Starting phenix.real_space_refine on Sun May 3 02:08:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21fy_67634/05_2026/21fy_67634_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/21fy_67634/05_2026/21fy_67634.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/21fy_67634/05_2026/21fy_67634.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21fy_67634/05_2026/21fy_67634.map" model { file = "/net/cci-nas-00/data/ceres_data/21fy_67634/05_2026/21fy_67634_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21fy_67634/05_2026/21fy_67634_neut.cif" } resolution = 2.85 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= 0.003 sd= 0.043 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 Fe 8 7.16 5 P 2 5.49 5 S 74 5.16 5 C 6212 2.51 5 N 1748 2.21 5 O 1868 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9912 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3063 Classifications: {'peptide': 390} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 376} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 3063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3063 Classifications: {'peptide': 390} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 376} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1885 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 10, 'TRANS': 228} Chain: "D" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1885 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 10, 'TRANS': 228} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7472 SG CYS C 176 22.936 38.977 41.648 1.00107.79 S ATOM 7965 SG CYS C 237 25.350 38.968 37.658 1.00 99.81 S ATOM 7455 SG CYS C 173 21.407 34.294 37.335 1.00 97.35 S ATOM 6812 SG CYS C 92 26.609 33.428 41.292 1.00 79.99 S ATOM 9357 SG CYS D 176 98.210 68.560 41.575 1.00103.91 S ATOM 9850 SG CYS D 237 95.593 68.583 37.744 1.00100.86 S ATOM 9340 SG CYS D 173 99.450 73.135 37.325 1.00 87.41 S ATOM 8697 SG CYS D 92 94.454 74.202 41.431 1.00 77.06 S Time building chain proxies: 2.50, per 1000 atoms: 0.25 Number of scatterers: 9912 At special positions: 0 Unit cell: (121.8, 108.36, 75.6, 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) Fe 8 26.01 S 74 16.00 P 2 15.00 O 1868 8.00 N 1748 7.00 C 6212 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 377.7 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 C 301 " pdb="FE2 SF4 C 301 " - pdb=" SG CYS C 237 " pdb="FE3 SF4 C 301 " - pdb=" SG CYS C 173 " pdb="FE4 SF4 C 301 " - pdb=" SG CYS C 92 " pdb="FE1 SF4 C 301 " - pdb=" SG CYS C 176 " pdb=" SF4 D 301 " pdb="FE2 SF4 D 301 " - pdb=" SG CYS D 237 " pdb="FE3 SF4 D 301 " - pdb=" SG CYS D 173 " pdb="FE4 SF4 D 301 " - pdb=" SG CYS D 92 " pdb="FE1 SF4 D 301 " - pdb=" SG CYS D 176 " Number of angles added : 24 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2304 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 10 sheets defined 46.9% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 16 through 25 removed outlier: 4.116A pdb=" N GLN A 25 " --> pdb=" O GLU A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 63 removed outlier: 3.581A pdb=" N TRP A 45 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A 61 " --> pdb=" O GLN A 57 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL A 62 " --> pdb=" O ILE A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 67 No H-bonds generated for 'chain 'A' and resid 65 through 67' Processing helix chain 'A' and resid 74 through 90 Processing helix chain 'A' and resid 104 through 116 removed outlier: 3.696A pdb=" N ARG A 116 " --> pdb=" O ARG A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 141 Processing helix chain 'A' and resid 162 through 174 removed outlier: 4.062A pdb=" N ILE A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.591A pdb=" N GLY A 238 " --> pdb=" O GLY A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 282 removed outlier: 3.614A pdb=" N GLU A 261 " --> pdb=" O ARG A 257 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N ALA A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N THR A 265 " --> pdb=" O GLU A 261 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET A 267 " --> pdb=" O MET A 263 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 317 Processing helix chain 'A' and resid 336 through 343 Processing helix chain 'A' and resid 345 through 351 Processing helix chain 'A' and resid 362 through 383 removed outlier: 3.746A pdb=" N LEU A 383 " --> pdb=" O ARG A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.725A pdb=" N GLU A 388 " --> pdb=" O PRO A 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 24 Processing helix chain 'B' and resid 41 through 63 removed outlier: 3.585A pdb=" N TRP B 45 " --> pdb=" O HIS B 41 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA B 47 " --> pdb=" O PHE B 43 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU B 61 " --> pdb=" O GLN B 57 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL B 62 " --> pdb=" O ILE B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 67 No H-bonds generated for 'chain 'B' and resid 65 through 67' Processing helix chain 'B' and resid 74 through 90 Processing helix chain 'B' and resid 104 through 116 removed outlier: 3.698A pdb=" N ARG B 116 " --> pdb=" O ARG B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 141 removed outlier: 3.552A pdb=" N LEU B 137 " --> pdb=" O ASP B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 174 removed outlier: 3.986A pdb=" N ILE B 166 " --> pdb=" O ASP B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 239 Processing helix chain 'B' and resid 245 through 282 removed outlier: 3.639A pdb=" N GLU B 261 " --> pdb=" O ARG B 257 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ALA B 264 " --> pdb=" O LYS B 260 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N THR B 265 " --> pdb=" O GLU B 261 