Starting phenix.real_space_refine on Mon Aug 25 12:28:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hga_52132/08_2025/9hga_52132.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hga_52132/08_2025/9hga_52132.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hga_52132/08_2025/9hga_52132.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hga_52132/08_2025/9hga_52132.map" model { file = "/net/cci-nas-00/data/ceres_data/9hga_52132/08_2025/9hga_52132.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hga_52132/08_2025/9hga_52132.cif" } resolution = 3.62 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= 0.000 sd= 0.007 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: 5 Type Number sf(0) Gaussians S 44 5.16 5 C 8915 2.51 5 N 2463 2.21 5 O 2794 1.98 5 H 13795 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28011 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 12129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 12129 Classifications: {'peptide': 785} Link IDs: {'PTRANS': 29, 'TRANS': 755} Chain: "B" Number of atoms: 5518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5518 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 11, 'TRANS': 358} Chain: "C" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 845 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 6, 'TRANS': 51} Chain: "D" Number of atoms: 3348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3348 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 12, 'TRANS': 196} Chain breaks: 1 Chain: "E" Number of atoms: 1291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1291 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 5, 'TRANS': 78} Chain: "F" Number of atoms: 4754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 4754 Classifications: {'peptide': 305} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 296} Chain breaks: 1 Chain: "G" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 126 Classifications: {'peptide': 7} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'UX8:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 4.22, per 1000 atoms: 0.15 Number of scatterers: 28011 At special positions: 0 Unit cell: (100.74, 124.1, 154.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 O 2794 8.00 N 2463 7.00 C 8915 6.00 H 13795 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.55 Conformation dependent library (CDL) restraints added in 817.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3342 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 17 sheets defined 30.3% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 38 through 46 Processing helix chain 'A' and resid 55 through 70 removed outlier: 4.043A pdb=" N GLY A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 118 Processing helix chain 'A' and resid 129 through 145 Processing helix chain 'A' and resid 189 through 196 removed outlier: 4.110A pdb=" N HIS A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 232 Processing helix chain 'A' and resid 280 through 289 removed outlier: 3.967A pdb=" N GLN A 286 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU A 287 " --> pdb=" O GLU A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 316 Processing helix chain 'A' and resid 361 through 368 removed outlier: 3.799A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 393 removed outlier: 3.827A pdb=" N GLY A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 500 Processing helix chain 'A' and resid 542 through 552 removed outlier: 3.596A pdb=" N TYR A 548 " --> pdb=" O ALA A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'A' and resid 691 through 695 removed outlier: 3.643A pdb=" N GLY A 695 " --> pdb=" O THR A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 731 No H-bonds generated for 'chain 'A' and resid 729 through 731' Processing helix chain 'C' and resid 31 through 37 removed outlier: 3.549A pdb=" N VAL C 35 " --> pdb=" O TYR C 31 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER C 36 " --> pdb=" O LYS C 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 46 Processing helix chain 'D' and resid 47 through 62 removed outlier: 3.865A pdb=" N ALA D 51 " --> pdb=" O ASN D 47 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR D 53 " --> pdb=" O ARG D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 82 Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 104 through 121 removed outlier: 3.797A pdb=" N VAL D 108 " --> pdb=" O ASN D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 160 through 189 Processing helix chain 'D' and resid 192 through 205 Processing helix chain 'D' and resid 208 through 225 Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 227 through 242 removed outlier: 3.877A pdb=" N LYS D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 46 removed outlier: 3.734A pdb=" N ILE E 46 " --> pdb=" O ASP E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 59 Processing helix chain 'F' and resid 39 through 56 removed outlier: 3.649A pdb=" N ASP F 43 " --> pdb=" O GLU F 39 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA F 54 " --> pdb=" O LYS F 50 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN F 55 " --> pdb=" O