp) cc_final: 0.8110 (mtp) REVERT: E 190 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7812 (tt0) REVERT: E 225 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7805 (mp0) REVERT: B 54 MET cc_start: 0.7386 (OUTLIER) cc_final: 0.6907 (mmm) REVERT: B 101 LEU cc_start: 0.7097 (tt) cc_final: 0.6437 (mt) REVERT: B 324 ARG cc_start: 0.8092 (ttm-80) cc_final: 0.7881 (ttm-80) REVERT: B 369 GLN cc_start: 0.7517 (pt0) cc_final: 0.7093 (mt0) REVERT: F 172 GLU cc_start: 0.6879 (tm-30) cc_final: 0.6644 (tm-30) REVERT: F 225 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7705 (mp0) REVERT: C 184 GLN cc_start: 0.7327 (pp30) cc_final: 0.7058 (pp30) REVERT: D 22 TYR cc_start: 0.7908 (t80) cc_final: 0.7542 (t80) outliers start: 41 outliers final: 22 residues processed: 378 average time/residue: 1.3302 time to fit residues: 555.9523 Evaluate side-chains 367 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 344 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 20 GLN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 155 ASP Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain F residue 30 CYS Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 155 ASP Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 288 SER Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 374 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 147 optimal weight: 0.6980 chunk 141 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 173 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 186 ASN A 361 GLN ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 HIS F 158 ASN F 186 ASN ** C 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 GLN C 361 GLN D 369 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.157730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.136219 restraints weight = 65745.525| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 1.73 r_work: 0.3798 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3668 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 15650 Z= 0.241 Angle : 0.602 7.447 21224 Z= 0.316 Chirality : 0.044 0.156 2486 Planarity : 0.005 0.068 2738 Dihedral : 4.819 38.343 2104 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.87 % Allowed : 20.85 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.19), residues: 1954 helix: 0.97 (0.17), residues: 916 sheet: -0.68 (0.29), residues: 294 loop : -0.93 (0.24), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 402 TYR 0.009 0.001 TYR F 219 PHE 0.014 0.002 PHE C 135 TRP 0.008 0.001 TRP D 199 HIS 0.008 0.002 HIS A 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.24 (15628) covalent geometry : angle 0.59596 / 0.32 (21212) hydrogen bonds : bond 0.05016 / 3.28 ( 809) hydrogen bonds : angle 5.10032 / 3.68 ( 2304) metal coordination : bond 0.01705 / 0.99 ( 20) metal coordination : angle 3.64171 / 2.14 ( 12) Misc. bond : bond 0.02008 / 0.99 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 360 time to evaluate : 0.817 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: E 184 MET cc_start: 0.8431 (mtp) cc_final: 0.8090 (mtp) REVERT: E 227 PHE cc_start: 0.8330 (t80) cc_final: 0.8121 (t80) REVERT: A 184 GLN cc_start: 0.7270 (pp30) cc_final: 0.7022 (pp30) REVERT: B 47 ILE cc_start: 0.7656 (OUTLIER) cc_final: 0.7436 (tp) REVERT: B 54 MET cc_start: 0.7428 (OUTLIER) cc_final: 0.6834 (mmm) REVERT: F 63 LEU cc_start: 0.7810 (tp) cc_final: 0.7610 (tt) REVERT: F 172 GLU cc_start: 0.6835 (tm-30) cc_final: 0.6632 (tm-30) REVERT: F 225 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7704 (mp0) REVERT: C 184 GLN cc_start: 0.7309 (pp30) cc_final: 0.7024 (pp30) REVERT: D 22 TYR cc_start: 0.7939 (t80) cc_final: 0.7574 (t80) REVERT: D 85 TRP cc_start: 0.6890 (OUTLIER) cc_final: 0.6497 (m100) outliers start: 48 outliers final: 26 residues processed: 385 average time/residue: 1.3546 time to fit residues: 575.9334 Evaluate side-chains 386 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 357 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 155 ASP Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain F residue 30 CYS Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 155 ASP Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 85 TRP Chi-restraints excluded: chain D residue 288 SER Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 302 GLN Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 374 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 122 optimal weight: 2.9990 chunk 169 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 144 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN B 15 GLN B 222 HIS B 233 HIS B 369 GLN F 186 ASN ** C 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 HIS C 284 GLN C 361 GLN D 369 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.157377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.135894 restraints weight = 65781.628| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 1.72 r_work: 0.3795 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3665 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 15650 Z= 0.233 Angle : 0.604 6.586 21224 Z= 0.317 Chirality : 0.044 0.161 2486 Planarity : 0.005 0.082 2738 Dihedral : 4.854 37.373 2104 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.11 % Allowed : 21.03 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.19), residues: 1954 helix: 0.92 (0.17), residues: 918 sheet: -0.82 (0.29), residues: 294 loop : -1.03 (0.23), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 324 TYR 0.009 0.001 TYR A 22 PHE 0.013 0.002 PHE C 135 TRP 0.011 0.002 TRP D 85 HIS 0.008 0.001 HIS A 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.23 (15628) covalent geometry : angle 0.59764 / 0.32 (21212) hydrogen bonds : bond 0.04902 / 3.21 ( 809) hydrogen bonds : angle 5.04374 / 3.65 ( 2304) metal coordination : bond 0.01756 / 1.06 ( 20) metal coordination : angle 3.60841 / 2.11 ( 12) Misc. bond : bond 0.02005 / 0.99 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 358 time to evaluate : 0.795 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: E 152 HIS cc_start: 0.8060 (OUTLIER) cc_final: 0.7782 (m90) REVERT: E 184 MET cc_start: 0.8438 (mtp) cc_final: 0.8109 (mtp) REVERT: A 167 MET cc_start: 0.7700 (ptm) cc_final: 0.7321 (ptm) REVERT: A 184 GLN cc_start: 0.7216 (pp30) cc_final: 0.6938 (pp30) REVERT: B 101 LEU cc_start: 0.6516 (tt) cc_final: 0.6193 (mt) REVERT: F 136 ASP cc_start: 0.7873 (m-30) cc_final: 0.7567 (m-30) REVERT: F 172 GLU cc_start: 0.6990 (tm-30) cc_final: 0.6782 (tm-30) REVERT: F 184 MET cc_start: 0.8457 (mtp) cc_final: 0.8170 (mtp) REVERT: C 184 GLN cc_start: 0.7310 (pp30) cc_final: 0.7012 (pp30) REVERT: D 101 LEU cc_start: 0.7122 (tt) cc_final: 0.6475 (mt) REVERT: D 369 GLN cc_start: 0.7832 (pt0) cc_final: 0.7510 (pt0) outliers start: 52 outliers final: 31 residues processed: 386 average time/residue: 1.4256 time to fit residues: 607.0266 Evaluate side-chains 380 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 348 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 155 ASP Chi-restraints excluded: chain E residue 160 ASP Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 306 ARG Chi-restraints excluded: chain F residue 30 CYS Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 155 ASP Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 396 ASN Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 288 SER Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 302 GLN Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 374 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 170 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 168 optimal weight: 0.0980 chunk 25 optimal weight: 2.9990 chunk 79 optimal weight: 0.1980 chunk 189 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 HIS A 223 ASN A 361 GLN B 15 GLN B 222 HIS B 233 HIS F 186 ASN C 131 HIS C 284 GLN C 361 GLN D 193 GLN D 222 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.158224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.136656 restraints weight = 65866.968| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 1.74 r_work: 0.3805 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3676 