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET B 267 " --> pdb=" O MET B 263 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU B 268 " --> pdb=" O ALA B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 317 Processing helix chain 'B' and resid 336 through 343 Processing helix chain 'B' and resid 345 through 351 Processing helix chain 'B' and resid 362 through 383 removed outlier: 3.650A pdb=" N LEU B 383 " --> pdb=" O ARG B 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 29 removed outlier: 3.958A pdb=" N ALA C 19 " --> pdb=" O GLY C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 57 removed outlier: 3.802A pdb=" N ARG C 50 " --> pdb=" O PRO C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 80 removed outlier: 3.561A pdb=" N VAL C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 104 removed outlier: 4.977A pdb=" N LYS C 99 " --> pdb=" O GLN C 95 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N VAL C 100 " --> pdb=" O LEU C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 119 Processing helix chain 'C' and resid 120 through 130 removed outlier: 3.589A pdb=" N ILE C 124 " --> pdb=" O GLU C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 143 Processing helix chain 'C' and resid 148 through 157 Processing helix chain 'C' and resid 161 through 166 removed outlier: 3.523A pdb=" N LYS C 165 " --> pdb=" O PRO C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 189 removed outlier: 3.597A pdb=" N TRP C 184 " --> pdb=" O GLY C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 206 removed outlier: 4.032A pdb=" N PHE C 195 " --> pdb=" O PHE C 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 29 removed outlier: 3.942A pdb=" N ALA D 19 " --> pdb=" O GLY D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 57 removed outlier: 4.274A pdb=" N GLN D 49 " --> pdb=" O HIS D 45 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG D 50 " --> pdb=" O PRO D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 80 removed outlier: 3.520A pdb=" N VAL D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 104 removed outlier: 5.083A pdb=" N LYS D 99 " --> pdb=" O GLN D 95 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N VAL D 100 " --> pdb=" O LEU D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 119 Processing helix chain 'D' and resid 120 through 130 removed outlier: 3.648A pdb=" N ILE D 124 " --> pdb=" O GLU D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 143 Processing helix chain 'D' and resid 145 through 157 removed outlier: 3.762A pdb=" N CYS D 149 " --> pdb=" O ASN D 145 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU D 150 " --> pdb=" O ARG D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 166 removed outlier: 3.550A pdb=" N LYS D 165 " --> pdb=" O PRO D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 189 removed outlier: 3.922A pdb=" N TRP D 184 " --> pdb=" O GLY D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 206 removed outlier: 4.089A pdb=" N PHE D 195 " --> pdb=" O PHE D 191 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 6 removed outlier: 7.166A pdb=" N ILE A 5 " --> pdb=" O ALA A 321 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 69 through 72 removed outlier: 6.566A pdb=" N TYR A 177 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N SER A 201 " --> pdb=" O TYR A 177 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL A 179 " --> pdb=" O SER A 201 " (cutoff:3.500A) removed outlier: 9.155A pdb=" N SER A 203 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE A 146 " --> pdb=" O ILE A 176 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N HIS A 178 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL A 148 " --> pdb=" O HIS A 178 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N ASP A 180 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N HIS A 96 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N SER A 149 " --> pdb=" O HIS A 96 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE A 98 " --> pdb=" O SER A 149 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE A 97 " --> pdb=" O THR A 122 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N LEU A 124 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N THR A 99 " --> pdb=" O LEU A 124 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 287 through 289 Processing sheet with id=AA4, first strand: chain 'A' and resid 327 through 329 Processing sheet with id=AA5, first strand: chain 'B' and resid 5 through 6 removed outlier: 7.112A pdb=" N ILE B 5 " --> pdb=" O ALA B 321 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 69 through 72 removed outlier: 6.668A pdb=" N ILE B 146 " --> pdb=" O ILE B 176 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N HIS B 178 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL B 148 " --> pdb=" O HIS B 178 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N ASP B 180 " --> pdb=" O VAL B 148 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N HIS B 96 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N SER B 149 " --> pdb=" O HIS B 96 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE B 98 " --> pdb=" O SER B 149 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE B 97 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LEU B 124 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N THR B 99 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 287 through 290 removed outlier: 4.672A pdb=" N ASN B 302 " --> pdb=" O ASN B 290 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 327 through 329 Processing sheet with id=AA9, first strand: chain 'C' and resid 64 through 66 removed outlier: 8.591A pdb=" N THR C 64 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N VAL C 36 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N VAL C 66 