LEU F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 88 removed outlier: 3.523A pdb=" N GLU F 72 " --> pdb=" O HIS F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 103 removed outlier: 3.879A pdb=" N ALA F 101 " --> pdb=" O ASP F 97 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASN F 102 " --> pdb=" O GLN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 117 removed outlier: 3.526A pdb=" N SER F 116 " --> pdb=" O GLN F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 123 removed outlier: 4.073A pdb=" N LEU F 123 " --> pdb=" O TYR F 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 120 through 123' Processing helix chain 'F' and resid 124 through 150 removed outlier: 3.588A pdb=" N TYR F 128 " --> pdb=" O ASN F 124 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER F 139 " --> pdb=" O GLU F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 166 Processing helix chain 'F' and resid 188 through 209 removed outlier: 3.577A pdb=" N GLY F 209 " --> pdb=" O GLN F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 220 Processing helix chain 'F' and resid 224 through 228 Processing helix chain 'F' and resid 237 through 239 No H-bonds generated for 'chain 'F' and resid 237 through 239' Processing helix chain 'F' and resid 240 through 250 removed outlier: 4.235A pdb=" N ALA F 246 " --> pdb=" O ILE F 242 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR F 249 " --> pdb=" O GLN F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 391 through 421 removed outlier: 3.806A pdb=" N ASP F 395 " --> pdb=" O ALA F 391 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ARG F 396 " --> pdb=" O ALA F 392 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 88 removed outlier: 3.537A pdb=" N GLN A 87 " --> pdb=" O ARG A 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 4.564A pdb=" N ILE A 94 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N LEU A 165 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N SER A 96 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N LEU A 167 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N THR A 98 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N PHE A 169 " --> pdb=" O THR A 98 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N SER A 100 " --> pdb=" O PHE A 169 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 183 removed outlier: 7.641A pdb=" N VAL A 256 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE A 180 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL A 258 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ILE A 182 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ILE A 260 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER A 242 " --> pdb=" O ASN A 259 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N THR A 261 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ILE A 240 " --> pdb=" O THR A 261 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 267 through 275 removed outlier: 4.360A pdb=" N GLU A 294 " --> pdb=" O LEU A 268 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 294 through 295 current: chain 'A' and resid 334 through 342 Processing sheet with id=AA5, first strand: chain 'A' and resid 348 through 355 removed outlier: 6.280A pdb=" N VAL A 412 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LYS A 351 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N GLN A 411 " --> pdb=" O ARG A 404 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ARG A 404 " --> pdb=" O GLN A 411 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ASP A 413 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N THR A 402 " --> pdb=" O ASP A 413 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL A 415 " --> pdb=" O THR A 400 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N THR A 400 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LYS A 417 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL A 398 " --> pdb=" O LYS A 417 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LYS A 419 " --> pdb=" O GLU A 396 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 425 through 433 removed outlier: 5.174A pdb=" N LEU A 485 " --> pdb=" O PRO A 476 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL A 483 " --> pdb=" O PHE A 478 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 483 through 485 current: chain 'A' and resid 505 through 518 removed outlier: 3.523A pdb=" N ALA A 527 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY A 590 " --> pdb=" O TYR A 618 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 44 through 51 removed outlier: 6.822A pdb=" N SER B 389 " --> pdb=" O ALA B 47 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N SER B 49 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL B 387 " --> pdb=" O SER B 49 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU B 378 " --> pdb=" O ILE B 390 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 66 through 68 removed outlier: 6.970A pdb=" N VAL B 81 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N SER B 94 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ALA B 83 " --> pdb=" O ILE B 92 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 