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 15650 Z= 0.172 Angle : 0.574 6.530 21224 Z= 0.299 Chirality : 0.042 0.169 2486 Planarity : 0.005 0.082 2738 Dihedral : 4.700 36.914 2104 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.75 % Allowed : 22.46 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.19), residues: 1954 helix: 1.21 (0.17), residues: 904 sheet: -0.85 (0.29), residues: 300 loop : -0.86 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 23 TYR 0.008 0.001 TYR A 22 PHE 0.011 0.001 PHE A 135 TRP 0.005 0.001 TRP E 19 HIS 0.006 0.001 HIS A 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (15628) covalent geometry : angle 0.56911 / 0.30 (21212) hydrogen bonds : bond 0.04489 / 2.93 ( 809) hydrogen bonds : angle 4.90692 / 3.55 ( 2304) metal coordination : bond 0.01651 / 1.00 ( 20) metal coordination : angle 3.06112 / 1.77 ( 12) Misc. bond : bond 0.01997 / 0.99 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 354 time to evaluate : 0.720 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: E 152 HIS cc_start: 0.8031 (OUTLIER) cc_final: 0.7759 (m90) REVERT: E 184 MET cc_start: 0.8420 (mtp) cc_final: 0.8093 (mtp) REVERT: E 248 GLN cc_start: 0.8006 (tm-30) cc_final: 0.7728 (tm-30) REVERT: A 167 MET cc_start: 0.7648 (ptm) cc_final: 0.7228 (ptm) REVERT: A 184 GLN cc_start: 0.7250 (pp30) cc_final: 0.6974 (pp30) REVERT: F 34 GLN cc_start: 0.6981 (mm-40) cc_final: 0.6754 (mm-40) REVERT: F 136 ASP cc_start: 0.7864 (m-30) cc_final: 0.7576 (m-30) REVERT: F 191 ILE cc_start: 0.8539 (OUTLIER) cc_final: 0.8087 (mt) REVERT: C 184 GLN cc_start: 0.7285 (pp30) cc_final: 0.6988 (pp30) REVERT: C 302 GLN cc_start: 0.8170 (mt0) cc_final: 0.7963 (mt0) REVERT: D 54 MET cc_start: 0.7503 (OUTLIER) cc_final: 0.5189 (mpp) REVERT: D 101 LEU cc_start: 0.7091 (tt) cc_final: 0.6425 (mt) REVERT: D 369 GLN cc_start: 0.7796 (pt0) cc_final: 0.7448 (pt0) outliers start: 46 outliers final: 35 residues processed: 377 average time/residue: 1.3720 time to fit residues: 571.8196 Evaluate side-chains 381 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 343 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 20 GLN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 155 ASP Chi-restraints excluded: chain E residue 160 ASP Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain B residue 12 GLN Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 306 ARG Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain F residue 30 CYS Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 155 ASP Chi-restraints excluded: chain F residue 191 ILE Chi-restraints excluded: chain C residue 9 HIS Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 396 ASN Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 54 MET Chi-restraints excluded: chain D residue 288 SER Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 302 GLN Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 374 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 177 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 179 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 223 ASN B 233 HIS B 369 GLN F 186 ASN C 284 GLN C 361 GLN D 222 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.158287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.136753 restraints weight = 65885.815| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 1.74 r_work: 0.3805 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3676 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 15650 Z= 0.169 Angle : 0.578 6.386 21224 Z= 0.301 Chirality : 0.042 0.146 2486 Planarity : 0.005 0.088 2738 Dihedral : 4.659 36.462 2104 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.81 % Allowed : 22.40 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.19), residues: 1954 helix: 1.20 (0.17), residues: 916 sheet: -0.59 (0.30), residues: 280 loop : -1.02 (0.23), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 23 TYR 0.007 0.001 TYR A 87 PHE 0.013 0.001 PHE C 135 TRP 0.015 0.001 TRP E 176 HIS 0.008 0.001 HIS D 