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ASN C 38 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL C 8 " --> pdb=" O THR C 35 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N PHE C 37 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N CYS C 10 " --> pdb=" O PHE C 37 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N ILE C 39 " --> pdb=" O CYS C 10 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 64 through 66 removed outlier: 6.070A pdb=" N VAL D 36 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N VAL D 66 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ASN D 38 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL D 8 " --> pdb=" O THR D 35 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N PHE D 37 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N CYS D 10 " --> pdb=" O PHE D 37 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N ILE D 39 " --> pdb=" O CYS D 10 " (cutoff:3.500A) 399 hydrogen bonds defined for protein. 1167 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: 1.36 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 4274 1.43 - 1.65: 5704 1.65 - 1.86: 108 1.86 - 2.07: 0 2.07 - 2.28: 24 Bond restraints: 10110 Sorted by residual: bond pdb=" NZ LLP A 206 " pdb=" C4' LLP A 206 " ideal model delta sigma weight residual 1.273 1.483 -0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" NZ LLP B 206 " pdb=" C4' LLP B 206 " ideal model delta sigma weight residual 1.273 1.472 -0.199 2.00e-02 2.50e+03 9.85e+01 bond pdb=" OP4 LLP A 206 " pdb=" P LLP A 206 " ideal model delta sigma weight residual 1.726 1.610 0.116 2.00e-02 2.50e+03 3.35e+01 bond pdb=" OP4 LLP B 206 " pdb=" P LLP B 206 " ideal model delta sigma weight residual 1.726 1.612 0.114 2.00e-02 2.50e+03 3.26e+01 bond pdb=" C2 LLP B 206 " pdb=" N1 LLP B 206 " ideal model delta sigma weight residual 1.319 1.375 -0.056 2.00e-02 2.50e+03 7.71e+00 ... (remaining 10105 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 13553 2.75 - 5.49: 87 5.49 - 8.24: 15 8.24 - 10.99: 3 10.99 - 13.74: 4 Bond angle restraints: 13662 Sorted by residual: angle pdb=" CE LLP A 206 " pdb=" NZ LLP A 206 " pdb=" C4' LLP A 206 " ideal model delta sigma weight residual 119.26 132.50 -13.24 3.00e+00 1.11e-01 1.95e+01 angle pdb=" CE LLP B 206 " pdb=" NZ LLP B 206 " pdb=" C4' LLP B 206 " ideal model delta sigma weight residual 119.26 131.26 -12.00 3.00e+00 1.11e-01 1.60e+01 angle pdb=" CA LEU A 383 " pdb=" CB LEU A 383 " pdb=" CG LEU A 383 " ideal model delta sigma weight residual 116.30 130.04 -13.74 3.50e+00 8.16e-02 1.54e+01 angle pdb=" CA LEU B 383 " pdb=" CB LEU B 383 " pdb=" CG LEU B 383 " ideal model delta sigma weight residual 116.30 128.46 -12.16 3.50e+00 8.16e-02 1.21e+01 angle pdb=" CB MET C 163 " pdb=" CG MET C 163 " pdb=" SD MET C 163 " ideal model delta sigma weight residual 112.70 121.55 -8.85 3.00e+00 1.11e-01 8.70e+00 ... (remaining 13657 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 5067 17.94 - 35.88: 723 35.88 - 53.82: 228 53.82 - 71.76: 43 71.76 - 89.69: 25 Dihedral angle restraints: 6086 sinusoidal: 2492 harmonic: 3594 Sorted by residual: dihedral pdb=" CA CYS D 14 " pdb=" C CYS D 14 " pdb=" N GLY D 15 " pdb=" CA GLY D 15 " ideal model delta harmonic sigma weight residual 180.00 161.52 18.48 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA CYS C 14 " pdb=" C CYS C 14 " pdb=" N GLY C 15 " pdb=" CA GLY C 15 " ideal model delta harmonic sigma weight residual 180.00 161.87 18.13 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA ASP D 141 " pdb=" CB ASP D 141 " pdb=" CG ASP D 141 " pdb=" OD1 ASP D 141 " ideal model delta sinusoidal sigma weight residual -30.00 -87.39 57.39 1 2.00e+01 2.50e-03 1.11e+01 ... (remaining 6083 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 960 0.037 - 0.073: 363 0.073 - 0.110: 136 0.110 - 0.147: 29 0.147 - 0.183: 4 Chirality restraints: 1492 Sorted by residual: chirality pdb=" CG LEU B 348 " pdb=" CB LEU B 348 " pdb=" CD1 LEU B 348 " pdb=" CD2 LEU B 348 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.39e-01 chirality pdb=" CG LEU B 383 " pdb=" CB LEU B 383 " pdb=" CD1 LEU B 383 " pdb=" CD2 LEU B 383 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.29e-01 chirality pdb=" CG LEU A 383 " pdb=" CB LEU A 383 " pdb=" CD1 LEU A 383 " pdb=" CD2 LEU A 383 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 6.95e-01 ... (remaining 1489 not shown) Planarity restraints: 1780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CE LLP B 206 " -0.191 2.00e-02 2.50e+03 1.83e-01 3.35e+02 pdb=" NZ LLP B 206 " 0.215 2.00e-02 2.50e+03 pdb=" C4 LLP B 206 " -0.171 2.00e-02 2.50e+03 pdb=" C4' LLP B 206 " 0.148 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CE LLP A 206 " 0.159 2.00e-02 2.50e+03 1.50e-01 2.25e+02 pdb=" NZ LLP A 206 " -0.192 2.00e-02 2.50e+03 pdb=" C4 LLP A 206 " 0.133 2.00e-02 2.50e+03 pdb=" C4' LLP A 206 " -0.101 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 LLP A 206 " 0.008 2.00e-02 2.50e+03 6.81e-02 1.16e+02 pdb=" C2' LLP A 206 " 0.032 2.00e-02 2.50e+03 pdb=" C3 LLP A 206 " -0.046 2.00e-02 2.50e+03 pdb=" C4 LLP A 206 " -0.066 2.00e-02 2.50e+03 pdb=" C4' LLP A 206 " 0.161 2.00e-02 2.50e+03 pdb=" C5 LLP A 206 " -0.020 2.00e-02 2.50e+03 pdb=" C5' LLP A 206 " -0.060 2.00e-02 2.50e+03 pdb=" C6 LLP A 206 " 0.026 2.00e-02 2.50e+03 pdb=" N1 LLP A 206 " 0.046 2.00e-02 2.50e+03 pdb=" O3 LLP A 206 " -0.080 2.00e-02 2.50e+03 ... (remaining 1777 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 617 2.73 - 3.27: 9423 3.27 - 3.82: 15939 3.82 - 4.36: 18812 4.36 - 4.90: 32860 Nonbonded interactions: 77651 Sorted by model distance: nonbonded pdb=" OG1 THR C 117 " pdb=" O PHE C 144 " model vdw 2.190 3.040 nonbonded pdb=" OG1 THR D 117 " pdb=" O PHE D 144 " model vdw 2.191 3.040 nonbonded pdb=" NZ LYS D 85 " pdb=" O LEU D 209 " model vdw 2.199 3.120 nonbonded pdb=" OH TYR C 168 " pdb=" OD2 ASP C 190 " model vdw 2.248 3.040 nonbonded pdb=" O VAL C 100 " pdb=" OG SER C 103 " model vdw 2.253 3.040 ... (remaining 77646 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.430 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 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 : 0.005 0.210 10118 Z= 0.251 Angle : 0.964 40.513 13686 Z= 0.308 Chirality : 0.045 0.183 1492 Planarity : 0.007 0.183 1780 Dihedral : 19.115 89.695 3782 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.36 % Allowed : 32.92 % Favored : 64.