116 through 117 removed outlier: 6.819A pdb=" N VAL B 131 " --> pdb=" O GLN B 144 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLN B 144 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ALA B 133 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 156 through 158 removed outlier: 3.500A pdb=" N VAL B 156 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N TRP B 183 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASN B 175 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N VAL B 181 " --> pdb=" O ASN B 175 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 201 through 202 removed outlier: 6.597A pdb=" N VAL B 216 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLN B 229 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ALA B 218 " --> pdb=" O ILE B 227 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 252 through 254 removed outlier: 6.411A pdb=" N LEU B 267 " --> pdb=" O LYS B 280 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LYS B 280 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ALA B 269 " --> pdb=" O MET B 278 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 290 through 292 removed outlier: 6.953A pdb=" N VAL B 305 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N THR B 318 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ALA B 307 " --> pdb=" O LEU B 316 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 331 through 333 removed outlier: 3.650A pdb=" N VAL B 339 " --> pdb=" O HIS B 347 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ASN B 350 " --> pdb=" O PHE B 356 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N PHE B 356 " --> pdb=" O ASN B 350 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 32 through 35 removed outlier: 3.614A pdb=" N THR E 94 " --> pdb=" O ASN E 103 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 28 through 32 removed outlier: 3.530A pdb=" N GLY F 35 " --> pdb=" O VAL F 32 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 230 through 235 removed outlier: 5.199A pdb=" N GLN F 230 " --> pdb=" O HIS F 178 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N HIS F 178 " --> pdb=" O GLN F 230 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLY F 232 " --> pdb=" O LEU F 176 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU F 176 " --> pdb=" O GLY F 232 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N SER F 177 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N VAL F 270 " --> pdb=" O SER F 177 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ILE F 179 " --> pdb=" O LEU F 268 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N LEU F 268 " --> pdb=" O ILE F 179 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ILE F 181 " --> pdb=" O HIS F 266 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N HIS F 266 " --> pdb=" O ILE F 181 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N HIS F 266 " --> pdb=" O PRO F 258 " (cutoff:3.500A) 619 hydrogen bonds defined for protein. 1752 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: 5.47 Time building geometry restraints manager: 3.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13795 1.03 - 1.23: 10 1.23 - 1.42: 6194 1.42 - 1.62: 8209 1.62 - 1.82: 86 Bond restraints: 28294 Sorted by residual: bond pdb=" CA UX8 G 3 " pdb=" C UX8 G 3 " ideal model delta sigma weight residual 1.525 1.351 0.174 2.10e-02 2.27e+03 6.83e+01 bond pdb=" N UX8 G 3 " pdb=" H UX8 G 3 " ideal model delta sigma weight residual 0.860 1.000 -0.140 2.00e-02 2.50e+03 4.91e+01 bond pdb=" NE1 UX8 G 3 " pdb=" HE1 UX8 G 3 " ideal model delta sigma weight residual 0.860 1.000 -0.140 2.00e-02 2.50e+03 4.89e+01 bond pdb=" CE3 UX8 G 3 " pdb=" HE3 UX8 G 3 " ideal model delta sigma weight residual 0.930 1.000 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" CZ2 UX8 G 3 " pdb=" HZ2 UX8 G 3 " ideal model delta sigma weight residual 0.930 1.000 -0.070 2.00e-02 2.50e+03 1.22e+01 ... (remaining 28289 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 50679 1.86 - 3.71: 220 3.71 - 5.57: 20 5.57 - 7.42: 5 7.42 - 9.28: 2 Bond angle restraints: 50926 Sorted by residual: angle pdb=" CA UX8 G 3 " pdb=" C UX8 G 3 " pdb=" O UX8 G 3 " ideal model delta sigma weight residual 120.80 130.08 -9.28 1.70e+00 3.46e-01 2.98e+01 angle pdb=" CA UX8 G 3 " pdb=" C UX8 G 3 " pdb=" N SER G 4 " ideal model delta sigma weight residual 116.20 110.48 5.72 2.00e+00 2.50e-01 8.19e+00 angle pdb=" CB UX8 G 3 " pdb=" CA UX8 G 3 " pdb=" HA UX8 G 3 " ideal model delta sigma weight residual 109.00 100.84 8.16 3.00e+00 1.11e-01 7.39e+00 angle pdb=" CB MET F 83 " pdb=" CG MET F 83 " pdb=" SD MET F 83 " ideal model delta sigma weight residual 112.70 119.63 -6.93 3.00e+00 1.11e-01 5.33e+00 angle pdb=" NE1 UX8 G 3 " pdb=" CD1 UX8 G 3 " pdb=" HD1 UX8 G 3 " ideal model delta sigma weight residual 120.19 127.05 -6.86 3.00e+00 1.11e-01 5.23e+00 ... (remaining 50921 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 11981 17.92 - 35.85: 981 35.85 - 53.77: 319 53.77 - 71.69: 66 71.69 - 89.61: 13 Dihedral angle restraints: 13360 sinusoidal: 7272 harmonic: 6088 Sorted by residual: dihedral pdb=" CB CYS A 690 " pdb=" SG CYS A 690 " pdb=" SG CYS A 