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (15628) covalent geometry : angle 0.57360 / 0.30 (21212) hydrogen bonds : bond 0.04418 / 2.90 ( 809) hydrogen bonds : angle 4.85164 / 3.52 ( 2304) metal coordination : bond 0.01610 / 0.97 ( 20) metal coordination : angle 3.09359 / 1.80 ( 12) Misc. bond : bond 0.01997 / 0.99 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 347 time to evaluate : 0.575 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: E 152 HIS cc_start: 0.8031 (OUTLIER) cc_final: 0.7811 (m-70) REVERT: E 167 PHE cc_start: 0.8430 (t80) cc_final: 0.8115 (t80) REVERT: E 184 MET cc_start: 0.8414 (mtp) cc_final: 0.8056 (mtp) REVERT: E 248 GLN cc_start: 0.7966 (tm-30) cc_final: 0.7724 (tm-30) REVERT: A 167 MET cc_start: 0.7632 (ptm) cc_final: 0.7241 (ptm) REVERT: A 184 GLN cc_start: 0.7252 (pp30) cc_final: 0.6982 (pp30) REVERT: B 83 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7207 (mm-30) REVERT: F 34 GLN cc_start: 0.6960 (mm-40) cc_final: 0.6740 (mm-40) REVERT: F 136 ASP cc_start: 0.7879 (m-30) cc_final: 0.7658 (m-30) REVERT: F 191 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.7997 (mt) REVERT: F 218 GLU cc_start: 0.6938 (mt-10) cc_final: 0.6681 (tt0) REVERT: C 184 GLN cc_start: 0.7289 (pp30) cc_final: 0.6992 (pp30) REVERT: C 302 GLN cc_start: 0.8174 (mt0) cc_final: 0.7955 (mt0) REVERT: D 22 TYR cc_start: 0.7943 (t80) cc_final: 0.7588 (t80) REVERT: D 54 MET cc_start: 0.7481 (OUTLIER) cc_final: 0.5113 (mpp) REVERT: D 369 GLN cc_start: 0.7795 (pt0) cc_final: 0.7441 (pt0) outliers start: 47 outliers final: 33 residues processed: 375 average time/residue: 1.2902 time to fit residues: 534.5205 Evaluate side-chains 378 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 341 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 20 GLN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 155 ASP Chi-restraints excluded: chain E residue 160 ASP Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain B residue 12 GLN Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain F residue 30 CYS Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 155 ASP Chi-restraints excluded: chain F residue 191 ILE Chi-restraints excluded: chain C residue 9 HIS Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 396 ASN Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 54 MET Chi-restraints excluded: chain D residue 288 SER Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 302 GLN Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 374 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 160 optimal weight: 0.7980 chunk 12 optimal weight: 0.4980 chunk 181 optimal weight: 0.9980 chunk 105 optimal weight: 0.2980 chunk 138 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 169 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 141 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 186 ASN A 361 GLN B 15 GLN F 186 ASN C 284 GLN C 361 GLN D 222 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.158957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.137412 restraints weight = 66042.688| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 1.75 r_work: 0.3814 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3685 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 15650 Z= 0.144 Angle : 0.565 8.111 21224 Z= 0.293 Chirality : 0.041 0.143 2486 Planarity : 0.005 0.089 2738 Dihedral : 4.521 36.126 2104 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.39 % Allowed : 23.00 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.19), residues: 1954 helix: 1.41 (0.17), residues: 906 sheet: -0.55 (0.30), residues: 280 loop : -0.93 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 23 TYR 0.007 0.001 TYR C 87 PHE 0.012 0.001 PHE F 138 TRP 0.007 0.001 TRP E 176 HIS 0.007 0.001 HIS D 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (15628) covalent geometry : angle 0.56126 / 0.29 (21212) hydrogen bonds : bond 0.04199 / 2.76 ( 809) hydrogen bonds : angle 4.74171 / 3.44 ( 2304) metal coordination : bond 0.01543 / 0.94 ( 20) metal coordination : angle 2.73276 / 