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.56 (0.25), residues: 1244 helix: 1.27 (0.23), residues: 526 sheet: 0.73 (0.45), residues: 158 loop : -0.57 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 112 TYR 0.009 0.001 TYR B 208 PHE 0.032 0.002 PHE C 126 TRP 0.008 0.001 TRP C 58 HIS 0.005 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00550 (10110) covalent geometry : angle 0.63560 (13662) hydrogen bonds : bond 0.15535 ( 399) hydrogen bonds : angle 5.87821 ( 1167) metal coordination : bond 0.00447 ( 8) metal coordination : angle 17.32888 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 284 time to evaluate : 0.360 Fit side-chains REVERT: A 8 ASP cc_start: 0.8452 (t0) cc_final: 0.8230 (t0) REVERT: A 309 GLU cc_start: 0.7391 (mp0) cc_final: 0.7084 (mp0) REVERT: B 135 LYS cc_start: 0.8218 (mmmm) cc_final: 0.8016 (mmmm) REVERT: B 198 ASP cc_start: 0.7862 (m-30) cc_final: 0.7601 (m-30) REVERT: B 283 ASP cc_start: 0.6881 (p0) cc_final: 0.6640 (p0) REVERT: B 334 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7216 (mm-30) REVERT: C 145 ASN cc_start: 0.7120 (p0) cc_final: 0.6915 (p0) REVERT: D 77 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7406 (mm-30) outliers start: 25 outliers final: 11 residues processed: 301 average time/residue: 0.6822 time to fit residues: 217.3059 Evaluate side-chains 256 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 245 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain C residue 170 ASN Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain D residue 170 ASN Chi-restraints excluded: chain D residue 217 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 123 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN A 161 GLN B 57 GLN C 68 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.144395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.117735 restraints weight = 13070.176| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.92 r_work: 0.3390 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10118 Z= 0.124 Angle : 0.862 36.548 13686 Z= 0.265 Chirality : 0.042 0.143 1492 Planarity : 0.004 0.053 1780 Dihedral : 4.835 57.163 1400 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.15 % Allowed : 29.15 % Favored : 66.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.85 (0.25), residues: 1244 helix: 1.62 (0.23), residues: 532 sheet: 0.88 (0.48), residues: 148 loop : -0.53 (0.28), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 379 TYR 0.007 0.001 TYR C 29 PHE 0.015 0.001 PHE D 12 TRP 0.010 0.001 TRP D 58 HIS 0.004 0.001 HIS B 247 Details of bonding type rmsd covalent geometry : bond 0.00289 (10110) covalent geometry : angle 0.50142 (13662) hydrogen bonds : bond 0.04483 ( 399) hydrogen bonds : angle 4.56956 ( 1167) metal coordination : bond 0.00443 ( 8) metal coordination : angle 16.75125 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 234 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: A 8 ASP cc_start: 0.8478 (t0) cc_final: 0.8221 (t0) REVERT: A 156 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7849 (mm-30) REVERT: A 236 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7596 (mm-30) REVERT: A 282 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8084 (ptpp) REVERT: A 315 MET cc_start: 0.8479 (tpp) cc_final: 0.8258 (ttp) REVERT: A 334 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7522 (mm-30) REVERT: B 221 LYS cc_start: 0.8412 (mtpp) cc_final: 0.8185 (tttp) REVERT: B 236 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7545 (mm-30) REVERT: C 77 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7724 (mt-10) REVERT: C 96 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7005 (mt) REVERT: D 97 LYS cc_start: 0.7732 (mttm) cc_final: 0.7531 (mmtp) REVERT: D 138 VAL cc_start: 0.7554 (OUTLIER) cc_final: 0.7325 (t) REVERT: D 163 MET cc_start: 0.7384 (mmm) cc_final: 0.7109 (tmm) REVERT: D 178 LYS cc_start: 0.7894 (mmtt) cc_final: 0.7536 (mmtt) outliers start: 44 outliers final: 11 residues processed: 258 average time/residue: 0.7140 time to fit residues: 194.5665 Evaluate side-chains 234 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 219 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 217 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 0.9980 chunk 49 optimal weight: 0.0060 chunk 58 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 109 optimal weight: 0.8980 chunk 123 optimal weight: 50.0000 chunk 16 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN D 48 ASN ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.145272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.118582 restraints weight = 13069.234| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.93 r_work: 0.3401 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10118 Z= 0.098 Angle : 0.840 36.090 13686 Z= 0.249 Chirality : 0.041 0.133 1492 Planarity : 0.003 0.048 1780 Dihedral : 4.663 59.822 1388 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.21 % Allowed : 31.32 % Favored : 65.