700 " pdb=" CB CYS A 700 " ideal model delta sinusoidal sigma weight residual -86.00 -150.57 64.57 1 1.00e+01 1.00e-02 5.48e+01 dihedral pdb=" CA ASP A 568 " pdb=" CB ASP A 568 " pdb=" CG ASP A 568 " pdb=" OD1 ASP A 568 " ideal model delta sinusoidal sigma weight residual -30.00 -84.82 54.82 1 2.00e+01 2.50e-03 1.02e+01 dihedral pdb=" CB GLU F 156 " pdb=" CG GLU F 156 " pdb=" CD GLU F 156 " pdb=" OE1 GLU F 156 " ideal model delta sinusoidal sigma weight residual 0.00 -84.38 84.38 1 3.00e+01 1.11e-03 9.62e+00 ... (remaining 13357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1920 0.063 - 0.127: 230 0.127 - 0.190: 4 0.190 - 0.254: 0 0.254 - 0.317: 1 Chirality restraints: 2155 Sorted by residual: chirality pdb=" CA UX8 G 3 " pdb=" N UX8 G 3 " pdb=" C UX8 G 3 " pdb=" CB UX8 G 3 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CA ILE F 181 " pdb=" N ILE F 181 " pdb=" C ILE F 181 " pdb=" CB ILE F 181 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" CA ILE A 290 " pdb=" N ILE A 290 " pdb=" C ILE A 290 " pdb=" CB ILE A 290 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 ... (remaining 2152 not shown) Planarity restraints: 4340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU D 219 " -0.007 2.00e-02 2.50e+03 1.52e-02 2.30e+00 pdb=" CD GLU D 219 " 0.026 2.00e-02 2.50e+03 pdb=" OE1 GLU D 219 " -0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU D 219 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN D 30 " -0.021 5.00e-02 4.00e+02 3.17e-02 1.61e+00 pdb=" N PRO D 31 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO D 31 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 31 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 153 " 0.020 5.00e-02 4.00e+02 3.11e-02 1.55e+00 pdb=" N PRO F 154 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO F 154 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO F 154 " 0.018 5.00e-02 4.00e+02 ... (remaining 4337 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1612 2.20 - 2.80: 56968 2.80 - 3.40: 74941 3.40 - 4.00: 98156 4.00 - 4.60: 149901 Nonbonded interactions: 381578 Sorted by model distance: nonbonded pdb=" OD2 ASP A 569 " pdb="HD21 ASN A 606 " model vdw 1.595 2.450 nonbonded pdb=" O LYS F 27 " pdb=" H GLU F 39 " model vdw 1.613 2.450 nonbonded pdb=" O GLY E 60 " pdb=" HH TYR E 75 " model vdw 1.613 2.450 nonbonded pdb=" HH TYR A 468 " pdb=" OE1 GLU A 470 " model vdw 1.616 2.450 nonbonded pdb=" OG1 THR B 309 " pdb=" H VAL B 314 " model vdw 1.623 2.450 ... (remaining 381573 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 4.600 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: 0.140 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 22.430 Find NCS groups from input model: 0.080 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: 0.010 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 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 : 0.002 0.174 14502 Z= 0.121 Angle : 0.444 9.276 19682 Z= 0.231 Chirality : 0.041 0.317 2155 Planarity : 0.002 0.032 2602 Dihedral : 14.834 89.614 5305 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 11.03 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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 aren not related in a simple way. whole: 1.01 (0.21), residues: 1797 helix: 2.51 (0.24), residues: 508 sheet: 0.52 (0.24), residues: 504 loop : -0.43 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 49 TYR 0.009 0.001 TYR D 184 PHE 0.009 0.001 PHE A 72 TRP 0.009 0.001 TRP A 546 HIS 0.002 0.000 HIS F 266 Details of bonding type rmsd covalent geometry : bond 0.00245 (14499) covalent geometry : angle 0.44363 (19680) SS BOND : bond 0.00224 ( 1) SS BOND : angle 1.22703 ( 2) hydrogen bonds : bond 0.19694 ( 619) hydrogen bonds : angle 7.26553 ( 1752) Misc. bond : bond 0.02867 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 52 ILE cc_start: 0.9417 (pt) cc_final: 0.9201 (tt) REVERT: E 50 MET cc_start: 0.8140 (mmp) cc_final: 0.7915 (mmp) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.2179 time to fit residues: 37.8152 Evaluate side-chains 109 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.0970 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.097442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.066713 restraints weight = 129355.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.069213 restraints weight = 48382.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.070698 restraints weight = 27190.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.071568 restraints weight = 19682.