1.58 ( 12) Misc. bond : bond 0.01993 / 0.99 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 346 time to evaluate : 1.046 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: E 129 LEU cc_start: 0.7697 (mt) cc_final: 0.7389 (mt) REVERT: E 152 HIS cc_start: 0.8004 (OUTLIER) cc_final: 0.7753 (m-70) REVERT: E 167 PHE cc_start: 0.8419 (t80) cc_final: 0.8190 (t80) REVERT: E 184 MET cc_start: 0.8413 (mtp) cc_final: 0.8060 (mtp) REVERT: E 190 GLU cc_start: 0.7821 (tt0) cc_final: 0.7363 (tt0) REVERT: E 248 GLN cc_start: 0.7958 (tm-30) cc_final: 0.7694 (tm-30) REVERT: A 167 MET cc_start: 0.7594 (ptm) cc_final: 0.7176 (ptm) REVERT: A 184 GLN cc_start: 0.7251 (pp30) cc_final: 0.6985 (pp30) REVERT: B 369 GLN cc_start: 0.7722 (pt0) cc_final: 0.7420 (pt0) REVERT: F 34 GLN cc_start: 0.6956 (mm-40) cc_final: 0.6740 (mm-40) REVERT: F 136 ASP cc_start: 0.7872 (m-30) cc_final: 0.7641 (m-30) REVERT: F 172 GLU cc_start: 0.7155 (tm-30) cc_final: 0.6862 (tm-30) REVERT: F 191 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.7997 (mt) REVERT: C 184 GLN cc_start: 0.7295 (pp30) cc_final: 0.7004 (pp30) REVERT: C 302 GLN cc_start: 0.8169 (mt0) cc_final: 0.7953 (mt0) REVERT: D 22 TYR cc_start: 0.7948 (t80) cc_final: 0.7598 (t80) REVERT: D 54 MET cc_start: 0.7445 (OUTLIER) cc_final: 0.5051 (mpp) REVERT: D 369 GLN cc_start: 0.7759 (pt0) cc_final: 0.7420 (pt0) outliers start: 40 outliers final: 30 residues processed: 371 average time/residue: 1.3229 time to fit residues: 542.0928 Evaluate side-chains 375 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 342 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 20 GLN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 155 ASP Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain B residue 12 GLN Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain F residue 30 CYS Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 155 ASP Chi-restraints excluded: chain F residue 191 ILE Chi-restraints excluded: chain C residue 9 HIS Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 396 ASN Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 54 MET Chi-restraints excluded: chain D residue 255 LYS Chi-restraints excluded: chain D residue 288 SER Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 302 GLN Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 374 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 169 optimal weight: 0.9980 chunk 181 optimal weight: 0.9980 chunk 160 optimal weight: 0.0980 chunk 148 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 1 optimal weight: 0.4980 chunk 100 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 158 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 361 GLN F 186 ASN C 284 GLN C 361 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.159027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.137456 restraints weight = 65860.991| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 1.75 r_work: 0.3815 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3686 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 15650 Z= 0.152 Angle : 0.595 13.204 21224 Z= 0.309 Chirality : 0.042 0.180 2486 Planarity : 0.005 0.092 2738 Dihedral : 4.518 35.899 2104 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.03 % Allowed : 23.60 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.19), residues: 1954 helix: 1.42 (0.17), residues: 906 sheet: -0.53 (0.30), residues: 280 loop : -0.96 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 23 TYR 0.007 0.001 TYR B 87 PHE 0.014 0.001 PHE E 227 TRP 0.007 0.001 TRP E 176 HIS 0.006 0.001 HIS D 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (15628) covalent geometry : angle 0.59176 / 0.31 (21212) hydrogen bonds : bond 0.04222 / 2.79 ( 809) hydrogen bonds : angle 4.73384 / 3.43 ( 2304) metal coordination : bond 0.01491 / 0.88 ( 20) metal coordination : angle 2.80730 / 1.63 ( 12) Misc. bond : bond 0.02304 / 1.13 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 347 time to evaluate : 0.810 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: E 152 