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.95 (0.25), residues: 1244 helix: 1.80 (0.23), residues: 532 sheet: 0.69 (0.46), residues: 162 loop : -0.54 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 173 TYR 0.006 0.001 TYR C 183 PHE 0.010 0.001 PHE D 144 TRP 0.010 0.001 TRP D 58 HIS 0.003 0.000 HIS B 247 Details of bonding type rmsd covalent geometry : bond 0.00222 (10110) covalent geometry : angle 0.47843 (13662) hydrogen bonds : bond 0.03802 ( 399) hydrogen bonds : angle 4.32321 ( 1167) metal coordination : bond 0.00782 ( 8) metal coordination : angle 16.48818 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 234 time to evaluate : 0.386 Fit side-chains REVERT: A 8 ASP cc_start: 0.8491 (t0) cc_final: 0.8226 (t0) REVERT: A 156 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7866 (mm-30) REVERT: A 236 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7537 (mm-30) REVERT: A 282 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8003 (ptpp) REVERT: A 334 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7481 (mm-30) REVERT: B 221 LYS cc_start: 0.8383 (mtpp) cc_final: 0.8158 (tttp) REVERT: B 224 VAL cc_start: 0.8906 (OUTLIER) cc_final: 0.8705 (p) REVERT: B 236 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7577 (mm-30) REVERT: C 77 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7718 (mt-10) REVERT: C 174 VAL cc_start: 0.8565 (t) cc_final: 0.8162 (m) REVERT: C 186 LYS cc_start: 0.7649 (tttm) cc_final: 0.7288 (tttt) REVERT: D 77 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7794 (mt-10) REVERT: D 85 LYS cc_start: 0.8534 (pttp) cc_final: 0.8311 (pttp) REVERT: D 163 MET cc_start: 0.7419 (mmm) cc_final: 0.7156 (mmm) REVERT: D 178 LYS cc_start: 0.7901 (mmtt) cc_final: 0.7441 (mmtt) outliers start: 34 outliers final: 17 residues processed: 246 average time/residue: 0.6917 time to fit residues: 180.0485 Evaluate side-chains 243 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 223 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 217 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN A 290 ASN B 129 ASN D 48 ASN ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.139194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.112443 restraints weight = 13235.040| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.91 r_work: 0.3307 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 10118 Z= 0.324 Angle : 0.999 43.253 13686 Z= 0.331 Chirality : 0.049 0.181 1492 Planarity : 0.005 0.053 1780 Dihedral : 5.628 75.841 1388 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.25 % Allowed : 30.28 % Favored : 65.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.49 (0.24), residues: 1244 helix: 1.48 (0.22), residues: 530 sheet: 0.36 (0.44), residues: 162 loop : -0.82 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 171 TYR 0.020 0.002 TYR B 6 PHE 0.023 0.003 PHE A 355 TRP 0.012 0.002 TRP D 58 HIS 0.006 0.002 HIS B 247 Details of bonding type rmsd covalent geometry : bond 0.00796 (10110) covalent geometry : angle 0.62931 (13662) hydrogen bonds : bond 0.06587 ( 399) hydrogen bonds : angle 4.79255 ( 1167) metal coordination : bond 0.00658 ( 8) metal coordination : angle 18.52682 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 240 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 92 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8107 (mtpp) REVERT: A 156 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7898 (mm-30) REVERT: A 236 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7663 (mm-30) REVERT: A 315 MET cc_start: 0.8490 (tpp) cc_final: 0.8279 (ttp) REVERT: A 334 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7435 (mm-30) REVERT: B 221 LYS cc_start: 0.8527 (mtpp) cc_final: 0.8325 (tttp) REVERT: C 24 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8006 (tt) REVERT: C 31 LYS cc_start: 0.8875 (ttmm) cc_final: 0.8673 (ttmm) REVERT: C 77 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7826 (mt-10) REVERT: C 96 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7163 (mt) REVERT: C 186 LYS cc_start: 0.7702 (tttm) cc_final: 0.7272 (tttt) REVERT: C 191 PHE cc_start: 0.5879 (OUTLIER) cc_final: 0.5190 (p90) REVERT: C 221 GLU cc_start: 0.5921 (OUTLIER) cc_final: 0.5337 (mp0) REVERT: D 43 GLU cc_start: 0.8078 (mp0) cc_final: 0.7818 (mp0) REVERT: D 77 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7865 (mt-10) REVERT: D 163 MET cc_start: 0.7439 (mmm) cc_final: 0.7084 (mmm) REVERT: D 178 LYS cc_start: 0.8046 (mmtt) cc_final: 0.7585 (mmtt) REVERT: D 191 PHE cc_start: 0.5465 (OUTLIER) cc_final: 0.4616 (p90) outliers start: 45 outliers final: 21 residues processed: 261 average time/residue: 0.7495 time to fit residues: 205.9859 Evaluate side-chains 264 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 236 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 101 ARG Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 181 MET Chi-restraints excluded: chain C residue 191 PHE Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain D residue 217 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 72 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 116 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 69 optimal weight: 0.0770 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN B 194 GLN B 229 GLN B 248 GLN C 68 ASN ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.143494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.116994 restraints weight = 13079.072| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.92 r_work: 0.3371 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10118 Z= 0.108 Angle : 0.881 39.098 13686 Z= 0.264 Chirality : 0.042 0.146 1492 Planarity : 0.004 0.045 1780 Dihedral : 4.787 56.113 1388 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.96 % Allowed : 31.23 % Favored : 64.