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.071942 restraints weight = 16579.504| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.0629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14502 Z= 0.150 Angle : 0.480 6.928 19682 Z= 0.261 Chirality : 0.041 0.152 2155 Planarity : 0.003 0.035 2602 Dihedral : 3.426 17.011 1987 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.20 % Allowed : 10.77 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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 aren not related in a simple way. whole: 0.79 (0.20), residues: 1797 helix: 2.37 (0.23), residues: 516 sheet: 0.30 (0.23), residues: 500 loop : -0.57 (0.23), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 281 TYR 0.008 0.001 TYR D 184 PHE 0.006 0.001 PHE A 517 TRP 0.007 0.001 TRP A 776 HIS 0.003 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00306 (14499) covalent geometry : angle 0.47995 (19680) SS BOND : bond 0.00352 ( 1) SS BOND : angle 1.28685 ( 2) hydrogen bonds : bond 0.04835 ( 619) hydrogen bonds : angle 5.56354 ( 1752) Misc. bond : bond 0.00102 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 109 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 187 GLU cc_start: 0.9057 (tm-30) cc_final: 0.8533 (tm-30) outliers start: 3 outliers final: 2 residues processed: 111 average time/residue: 0.2393 time to fit residues: 40.2993 Evaluate side-chains 109 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 107 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain F residue 42 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 79 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 147 optimal weight: 0.9990 chunk 172 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 118 optimal weight: 0.6980 chunk 100 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.097175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.066053 restraints weight = 130531.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.068606 restraints weight = 47766.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.070137 restraints weight = 26673.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.071022 restraints weight = 19257.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.071517 restraints weight = 16202.552| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.0907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14502 Z= 0.122 Angle : 0.453 5.215 19682 Z= 0.242 Chirality : 0.041 0.140 2155 Planarity : 0.003 0.037 2602 Dihedral : 3.477 17.486 1987 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.33 % Allowed : 11.10 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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 aren not related in a simple way. whole: 0.72 (0.20), residues: 1797 helix: 2.43 (0.23), residues: 511 sheet: 0.21 (0.23), residues: 491 loop : -0.62 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 162 TYR 0.009 0.001 TYR A 468 PHE 0.007 0.001 PHE A 31 TRP 0.008 0.001 TRP A 776 HIS 0.003 0.001 HIS B 64 Details of bonding type rmsd covalent geometry : bond 0.00258 (14499) covalent geometry : angle 0.45255 (19680) SS BOND : bond 0.00311 ( 1) SS BOND : angle 1.21575 ( 2) hydrogen bonds : bond 0.03803 ( 619) hydrogen bonds : angle 5.11622 ( 1752) Misc. bond : bond 0.00017 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 115 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 187 GLU cc_start: 0.9026 (tm-30) cc_final: 0.8412 (tm-30) outliers start: 5 outliers final: 3 residues processed: 120 average time/residue: 0.2332 time to fit residues: 43.0361 Evaluate side-chains 111 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 108 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 426 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 133 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 158 optimal weight: 10.0000 chunk 177 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 165 optimal weight: 20.0000 chunk 60 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.095946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.064940 restraints weight = 130510.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.067416 restraints weight = 48139.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.068935 restraints weight = 27125.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.069634 restraints weight = 19640.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.070217 restraints weight = 16922.920| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14502 Z= 0.196 Angle : 0.475 5.839 19682 Z= 0.257 Chirality : 0.041 0.136 2155 Planarity : 0.003 0.036 2602 Dihedral : 3.567 17.214 1987 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.59 % Allowed : 11.62 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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 aren not related in a simple way. whole: 0.58 (0.20), residues: 1797 helix: 2.31 (0.23), residues: 511 sheet: 0.12 (0.23), residues: 496 loop : -0.71 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 281 TYR 0.011 0.001 TYR A 468 PHE 0.007 0.001 PHE A 72 TRP 0.008 0.001 TRP A 776 HIS 0.003 0.001 HIS B 64 Details of bonding type rmsd covalent geometry : bond 0.00413 (14499) covalent geometry : angle 0.47494 (19680) SS BOND : bond 0.00138 ( 1) SS BOND : angle 0.90220 ( 2) hydrogen bonds : bond 0.03640 ( 619) hydrogen bonds : angle 5.12489 ( 1752) Misc. bond : bond 0.00062 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LEU cc_start: 0.9522 (tp) cc_final: 0.9300 (tt) REVERT: A 607 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7837 (mt-10) REVERT: D 187 GLU cc_start: 0.9006 (tm-30) cc_final: 0.8353 (tm-30) outliers start: 9 outliers final: 6 residues processed: 115 average time/residue: 0.2341 time to fit residues: 41.3707 Evaluate side-chains 110 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 104 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 106 GLN Chi-restraints excluded: chain F residue 426 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 26 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 174 optimal weight: 30.0000 chunk 28 optimal weight: 1.9990 chunk 172 optimal weight: 10.0000 chunk 120 optimal weight: 0.9980 chunk 67 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 78 optimal weight: 0.0000 chunk 85 optimal weight: 5.