HIS cc_start: 0.7996 (OUTLIER) cc_final: 0.7748 (m-70) REVERT: E 167 PHE cc_start: 0.8412 (t80) cc_final: 0.8150 (t80) REVERT: E 184 MET cc_start: 0.8418 (mtp) cc_final: 0.8067 (mtp) REVERT: E 190 GLU cc_start: 0.7858 (tt0) cc_final: 0.7616 (tt0) REVERT: E 191 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8066 (mt) REVERT: E 248 GLN cc_start: 0.7949 (tm-30) cc_final: 0.7685 (tm-30) REVERT: A 167 MET cc_start: 0.7605 (ptm) cc_final: 0.7193 (ptm) REVERT: A 184 GLN cc_start: 0.7254 (pp30) cc_final: 0.6984 (pp30) REVERT: B 167 MET cc_start: 0.7018 (ptp) cc_final: 0.6666 (ptm) REVERT: B 176 MET cc_start: 0.6866 (tpp) cc_final: 0.6649 (tpp) REVERT: B 369 GLN cc_start: 0.7711 (pt0) cc_final: 0.7416 (pt0) REVERT: F 34 GLN cc_start: 0.6937 (mm-40) cc_final: 0.6727 (mm-40) REVERT: F 136 ASP cc_start: 0.7877 (m-30) cc_final: 0.7632 (m-30) REVERT: F 172 GLU cc_start: 0.7148 (tm-30) cc_final: 0.6841 (tm-30) REVERT: F 184 MET cc_start: 0.8433 (mtp) cc_final: 0.8002 (mtp) REVERT: F 191 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.7965 (mt) REVERT: C 62 GLU cc_start: 0.8142 (mp0) cc_final: 0.7940 (mp0) REVERT: C 184 GLN cc_start: 0.7305 (pp30) cc_final: 0.7009 (pp30) REVERT: C 289 MET cc_start: 0.8724 (mtt) cc_final: 0.8473 (mtp) REVERT: C 302 GLN cc_start: 0.8168 (mt0) cc_final: 0.7954 (mt0) REVERT: D 22 TYR cc_start: 0.7958 (t80) cc_final: 0.7594 (t80) REVERT: D 54 MET cc_start: 0.7397 (OUTLIER) cc_final: 0.4913 (mpp) REVERT: D 369 GLN cc_start: 0.7766 (pt0) cc_final: 0.7428 (pt0) outliers start: 34 outliers final: 29 residues processed: 368 average time/residue: 1.4013 time to fit residues: 568.9352 Evaluate side-chains 375 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 342 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 155 ASP Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain B residue 12 GLN Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain F residue 30 CYS Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 155 ASP Chi-restraints excluded: chain F residue 191 ILE Chi-restraints excluded: chain C residue 9 HIS Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 396 ASN Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 54 MET Chi-restraints excluded: chain D residue 255 LYS Chi-restraints excluded: chain D residue 288 SER Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 302 GLN Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 374 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 111 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 151 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 187 optimal weight: 1.9990 chunk 20 optimal weight: 0.2980 chunk 12 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 361 GLN C 284 GLN C 361 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.159090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.137500 restraints weight = 66263.138| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 1.76 r_work: 0.3816 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3685 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 15650 Z= 0.146 Angle : 0.575 8.140 21224 Z= 0.297 Chirality : 0.041 0.185 2486 Planarity : 0.005 0.104 2738 Dihedral : 4.494 35.523 2104 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.15 % Allowed : 23.48 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.19), residues: 1954 helix: 1.49 (0.17), residues: 906 sheet: -0.53 (0.30), residues: 280 loop : -0.94 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 23 TYR 0.006 0.001 TYR C 87 PHE 0.012 0.001 PHE F 138 TRP 0.006 0.001 TRP E 19 HIS 0.008 0.001 HIS D 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (15628) covalent geometry : angle 0.57112 / 0.30 (21212) hydrogen bonds : bond 0.04146 / 2.73 ( 809) hydrogen bonds : angle 4.68688 / 3.40 ( 2304) metal coordination : bond 0.01594 / 1.00 ( 20) metal coordination : angle 2.84115 / 1.65 ( 12) Misc. bond : bond 0.02127 / 1.05 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17550.37 seconds wall clock time: 295 minutes 50.62 seconds (17750.62 seconds total)