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.84 (0.25), residues: 1244 helix: 1.76 (0.23), residues: 532 sheet: 0.77 (0.47), residues: 158 loop : -0.70 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 379 TYR 0.010 0.001 TYR B 208 PHE 0.013 0.001 PHE D 51 TRP 0.012 0.001 TRP D 58 HIS 0.004 0.001 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00250 (10110) covalent geometry : angle 0.52157 (13662) hydrogen bonds : bond 0.04015 ( 399) hydrogen bonds : angle 4.32344 ( 1167) metal coordination : bond 0.00537 ( 8) metal coordination : angle 16.95064 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 239 time to evaluate : 0.455 Fit side-chains REVERT: A 8 ASP cc_start: 0.8503 (t0) cc_final: 0.8216 (t0) REVERT: A 156 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7879 (mm-30) REVERT: A 236 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7589 (mm-30) REVERT: A 282 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8060 (ptpp) REVERT: A 334 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7360 (mm-30) REVERT: A 340 ARG cc_start: 0.8647 (ttm-80) cc_final: 0.8264 (ttp-170) REVERT: B 208 TYR cc_start: 0.8657 (m-80) cc_final: 0.8409 (m-80) REVERT: B 236 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7680 (mm-30) REVERT: C 77 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7660 (mt-10) REVERT: C 96 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.6996 (mt) REVERT: C 174 VAL cc_start: 0.8543 (t) cc_final: 0.8183 (m) REVERT: C 186 LYS cc_start: 0.7544 (tttm) cc_final: 0.7098 (tttt) REVERT: C 191 PHE cc_start: 0.5467 (OUTLIER) cc_final: 0.4999 (p90) REVERT: C 221 GLU cc_start: 0.5921 (OUTLIER) cc_final: 0.5358 (mp0) REVERT: D 43 GLU cc_start: 0.8081 (mp0) cc_final: 0.7860 (mp0) REVERT: D 77 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7823 (mt-10) REVERT: D 163 MET cc_start: 0.7366 (mmm) cc_final: 0.6973 (mmm) REVERT: D 178 LYS cc_start: 0.8005 (mmtt) cc_final: 0.7556 (mmtt) REVERT: D 191 PHE cc_start: 0.5140 (OUTLIER) cc_final: 0.4528 (p90) REVERT: D 198 MET cc_start: 0.7971 (tpt) cc_final: 0.7734 (tpp) REVERT: D 221 GLU cc_start: 0.6589 (OUTLIER) cc_final: 0.5694 (mp0) outliers start: 42 outliers final: 22 residues processed: 254 average time/residue: 0.7079 time to fit residues: 189.9752 Evaluate side-chains 262 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 233 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 181 MET Chi-restraints excluded: chain C residue 191 PHE Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 221 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 59 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 8.9990 chunk 73 optimal weight: 0.7980 chunk 68 optimal weight: 0.0970 chunk 83 optimal weight: 0.8980 chunk 118 optimal weight: 0.6980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 GLN A 57 GLN B 248 GLN ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.143729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.117126 restraints weight = 13071.343| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.90 r_work: 0.3376 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10118 Z= 0.110 Angle : 0.861 38.114 13686 Z= 0.257 Chirality : 0.042 0.143 1492 Planarity : 0.004 0.042 1780 Dihedral : 4.738 58.235 1388 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.25 % Allowed : 31.04 % Favored : 64.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.96 (0.25), residues: 1244 helix: 1.88 (0.23), residues: 532 sheet: 0.77 (0.47), residues: 158 loop : -0.65 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 379 TYR 0.008 0.001 TYR B 208 PHE 0.012 0.001 PHE D 126 TRP 0.012 0.001 TRP D 58 HIS 0.003 0.001 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00256 (10110) covalent geometry : angle 0.50589 (13662) hydrogen bonds : bond 0.04041 ( 399) hydrogen bonds : angle 4.25931 ( 1167) metal coordination : bond 0.00558 ( 8) metal coordination : angle 16.64523 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 248 time to evaluate : 0.405 Fit side-chains REVERT: A 8 ASP cc_start: 0.8498 (t0) cc_final: 0.8218 (t0) REVERT: A 156 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7878 (mm-30) REVERT: A 236 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7562 (mm-30) REVERT: A 282 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8034 (ptpp) REVERT: A 334 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7302 (mm-30) REVERT: A 340 ARG cc_start: 0.8599 (ttm-80) cc_final: 0.8161 (ttp-170) REVERT: B 236 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7674 (mm-30) REVERT: C 77 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7728 (mt-10) REVERT: C 96 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.6960 (mt) REVERT: C 191 PHE cc_start: 0.5353 (OUTLIER) cc_final: 0.4865 (p90) REVERT: C 198 MET cc_start: 0.7961 (tpt) cc_final: 0.7751 (tpp) REVERT: C 221 GLU cc_start: 0.5904 (OUTLIER) cc_final: 0.5325 (mp0) REVERT: D 77 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7810 (mt-10) REVERT: D 163 MET cc_start: 0.7354 (mmm) cc_final: 0.6960 (mmm) REVERT: D 174 VAL cc_start: 0.8686 (t) cc_final: 0.8369 (m) REVERT: D 178 LYS cc_start: 0.7989 (mmtt) cc_final: 0.7542 (mmtt) REVERT: D 191 PHE cc_start: 0.5138 (OUTLIER) cc_final: 0.4583 (p90) REVERT: D 198 MET cc_start: 0.7974 (tpt) cc_final: 0.7748 (tpp) REVERT: D 221 GLU cc_start: 0.6608 (OUTLIER) cc_final: 0.5735 (mp0) outliers start: 45 outliers final: 26 residues processed: 266 average time/residue: 0.7210 time to fit residues: 202.4500 Evaluate side-chains 279 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 246 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 191 PHE Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 181 MET Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 221 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 83 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 100 optimal weight: 0.0970 chunk 31 optimal weight: 4.9990 chunk 70 optimal weight: 0.1980 chunk 118 optimal weight: 1.9990 chunk 29 optimal weight: 0.0980 chunk 59 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 GLN A 57 GLN B 161 GLN B 248 GLN C 145 ASN ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.145094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.118567 restraints weight = 13028.159| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.90 r_work: 0.3397 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10118 Z= 0.095 Angle : 0.863 37.216 13686 Z= 0.260 Chirality : 0.041 0.135 1492 Planarity : 0.003 0.040 1780 Dihedral : 4.565 55.003 1388 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.87 % Allowed : 31.42 % Favored : 64.