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.096091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.065803 restraints weight = 131063.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.068363 restraints weight = 48063.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.069988 restraints weight = 26702.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.070790 restraints weight = 18959.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.071425 restraints weight = 15994.781| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14502 Z= 0.146 Angle : 0.457 6.112 19682 Z= 0.245 Chirality : 0.041 0.137 2155 Planarity : 0.003 0.042 2602 Dihedral : 3.586 17.309 1987 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.66 % Allowed : 11.95 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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 aren not related in a simple way. whole: 0.56 (0.20), residues: 1797 helix: 2.35 (0.23), residues: 509 sheet: 0.09 (0.23), residues: 488 loop : -0.72 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 207 TYR 0.010 0.001 TYR D 184 PHE 0.007 0.001 PHE A 72 TRP 0.008 0.001 TRP A 546 HIS 0.003 0.001 HIS B 64 Details of bonding type rmsd covalent geometry : bond 0.00310 (14499) covalent geometry : angle 0.45697 (19680) SS BOND : bond 0.00193 ( 1) SS BOND : angle 1.05564 ( 2) hydrogen bonds : bond 0.03476 ( 619) hydrogen bonds : angle 4.97369 ( 1752) Misc. bond : bond 0.00026 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LEU cc_start: 0.9524 (tp) cc_final: 0.9306 (tt) REVERT: A 607 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7835 (mt-10) outliers start: 10 outliers final: 8 residues processed: 116 average time/residue: 0.2058 time to fit residues: 36.5281 Evaluate side-chains 114 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain E residue 28 TYR Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 106 GLN Chi-restraints excluded: chain F residue 426 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 39 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 176 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 2 optimal weight: 20.0000 chunk 155 optimal weight: 0.7980 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 230 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.094411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.063232 restraints weight = 132130.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.065618 restraints weight = 49374.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.067100 restraints weight = 28214.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.067962 restraints weight = 20601.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.068432 restraints weight = 17407.548| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14502 Z= 0.248 Angle : 0.520 6.193 19682 Z= 0.282 Chirality : 0.041 0.131 2155 Planarity : 0.003 0.042 2602 Dihedral : 3.832 17.010 1987 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.92 % Allowed : 12.21 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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 aren not related in a simple way. whole: 0.23 (0.20), residues: 1797 helix: 2.06 (0.23), residues: 509 sheet: -0.10 (0.23), residues: 488 loop : -0.93 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 233 TYR 0.012 0.001 TYR D 205 PHE 0.011 0.001 PHE A 72 TRP 0.008 0.001 TRP A 776 HIS 0.003 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00517 (14499) covalent geometry : angle 0.51947 (19680) SS BOND : bond 0.00417 ( 1) SS BOND : angle 1.38949 ( 2) hydrogen bonds : bond 0.03615 ( 619) hydrogen bonds : angle 5.15446 ( 1752) Misc. bond : bond 0.00106 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7909 (mp10) REVERT: A 607 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7856 (mt-10) outliers start: 14 outliers final: 11 residues processed: 117 average time/residue: 0.2188 time to fit residues: 38.8636 Evaluate side-chains 113 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 466 GLN Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain E residue 28 TYR Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 106 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 103 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 93 optimal weight: 0.4980 chunk 57 optimal weight: 0.3980 chunk 76 optimal weight: 0.8980 chunk 164 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 chunk 173 optimal weight: 30.0000 chunk 85 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.096140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.065214 restraints weight = 129059.