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 1.00 (0.25), residues: 1244 helix: 1.93 (0.23), residues: 532 sheet: 0.79 (0.47), residues: 158 loop : -0.63 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 379 TYR 0.006 0.001 TYR B 208 PHE 0.012 0.001 PHE D 59 TRP 0.034 0.001 TRP D 58 HIS 0.003 0.000 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00216 (10110) covalent geometry : angle 0.52089 (13662) hydrogen bonds : bond 0.03524 ( 399) hydrogen bonds : angle 4.16580 ( 1167) metal coordination : bond 0.00560 ( 8) metal coordination : angle 16.44636 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 230 time to evaluate : 0.374 Fit side-chains REVERT: A 8 ASP cc_start: 0.8507 (t0) cc_final: 0.8233 (t0) REVERT: A 156 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7862 (mm-30) REVERT: A 236 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7555 (mm-30) REVERT: A 334 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7281 (mm-30) REVERT: A 340 ARG cc_start: 0.8536 (ttm-80) cc_final: 0.8191 (ttm-80) REVERT: B 236 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7673 (mm-30) REVERT: C 77 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7673 (mt-10) REVERT: C 174 VAL cc_start: 0.8544 (t) cc_final: 0.8176 (m) REVERT: C 191 PHE cc_start: 0.5204 (OUTLIER) cc_final: 0.4775 (p90) REVERT: C 198 MET cc_start: 0.7918 (tpt) cc_final: 0.7704 (tpp) REVERT: D 77 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7813 (mt-10) REVERT: D 163 MET cc_start: 0.7284 (mmm) cc_final: 0.6922 (mmm) REVERT: D 174 VAL cc_start: 0.8656 (t) cc_final: 0.8339 (m) REVERT: D 178 LYS cc_start: 0.7975 (mmtt) cc_final: 0.7531 (mmtt) REVERT: D 191 PHE cc_start: 0.4967 (OUTLIER) cc_final: 0.4393 (p90) REVERT: D 195 PHE cc_start: 0.8501 (t80) cc_final: 0.7726 (m-80) REVERT: D 198 MET cc_start: 0.7975 (tpt) cc_final: 0.7746 (tpp) REVERT: D 221 GLU cc_start: 0.6615 (OUTLIER) cc_final: 0.5746 (mp0) outliers start: 41 outliers final: 21 residues processed: 247 average time/residue: 0.7304 time to fit residues: 190.1811 Evaluate side-chains 253 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 228 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 181 MET Chi-restraints excluded: chain C residue 191 PHE Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 181 MET Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 221 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 80 optimal weight: 0.0000 chunk 26 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 92 optimal weight: 8.9990 chunk 0 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 73 optimal weight: 5.9990 overall best weight: 1.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN A 129 ASN C 145 ASN ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.141128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.114221 restraints weight = 13057.408| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.89 r_work: 0.3332 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10118 Z= 0.219 Angle : 0.941 40.707 13686 Z= 0.308 Chirality : 0.046 0.148 1492 Planarity : 0.004 0.045 1780 Dihedral : 5.289 71.985 1388 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.40 % Allowed : 31.70 % Favored : 64.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.73 (0.25), residues: 1244 helix: 1.77 (0.22), residues: 530 sheet: 0.44 (0.45), residues: 162 loop : -0.77 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 379 TYR 0.011 0.001 TYR B 6 PHE 0.018 0.002 PHE A 355 TRP 0.032 0.002 TRP D 58 HIS 0.006 0.001 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00538 (10110) covalent geometry : angle 0.60459 (13662) hydrogen bonds : bond 0.05601 ( 399) hydrogen bonds : angle 4.56865 ( 1167) metal coordination : bond 0.00461 ( 8) metal coordination : angle 17.22874 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 233 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: A 92 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.8225 (mtpp) REVERT: A 220 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.8113 (ptm-80) REVERT: A 236 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7660 (mm-30) REVERT: A 315 MET cc_start: 0.8474 (tpp) cc_final: 0.8240 (ttp) REVERT: A 334 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7393 (mm-30) REVERT: A 340 ARG cc_start: 0.8643 (ttm-80) cc_final: 0.8313 (ttp-170) REVERT: B 48 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7429 (tm-30) REVERT: B 236 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7639 (mm-30) REVERT: C 77 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7785 (mt-10) REVERT: C 96 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7022 (mt) REVERT: C 191 PHE cc_start: 0.5349 (OUTLIER) cc_final: 0.4732 (p90) REVERT: D 77 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7824 (mt-10) REVERT: D 163 MET cc_start: 0.7269 (mmm) cc_final: 0.6893 (mmm) REVERT: D 174 VAL cc_start: 0.8733 (t) cc_final: 0.8383 (m) REVERT: D 178 LYS cc_start: 0.8048 (mmtt) cc_final: 0.7620 (mmtt) REVERT: D 191 PHE cc_start: 0.5152 (OUTLIER) cc_final: 0.4538 (p90) REVERT: D 198 MET cc_start: 0.8023 (tpt) cc_final: 0.7809 (tpp) REVERT: D 221 GLU cc_start: 0.6658 (OUTLIER) cc_final: 0.5805 (mp0) outliers start: 36 outliers final: 20 residues processed: 247 average time/residue: 0.7689 time to fit residues: 199.8395 Evaluate side-chains 264 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 236 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 181 MET Chi-restraints excluded: chain C residue 191 PHE Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 221 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 88 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 123 optimal weight: 8.9990 chunk 49 optimal weight: 0.0370 chunk 81 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 1 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 overall best weight: 0.