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.067728 restraints weight = 47468.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.069239 restraints weight = 26610.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.070119 restraints weight = 19239.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.070598 restraints weight = 16205.308| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 14502 Z= 0.095 Angle : 0.456 6.310 19682 Z= 0.242 Chirality : 0.042 0.141 2155 Planarity : 0.003 0.046 2602 Dihedral : 3.679 17.539 1987 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.53 % Allowed : 12.80 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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 aren not related in a simple way. whole: 0.47 (0.20), residues: 1797 helix: 2.35 (0.23), residues: 506 sheet: -0.09 (0.23), residues: 489 loop : -0.74 (0.23), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 135 TYR 0.012 0.001 TYR D 184 PHE 0.007 0.001 PHE A 72 TRP 0.009 0.001 TRP B 348 HIS 0.003 0.000 HIS B 64 Details of bonding type rmsd covalent geometry : bond 0.00203 (14499) covalent geometry : angle 0.45612 (19680) SS BOND : bond 0.00251 ( 1) SS BOND : angle 1.07837 ( 2) hydrogen bonds : bond 0.03292 ( 619) hydrogen bonds : angle 4.81849 ( 1752) Misc. bond : bond 0.00059 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 607 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7854 (mt-10) outliers start: 8 outliers final: 7 residues processed: 118 average time/residue: 0.2331 time to fit residues: 42.0508 Evaluate side-chains 114 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain E residue 28 TYR Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 106 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 173 optimal weight: 20.0000 chunk 101 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 25 optimal weight: 8.9990 chunk 110 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 86 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 171 optimal weight: 20.0000 chunk 80 optimal weight: 3.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.095421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.064390 restraints weight = 130761.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.066842 restraints weight = 48589.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.068346 restraints weight = 27458.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.069197 restraints weight = 19992.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.069648 restraints weight = 16882.074| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14502 Z= 0.153 Angle : 0.468 6.182 19682 Z= 0.249 Chirality : 0.041 0.134 2155 Planarity : 0.003 0.039 2602 Dihedral : 3.682 17.022 1987 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.59 % Allowed : 12.74 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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 aren not related in a simple way. whole: 0.40 (0.20), residues: 1797 helix: 2.29 (0.23), residues: 506 sheet: -0.11 (0.23), residues: 488 loop : -0.78 (0.23), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 127 TYR 0.011 0.001 TYR D 184 PHE 0.013 0.001 PHE A 652 TRP 0.007 0.001 TRP A 776 HIS 0.002 0.001 HIS B 64 Details of bonding type rmsd covalent geometry : bond 0.00324 (14499) covalent geometry : angle 0.46754 (19680) SS BOND : bond 0.00326 ( 1) SS BOND : angle 1.22365 ( 2) hydrogen bonds : bond 0.03280 ( 619) hydrogen bonds : angle 4.84087 ( 1752) Misc. bond : bond 0.00040 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7856 (mp10) REVERT: A 607 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7829 (mt-10) REVERT: B 282 GLU cc_start: 0.8254 (mt-10) cc_final: 0.8002 (mm-30) outliers start: 9 outliers final: 8 residues processed: 111 average time/residue: 0.2396 time to fit residues: 40.4258 Evaluate side-chains 111 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 466 GLN Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain E residue 28 TYR Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 106 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 23 optimal weight: 3.9990 chunk 42 optimal weight: 0.3980 chunk 134 optimal weight: 1.9990 chunk 147 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 150 optimal weight: 30.0000 chunk 15 optimal weight: 0.8980 chunk 174 optimal weight: 30.0000 chunk 26 optimal weight: 1.9990 chunk 158 optimal weight: 20.0000 chunk 65 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.096144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.064976 restraints weight = 131217.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.067505 restraints weight = 48856.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.069020 restraints weight = 27555.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.069940 restraints weight = 20009.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.070275 restraints weight = 16761.848| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 14502 Z= 0.096 Angle : 0.450 5.830 19682 Z= 0.238 Chirality : 0.041 0.139 2155 Planarity : 0.003 0.045 2602 Dihedral : 3.608 17.057 1987 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.53 % Allowed : 12.93 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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 aren not related in a simple way. whole: 0.56 (0.21), residues: 1797 helix: 2.48 (0.23), residues: 503 sheet: -0.11 (0.23), residues: 494 loop : -0.66 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 64 TYR 0.011 0.001 TYR D 184 PHE 0.015 0.001 PHE A 197 TRP 0.008 0.001 TRP B 348 HIS 0.002 0.001 HIS B 64 Details of bonding type rmsd covalent geometry : bond 0.00210 (14499) covalent geometry : angle 0.45021 (19680) SS BOND : bond 0.00226 ( 1) SS BOND : angle 1.04391 ( 2) hydrogen bonds : bond 0.03119 ( 619) hydrogen bonds : angle 4.65551 ( 1752) Misc. bond : bond 0.00043 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 117 average time/residue: 0.2211 time to fit residues: 39.5563 Evaluate side-chains 113 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 107 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 466 GLN Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 106 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 23 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 136 optimal weight: 1.9990 chunk 173 optimal weight: 40.0000 chunk 70 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 56 optimal weight: 0.0030 overall best weight: 1.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.095570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.064737 restraints weight = 129218.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.067226 restraints weight = 47932.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.068727 restraints weight = 26989.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.069483 restraints weight = 19541.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.070028 restraints weight = 16719.487| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14502 Z= 0.147 Angle : 0.466 5.792 19682 Z= 0.247 Chirality : 0.041 0.135 2155 Planarity : 0.003 0.036 2602 Dihedral : 3.635 16.485 1987 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.53 % Allowed : 13.07 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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 aren not related in a simple way. whole: 0.49 (0.21), residues: 1797 helix: 2.43 (0.23), residues: 503 sheet: -0.13 (0.23), residues: 494 loop : -0.72 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 547 TYR 0.011 0.001 TYR D 184 PHE 0.017 0.001 PHE A 72 TRP 0.007 0.001 TRP A 776 HIS 0.002 0.001 HIS B 64 Details of bonding type rmsd covalent geometry : bond 0.00314 (14499) covalent geometry : angle 0.46552 (19680) SS BOND : bond 0.00330 ( 1) SS BOND : angle 1.16588 ( 2) hydrogen bonds : bond 0.03156 ( 619) hydrogen bonds : angle 4.72397 ( 1752) Misc. bond : bond 0.00035 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3594 Ramachandran restraints generated. 1797 Oldfield, 0 Emsley, 1797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7871 (mp10) REVERT: B 282 GLU cc_start: 0.8288 (mt-10) cc_final: 0.8029 (mm-30) outliers start: 8 outliers final: 7 residues processed: 112 average time/residue: 0.2191 time to fit residues: 37.3991 Evaluate side-chains 113 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 466 GLN Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 106 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 40 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 158 optimal weight: 20.0000 chunk 152 optimal weight: 6.9990 chunk 167 optimal weight: 20.0000 chunk 10 optimal weight: 5.9990 chunk 153 optimal weight: 9.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.095156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.064273 restraints weight = 130402.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.066744 restraints weight = 48678.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.068228 restraints weight = 27459.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.069087 restraints weight = 19929.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.069455 restraints weight = 16801.886| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 14502 Z= 0.168 Angle : 0.475 5.612 19682 Z= 0.253 Chirality : 0.041 0.133 2155 Planarity : 0.003 0.045 2602 Dihedral : 3.692 16.210 1987 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.66 % Allowed : 13.07 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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 aren not related in a simple way. whole: 0.43 (0.20), residues: 1797 helix: 2.36 (0.23), residues: 503 sheet: -0.12 (0.23), residues: 490 loop : -0.78 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 281 TYR 0.011 0.001 TYR D 184 PHE 0.014 0.001 PHE A 197 TRP 0.008 0.001 TRP A 776 HIS 0.002 0.001 HIS B 64 Details of bonding type rmsd covalent geometry : bond 0.00355 (14499) covalent geometry : angle 0.47533 (19680) SS BOND : bond 0.00322 ( 1) SS BOND : angle 1.17466 ( 2) hydrogen bonds : bond 0.03200 ( 619) hydrogen bonds : angle 4.78013 ( 1752) Misc. bond : bond 0.00042 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4112.32 seconds wall clock time: 70 minutes 49.95 seconds (4249.95 seconds total)