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 GLN A 57 GLN B 25 GLN B 194 GLN B 248 GLN ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.143103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.116291 restraints weight = 12934.307| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.88 r_work: 0.3366 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10118 Z= 0.131 Angle : 0.903 39.290 13686 Z= 0.282 Chirality : 0.043 0.172 1492 Planarity : 0.004 0.044 1780 Dihedral : 4.839 60.811 1388 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.74 % Allowed : 32.55 % Favored : 64.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.88 (0.25), residues: 1244 helix: 1.87 (0.23), residues: 530 sheet: 0.61 (0.46), residues: 158 loop : -0.69 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 379 TYR 0.008 0.001 TYR B 208 PHE 0.012 0.001 PHE D 126 TRP 0.036 0.001 TRP D 58 HIS 0.003 0.001 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00313 (10110) covalent geometry : angle 0.56601 (13662) hydrogen bonds : bond 0.04339 ( 399) hydrogen bonds : angle 4.36114 ( 1167) metal coordination : bond 0.00479 ( 8) metal coordination : angle 16.80573 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 238 time to evaluate : 0.386 Fit side-chains REVERT: A 8 ASP cc_start: 0.8485 (t0) cc_final: 0.8217 (t0) REVERT: A 236 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7612 (mm-30) REVERT: A 334 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7341 (mm-30) REVERT: A 340 ARG cc_start: 0.8576 (ttm-80) cc_final: 0.8186 (ttp-170) REVERT: B 236 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7707 (mm-30) REVERT: C 77 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7659 (mt-10) REVERT: C 96 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.6973 (mt) REVERT: C 191 PHE cc_start: 0.5200 (OUTLIER) cc_final: 0.4639 (p90) REVERT: C 198 MET cc_start: 0.7969 (tpt) cc_final: 0.7765 (tpp) REVERT: D 77 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7802 (mt-10) REVERT: D 163 MET cc_start: 0.7224 (mmm) cc_final: 0.6855 (mmm) REVERT: D 174 VAL cc_start: 0.8646 (t) cc_final: 0.8303 (m) REVERT: D 178 LYS cc_start: 0.8018 (mmtt) cc_final: 0.7589 (mmtt) REVERT: D 191 PHE cc_start: 0.4928 (OUTLIER) cc_final: 0.4347 (p90) REVERT: D 221 GLU cc_start: 0.6614 (OUTLIER) cc_final: 0.5754 (mp0) outliers start: 29 outliers final: 20 residues processed: 247 average time/residue: 0.7515 time to fit residues: 195.7140 Evaluate side-chains 255 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 230 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 181 MET Chi-restraints excluded: chain C residue 191 PHE Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 181 MET Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 221 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/iotbx/cli_parser.py", line 995, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1590, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1493, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1374, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.5753 > 50: distance: 38 - 71: 13.238 distance: 54 - 62: 5.529 distance: 62 - 63: 3.926 distance: 63 - 64: 4.956 distance: 63 - 66: 6.433 distance: 64 - 65: 4.150 distance: 64 - 71: 3.201 distance: 66 - 67: 6.726 distance: 68 - 69: 4.900 distance: 69 - 70: 3.095 distance: 71 - 72: 9.877 distance: 72 - 73: 11.141 distance: 72 - 75: 4.136 distance: 73 - 74: 41.953 distance: 73 - 79: 17.762 distance: 75 - 76: 3.666 distance: 76 - 77: 8.576 distance: 76 - 78: 6.470 distance: 79 - 80: 5.688 distance: 80 - 81: 7.453 distance: 81 - 82: 31.142 distance: 81 - 83: 8.134 distance: 83 - 84: 6.930 distance: 84 - 85: 4.687 distance: 84 - 87: 4.532 distance: 85 - 86: 5.104 distance: 85 - 95: 5.670 distance: 87 - 88: 6.113 distance: 88 - 89: 4.949 distance: 88 - 90: 5.802 distance: 89 - 91: 3.647 distance: 90 - 92: 6.979 distance: 91 - 93: 4.612 distance: 92 - 93: 6.415 distance: 93 - 94: 8.050 distance: 95 - 96: 3.907 distance: 96 - 97: 7.849 distance: 96 - 99: 10.020 distance: 97 - 98: 4.712 distance: 97 - 103: 6.974 distance: 99 - 100: 11.820 distance: 100 - 101: 8.563 distance: 100 - 102: 7.595 distance: 104 - 105: 4.116 distance: 105 - 106: 4.544 distance: 105 - 111: 5.074 distance: 107 - 108: 5.400 distance: 108 - 109: 3.082 distance: 108 - 110: 8.700 distance: 111 - 112: 6.952 distance: 112 - 113: 5.196 distance: 112 - 115: 6.700 distance: 113 - 119: 3.814 distance: 115 - 116: 10.522 distance: 116 - 117: 4.296 distance: 116 - 118: 6.694 distance: 119 - 120: 5.560 distance: 120 - 121: 5.572 distance: 120 - 123: 5.661 distance: 121 - 122: 17.520 distance: 121 - 127: 3.862 distance: 123 - 124: 3.250 distance: 124 - 125: 9.489 distance: 124 - 126: 9.369 distance: 127 - 128: 10.641 distance: 128 - 129: 11.573 distance: 128 - 131: 10.159 distance: 129 - 130: 4.829 distance: 129 - 133: 5.501 distance: 131 - 132: 11.582 distance: 132 - 218: 12.444 distance: 133 - 134: 19.505 distance: 134 - 135: 4.662 distance: 134 - 137: 19.947 distance: 135 - 136: 4.721 distance: 135 - 140: 6.765 distance: 137 - 138: 14.574 distance: 150 - 168: 3.439